url
stringlengths 63
66
| repository_url
stringclasses 1
value | labels_url
stringlengths 77
80
| comments_url
stringlengths 72
75
| events_url
stringlengths 70
73
| html_url
stringlengths 52
56
| id
int64 3.39M
3.04B
| node_id
stringlengths 18
32
| number
int64 1
4.39k
| title
stringlengths 3
367
| user
dict | labels
listlengths 0
5
| state
stringclasses 2
values | locked
bool 2
classes | assignee
dict | assignees
listlengths 0
2
| milestone
null | comments
listlengths 0
30
| created_at
timestamp[s]date 2012-02-26 12:10:46
2025-05-02 18:11:41
| updated_at
timestamp[s]date 2012-02-26 14:52:41
2025-05-02 18:16:27
| closed_at
stringlengths 0
20
| author_association
stringclasses 3
values | type
stringclasses 1
value | active_lock_reason
stringclasses 2
values | sub_issues_summary
dict | body
stringlengths 0
119k
| closed_by
dict | reactions
dict | timeline_url
stringlengths 72
75
| performed_via_github_app
null | state_reason
stringclasses 4
values | is_pull_request
bool 2
classes | draft
bool 2
classes | pull_request
dict |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
https://api.github.com/repos/materialsproject/pymatgen/issues/3146
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3146/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3146/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3146/events
|
https://github.com/materialsproject/pymatgen/pull/3146
| 1,799,818,092
|
PR_kwDOACgets5VP858
| 3,146
|
read `mag` from OSZICAR
|
{
"login": "chiang-yuan",
"id": 41962462,
"node_id": "MDQ6VXNlcjQxOTYyNDYy",
"avatar_url": "https://avatars.githubusercontent.com/u/41962462?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chiang-yuan",
"html_url": "https://github.com/chiang-yuan",
"followers_url": "https://api.github.com/users/chiang-yuan/followers",
"following_url": "https://api.github.com/users/chiang-yuan/following{/other_user}",
"gists_url": "https://api.github.com/users/chiang-yuan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chiang-yuan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chiang-yuan/subscriptions",
"organizations_url": "https://api.github.com/users/chiang-yuan/orgs",
"repos_url": "https://api.github.com/users/chiang-yuan/repos",
"events_url": "https://api.github.com/users/chiang-yuan/events{/privacy}",
"received_events_url": "https://api.github.com/users/chiang-yuan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 2414169365,
"node_id": "MDU6TGFiZWwyNDE0MTY5MzY1",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20testing",
"name": "needs testing",
"color": "66ddab",
"default": false,
"description": "PRs that are not ready to merge due to lacking tests"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@chiang-yuan Yes, we definitely need a test for this.\r\n\r\nDo I understand correctly that your PR adds a `mag` key to any parsed `OSZICAR` even if that data is not present in the file? Will the value be `None` in that case?",
"Haven't tested different OSZICAR yet. Looks like OSZICAR test in test_ouptut.py doesn't test different combinations of available field. I am going to add a test considering if the field is missing. https://github.com/materialsproject/pymatgen/blob/1b04a0a626dae8ae42324ac1d99d151591519c6e/pymatgen/io/vasp/tests/test_outputs.py#L1422-L1428",
"Hi @janosh I think this PR is ready to be merged. Let me know if I can do anything to make it better!",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3146?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`100.00%`** and project coverage change: **`-0.56%`** :warning:\n> Comparison is base [(`d9fdfef`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/d9fdfefa4787c5121d76ea0e1c60927d7b320d43?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.62% compared to head [(`179d20a`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3146?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.06%.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3146 +/- ##\n==========================================\n- Coverage 74.62% 74.06% -0.56% \n==========================================\n Files 230 230 \n Lines 69403 69394 -9 \n Branches 16161 16160 -1 \n==========================================\n- Hits 51794 51399 -395 \n- Misses 14533 14954 +421 \n+ Partials 3076 3041 -35 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3146?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/io/vasp/outputs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3146?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vdmFzcC9vdXRwdXRzLnB5) | `88.12% <100.00%> (+0.20%)` | :arrow_up: |\n\n... and [7 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3146/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3146?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-07-11T22:02:20
| 2023-08-18T16:46:19
|
2023-08-18T16:46:19Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I tried to read `mag` from OSZICAR and found `mag` is not read from `ionic_MD_pattern`. Not sure if `mag` is available in all vasp md calculation.
@janosh should I add unit test for this? The OSZICAR in `test_files/OSZICAR` doesn't have all the available output fields like
```
2 T= 1239. E= 0.11712678E+03 F= -.20873815E+03 E0= -.20873814E+03 EK= 0.10092E+02 SP= 0.32E+03 SK= 0.10E-02 mag= -0.000
```
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3146/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3146/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3146",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3146",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3146.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3146.patch",
"merged_at": "2023-08-18T16:46:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3147
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3147/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3147/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3147/events
|
https://github.com/materialsproject/pymatgen/pull/3147
| 1,799,857,059
|
PR_kwDOACgets5VQFhI
| 3,147
|
Compress test files
|
{
"login": "mcgalcode",
"id": 15318848,
"node_id": "MDQ6VXNlcjE1MzE4ODQ4",
"avatar_url": "https://avatars.githubusercontent.com/u/15318848?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mcgalcode",
"html_url": "https://github.com/mcgalcode",
"followers_url": "https://api.github.com/users/mcgalcode/followers",
"following_url": "https://api.github.com/users/mcgalcode/following{/other_user}",
"gists_url": "https://api.github.com/users/mcgalcode/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mcgalcode/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mcgalcode/subscriptions",
"organizations_url": "https://api.github.com/users/mcgalcode/orgs",
"repos_url": "https://api.github.com/users/mcgalcode/repos",
"events_url": "https://api.github.com/users/mcgalcode/events{/privacy}",
"received_events_url": "https://api.github.com/users/mcgalcode/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks a lot @mcgalcode. This was a big chunk!"
] | 2023-07-11T22:41:14
| 2023-07-11T22:53:58
|
2023-07-11T22:53:40Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Fixes tests after compression of files in pymatgen/analysis.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3147/reactions",
"total_count": 1,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 1,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3147/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3147",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3147",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3147.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3147.patch",
"merged_at": "2023-07-11T22:53:40Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3148
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3148/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3148/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3148/events
|
https://github.com/materialsproject/pymatgen/issues/3148
| 1,801,443,872
|
I_kwDOACgets5rX9og
| 3,148
|
Incorrect formula for `estimate_nbands` method
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5414010766,
"node_id": "LA_kwDOACgets8AAAABQrM_jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20discussion",
"name": "needs discussion",
"color": "D96543",
"default": false,
"description": "Needs discussion to agree on actionable next steps"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This might well be true, but I expect this was written with reference to the [VASP docs](https://www.vasp.at/wiki/index.php/NBANDS). I'm not sure the appropriateness of referring to the source code here.",
"@mkhorton what do you mean? I thought that using the formula from the source code (which is distinct from the docs) would be desirable, as it would closer to the actual NBANDS used by VASP. ",
"VASP is not an open source code (meaning, a code released under an open source license).\r\n\r\nI'm not a lawyer, but generally it's not ok to reference a closed-source code to re-implement a feature into an open-source code, since it violates the terms of the original license.\r\n\r\nI don't know how much of that is context dependent; this is something trivial, and is essentially a single line to implement an alternative API to enable use of the original code (anyone using pymatgen for VASP would also need to hold a license for VASP themselves), but nevertheless ...",
"Closed by #3149 "
] | 2023-07-12T17:33:45
| 2023-07-20T22:16:27
|
2023-07-20T22:16:27Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
https://github.com/materialsproject/pymatgen/blob/71864db310569946703bfa8c3f42eaf69c533744/pymatgen/io/vasp/sets.py#L689
According to my version of the VASP source code, in `main.F`, the actual formula for NBANDS should be:
`max((valid_nelect+2)/2 + max(nions/2,3), valid_nelect*0.6)) + nmag`
with `nmag=0` always set for ISPIN=1 calcs
Also, `nmag` should be calculated as:
```
nmag = len([m for m in self.incar["MAGMOM"] if not np.allclose(m, 0)])
nmag =(nmag+1)/2 # this step is currently excluded from the code
```
It can later be increased (to be divisible by the number of cores, etc.), but that can't be accounted for without additional context for a given calc.
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3148/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3148/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3149
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3149/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3149/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3149/events
|
https://github.com/materialsproject/pymatgen/pull/3149
| 1,801,511,957
|
PR_kwDOACgets5VVwIf
| 3,149
|
fix `estimate_nbands` function
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@matthewkuner Thanks for spotting this!\r\n\r\nWould be great if @aaron-kaplan or someone else more qualified than me could sign off on this.\r\n\r\nAlso, @matthewkuner we need a unit test in `pymatgen/io/vasp/tests/test_sets.py` for this change in behavior. It should pass with and fail without this change. Maybe in `test_nelect`.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/71864db310569946703bfa8c3f42eaf69c533744/pymatgen/io/vasp/tests/test_sets.py#L233",
"> Would be great if @aaron-kaplan or someone else more qualified than me could sign off on this.\r\n\r\nYou tagged the wrong person. I'm not involved with this project.",
"@aaron-kaplan Apologies.\r\n\r\nI meant @esoteric-ephemera.",
"@matthewkuner, lines 694-695 seem wrong to me per our discussion:\r\n> nmag = len([m for m in self.incar[\"MAGMOM\"] if not np.allclose(m, 0)])\r\n> nmag = np.ceil((nmag+1)/2)\r\n\r\nThe lines of code in VASP's main.F are:\r\n> NMAG=SUM(T_INFO%ATOMOM(1:T_INFO%NIONS))\r\n> NMAG = (NMAG+1)/2\r\n\r\nwhich to me looks like VASP is simply summing the initial magnetic moments (ATOMOM), not counting the number of atoms with nonzero magnetic moments\r\n\r\nThe weird thing is that NMAG is an integer but ATOMOM is declared to be a float in poscar_struc.F. Fortran seems to do int + float = int + floor(float) when assigning to a variable. You probably want to double check your code against a few sets of INCAR's and OUTCAR's.\r\n\r\nAlso, @matthewkuner, if the user specifies NPAR (if 'NPAR' is in self.incar), you probably want to add a line as in main.F:\r\n> NBANDS=((NBANDS+NPAR-1)/NPAR)*NPAR\r\n\r\n@janosh, my name is unfortunately too common to get it as a username 😂",
"@matthewkuner: Copying over our brief convo from Slack, it would perhaps be nice (if you're willing to do so) to move the `estimate_nbands` definition out of the `DictSet` class. It would be nice to be able to call `estimate_nbands` for a given `Structure` without instantiating a `DictSet`.",
"@janosh @arosen93 @esoteric-ephemera Please see comments in [#3148](https://github.com/materialsproject/pymatgen/issues/3148#issuecomment-1635345159) by @mkhorton",
"The license concerns? Perhaps we can loop in someone from VASP and get their ok. Haven't looked into this myself, but taking @matthewkuner's word for it, I doubt VASP minds us fixing downstream repercussions arising from disparities between their docs and their actual implementation. Given it's a paid product, this should not have happened in the 1st place.",
"Perhaps @MichaelWolloch could help clarify or get us in touch with folks who can.\n\nI also see this as being a likely non-issue. ",
"Yes, agreed--just asking the VASP devs is the best course of action here. I also agree hopefully it's a non-issue, but good to check.",
"@janosh I've updated the tests and verified them to quick VASP calcs that I ran.",
"> Also, @matthewkuner, if the user specifies NPAR (if 'NPAR' is in self.incar), you probably want to add a line as in `main.F`:\r\n> `NBANDS=((NBANDS+NPAR-1)/NPAR)*NPAR`\r\n\r\nThanks @matthewkuner! Did you address this comment raised by @esoteric-ephemera?",
"@janosh I addressed everything from Aaron’s comment except for the NPAR stuff. I’ll do that tomorrow",
"I’m assuming since work is proceeding that VASP devs ok’d using `main.F` as a reference? Would it be possible to include a copy of the response here for the record?",
"No response yet from VASP. Not sure who to ping. @sudarshanv01 Do you have any suggestions?",
"@janosh @mkhorton I asked a similar question about NGX/Y/Z, and they basically just said that as long as it isn't a direct copy-paste, it should be fine. See: https://www.vasp.at/forum/viewtopic.php?p=24351#p24351\r\n\r\nConsidering it is being transcribed from one language to another, I think we are fine here. Let me know if you think my interpretation is too biased/generous to our efforts.",
"I think that’s reasonable. I just wanted to make sure there was a record. Perhaps this thread can be linked on that forum post as well just to be completely above board and leave it there if there are no objections.",
"Hi, and apologies for the late reply. I am on holidays this week and did not check my emails for a while. I have never dealt with this type of code base related issue, and am hesitant to comment either way. Maybe @henriquemiranda is in-office and knows more about VASPs policy here? Or can quickly ask someone more senior?\r\nCheers, M",
"This code has no tests whatsoever. Can someone pls add a unittest for it? @janosh Pls make sure that this is always done for any new code before merging.",
"@shyuep there are indeed new tests for this PR, check the second file changed",
"@matthewkuner Ah yes. However, it says skip if no PSP directory. That basically means it is not running at all on Github Actions. Can the test be modified to at change check a few POTCAR files? Since the code is not running on the CI, we can't detect any bugs until someone runs it on their computer."
] | 2023-07-12T18:07:45
| 2023-08-05T13:50:32
|
2023-07-20T21:54:09Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Fixes the `estimate_nbands` function. See #3148 for more context.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3149/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3149/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3149",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3149",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3149.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3149.patch",
"merged_at": "2023-07-20T21:54:09Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3150
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3150/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3150/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3150/events
|
https://github.com/materialsproject/pymatgen/pull/3150
| 1,801,566,935
|
PR_kwDOACgets5VV8Lh
| 3,150
|
Don't waste `pytest.approx()` function calls on integers
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-12T18:47:08
| 2023-07-12T20:20:40
|
2023-07-12T20:20:39Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3150/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3150/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3150",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3150",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3150.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3150.patch",
"merged_at": "2023-07-12T20:20:39Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3151
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3151/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3151/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3151/events
|
https://github.com/materialsproject/pymatgen/pull/3151
| 1,801,820,377
|
PR_kwDOACgets5VWz3H
| 3,151
|
`AseAtomsAdaptor`: Retain `tags` property when interconverting `Atoms` and `Structure`/`Molecule`
|
{
"login": "Andrew-S-Rosen",
"id": 8674072,
"node_id": "MDQ6VXNlcjg2NzQwNzI=",
"avatar_url": "https://avatars.githubusercontent.com/u/8674072?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Andrew-S-Rosen",
"html_url": "https://github.com/Andrew-S-Rosen",
"followers_url": "https://api.github.com/users/Andrew-S-Rosen/followers",
"following_url": "https://api.github.com/users/Andrew-S-Rosen/following{/other_user}",
"gists_url": "https://api.github.com/users/Andrew-S-Rosen/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Andrew-S-Rosen/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Andrew-S-Rosen/subscriptions",
"organizations_url": "https://api.github.com/users/Andrew-S-Rosen/orgs",
"repos_url": "https://api.github.com/users/Andrew-S-Rosen/repos",
"events_url": "https://api.github.com/users/Andrew-S-Rosen/events{/privacy}",
"received_events_url": "https://api.github.com/users/Andrew-S-Rosen/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5585129979,
"node_id": "LA_kwDOACgets8AAAABTOZR-w",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ase",
"name": "ase",
"color": "B8E879",
"default": false,
"description": "Atomic simulation environment"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"thanks @arosen93 !",
"@janosh --- why does ruff hate me? :(",
"Looks like `ruff` just had a new release that finds new issues on `master`. So nothing to do with your changes. Does this still need testing?",
"Ah I see. No, this should be done! "
] | 2023-07-12T22:01:30
| 2023-07-24T16:07:29
|
2023-07-22T03:33:42Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Currently, the `.tags` property of the ASE `Atoms` object is lost when interconverting between ASE `Atoms` and Pymatgen `Structure`/`Molecule`. I adopted the solution by @brookwander in https://github.com/ulissigroup/catapalt/issues/2 to ensure the tags do not get lost.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3151/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3151/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3151",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3151",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3151.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3151.patch",
"merged_at": "2023-07-22T03:33:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3152
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3152/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3152/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3152/events
|
https://github.com/materialsproject/pymatgen/issues/3152
| 1,801,917,011
|
I_kwDOACgets5rZxJT
| 3,152
|
Handle special values in `pmg config --add` CLI
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5729312941,
"node_id": "LA_kwDOACgets8AAAABVX5grQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/cli",
"name": "cli",
"color": "19872C",
"default": false,
"description": "Command line interface"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-12T23:53:57
| 2023-07-13T02:30:58
|
2023-07-13T02:30:57Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
You can't set any type other than `str` using the `pmg` CLI at the moment.
```sh
pmg config --add PMG_POTCAR_CHECKS False
```
will be stored as
```yaml
# ~/.config/.pmgrc.yaml
PMG_POTCAR_CHECKS: 'False'
```
which is truthy and so the opposite of expected behavior.
_Originally posted by @janosh in https://github.com/materialsproject/pymatgen/issues/3143#issuecomment-1633342975_
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3152/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3152/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3153
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3153/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3153/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3153/events
|
https://github.com/materialsproject/pymatgen/pull/3153
| 1,801,923,282
|
PR_kwDOACgets5VXKjY
| 3,153
|
Rename `PMG_DISABLE_POTCAR_CHECKS` to `PMG_POTCAR_CHECKS`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457867742,
"node_id": "LA_kwDOACgets8AAAABRVBz3g",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/breaking",
"name": "breaking",
"color": "41396E",
"default": false,
"description": "Breaking change"
},
{
"id": 5729312941,
"node_id": "LA_kwDOACgets8AAAABVX5grQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/cli",
"name": "cli",
"color": "19872C",
"default": false,
"description": "Command line interface"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-13T00:02:47
| 2023-07-13T02:30:57
|
2023-07-13T02:30:56Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3152
90a7c076d rename `PMG_DISABLE_POTCAR_CHECKS` to `PMG_POTCAR_CHECKS`
0729fc3f9 fix setting `bool` and `None` through `pmg` config CLI
0ef9ae7d2 document existence of `PMG_POTCAR_CHECKS` in all doc strings for `check_potcar: bool = True`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3153/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3153/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3153",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3153",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3153.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3153.patch",
"merged_at": "2023-07-13T02:30:56Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3154
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3154/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3154/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3154/events
|
https://github.com/materialsproject/pymatgen/issues/3154
| 1,803,785,035
|
I_kwDOACgets5rg5NL
| 3,154
|
MaterialsProject2020Compatibility doesn't handle oxidation states
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5680875673,
"node_id": "LA_kwDOACgets8AAAABUptImQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/mixing-schemes",
"name": "mixing-schemes",
"color": "44BAE9",
"default": false,
"description": "About mixing energies from different DFT functionals"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I think the fix is just to use el.symbol instead? Most of the time the compatibility is operated on MP entries. Most of which don't come with oxidation state decorated.",
"Yes, the fix is straightforward. Just baffled that it hasn't come up before."
] | 2023-07-13T21:25:55
| 2023-07-13T22:59:42
|
2023-07-13T22:59:42Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I'm surprised this didn't come up before. Opening this issue rather than quietly fixing to make sure I'm not missing something. It appears `MaterialsProject2020Compatibility` doesn't currently handle oxidation states.
```py
from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
from pymatgen.entries.computed_entries import ComputedStructureEntry
li_mn_o2 = Structure.from_file("o-LiMnO2_unit.cif")
cse = ComputedStructureEntry(
li_mn_o2,
-42,
parameters={
"hubbards": {"Mn": 3.9},
"run_type": "GGA+U"
}
)
MaterialsProject2020Compatibility(check_potcar=False).process_entries(
cse, clean=True, inplace=False
)
```
The above correction fails because this line
https://github.com/materialsproject/pymatgen/blob/edd80a85d61d06ec02c183950c5ed8fb7c0ec0bd/pymatgen/entries/compatibility.py#L175
uses the `Element.__str__` (which includes oxidation state e.g. `O2-`) rather than `symbol` to match dict keys which are element symbols.
<details><summary><code>o-LiMnO2_unit.cif</code></summary>
```cif
# generated using pymatgen
data_LiMnO2
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 2.86877900
_cell_length_b 4.63447500
_cell_length_c 5.83250700
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural LiMnO2
_chemical_formula_sum 'Li2 Mn2 O4'
_cell_volume 77.54484024
_cell_formula_units_Z 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Li+ 1.0
Mn3+ 3.0
O2- -2.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li+ Li0 1 0.50000000 0.50000000 0.37975050 1
Li+ Li1 1 0.00000000 0.00000000 0.62024950 1
Mn3+ Mn2 1 0.50000000 0.50000000 0.86325250 1
Mn3+ Mn3 1 0.00000000 0.00000000 0.13674750 1
O2- O4 1 0.50000000 0.00000000 0.36082450 1
O2- O5 1 0.00000000 0.50000000 0.09851350 1
O2- O6 1 0.50000000 0.00000000 0.90148650 1
O2- O7 1 0.00000000 0.50000000 0.63917550 1
```
</details>
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3154/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3154/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3155
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3155/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3155/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3155/events
|
https://github.com/materialsproject/pymatgen/pull/3155
| 1,803,820,659
|
PR_kwDOACgets5Vdqun
| 3,155
|
Fix "Incompatible POTCAR" error on ComputedEntries with oxidation states
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5680875673,
"node_id": "LA_kwDOACgets8AAAABUptImQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/mixing-schemes",
"name": "mixing-schemes",
"color": "44BAE9",
"default": false,
"description": "About mixing energies from different DFT functionals"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-13T22:01:29
| 2023-07-13T22:59:42
|
2023-07-13T22:59:41Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3154.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3155/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3155/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3155",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3155",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3155.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3155.patch",
"merged_at": "2023-07-13T22:59:41Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3156
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3156/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3156/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3156/events
|
https://github.com/materialsproject/pymatgen/issues/3156
| 1,804,560,445
|
I_kwDOACgets5rj2g9
| 3,156
|
Importing pymatgen messes up sys.path
|
{
"login": "pmrv",
"id": 2719909,
"node_id": "MDQ6VXNlcjI3MTk5MDk=",
"avatar_url": "https://avatars.githubusercontent.com/u/2719909?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pmrv",
"html_url": "https://github.com/pmrv",
"followers_url": "https://api.github.com/users/pmrv/followers",
"following_url": "https://api.github.com/users/pmrv/following{/other_user}",
"gists_url": "https://api.github.com/users/pmrv/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pmrv/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pmrv/subscriptions",
"organizations_url": "https://api.github.com/users/pmrv/orgs",
"repos_url": "https://api.github.com/users/pmrv/repos",
"events_url": "https://api.github.com/users/pmrv/events{/privacy}",
"received_events_url": "https://api.github.com/users/pmrv/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5585018768,
"node_id": "LA_kwDOACgets8AAAABTOSfkA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/pkg",
"name": "pkg",
"color": "EFE8DB",
"default": false,
"description": "Package health and distribution related stuff"
},
{
"id": 5585129979,
"node_id": "LA_kwDOACgets8AAAABTOZR-w",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ase",
"name": "ase",
"color": "B8E879",
"default": false,
"description": "Atomic simulation environment"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks for reporting this. @arosen93 The only sys.path that I noticed is in the io.ase. Did you add that? I am not sure of the purpose of it. Can you reverse it? @janosh \r\n",
"Nope, don't think that was me. @janosh, was that one you? Feel free to reverse. Otherwise, I'll take a look later today. ",
"Ah yes, it was @janosh based on the git blame. This needs to be reversed. We shouldn't be doing this kind of thing for test running. I am not sure why this is even a problem. But if it is for testing, I am sure there are other solutions that don't involve doing things like modifying sys.path.",
"I found a solution that works: `--import-mode=importlib` for pytest. This solution does nothing to the actual code. See https://docs.pytest.org/en/7.1.x/explanation/pythonpath.html",
"A 2023.7.14 release has been made that removed the sys.path. This version should now work. Thanks for reporting this.",
"`--import-mode=importlib` sounds great! Except for the caveat:\r\n\r\n> test modules are non-importable by each other. Also, utility modules in the tests directories are not automatically importable because the tests directory is no longer added to [sys.path](https://docs.python.org/3/library/sys.html#sys.path).\r\n\r\nI'm very surprised if we don't make use of that anywhere in the `pymatgen` test suite.",
"Cool, looks I have reason to be surprised; all tests still passing. `--import-mode=importlib` is clearly the better solution, sorry for the path issues.",
"I would be very surprised if tests import from each other. All tests are written on a per file testing basis.",
"I was referring to utility modules in the tests directories. I have those in several of my projects that are much smaller than `pymatgen`.",
"Thanks everyone for quickly resolving this!\n\n@janosh re utility modules: We have this case in multiple of our pyiron packages and there we just stick those in a `_test` module in the main package and haven't had problems so far. It doesn't impact the main package as well because it never imports that module.",
"Sounds like `_test` would end up in the source distribution (unless you explicitly exclude it)?",
"Correct, it does end up in the source distribution. It's a bit unaesthetic, but no issues otherwise."
] | 2023-07-14T09:42:32
| 2023-07-15T07:58:33
|
2023-07-14T13:51:21Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Since [v2023.06.23](https://github.com/materialsproject/pymatgen/releases/tag/v2023.06.23) importing `pymatgen` manipulates [sys.path](https://github.com/materialsproject/pymatgen/blame/63bbd23b57ca2c68eaca07e4915a70ef66e13405/pymatgen/io/ase.py#L26). This is somewhat annoying if you have a more complicated site setup.
I would suggest as a fix to move that hack either to the file with the affected tests or remove the path of `sys.path` again after you have checked that ase is installed in the file linked above (it seems `ase_loaded` that was previously checked is not used elsewhere in the code). I'm happy to make a PR to either effect if you're a bit strapped for time right now.
Some background as to why this breaks for us: We are in a setup where users and developers of our package share a conda environment. For users releases of our package are installed via conda. Developers shadow the installed package by manipulating their `sys.path` to import their development version of the software rather than the releases from conda. The hack above then manipulates our manipulation so that the package is imported from conda again. So it's just that the hack works a little bit too well. 😅
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3156/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3156/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3157
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3157/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3157/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3157/events
|
https://github.com/materialsproject/pymatgen/pull/3157
| 1,805,737,012
|
PR_kwDOACgets5VkQjG
| 3,157
|
Bug fix: `CollinearMagneticAnalyzer` should not fail when `Species.spin = None`
|
{
"login": "mattmcdermott",
"id": 40469694,
"node_id": "MDQ6VXNlcjQwNDY5Njk0",
"avatar_url": "https://avatars.githubusercontent.com/u/40469694?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mattmcdermott",
"html_url": "https://github.com/mattmcdermott",
"followers_url": "https://api.github.com/users/mattmcdermott/followers",
"following_url": "https://api.github.com/users/mattmcdermott/following{/other_user}",
"gists_url": "https://api.github.com/users/mattmcdermott/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mattmcdermott/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mattmcdermott/subscriptions",
"organizations_url": "https://api.github.com/users/mattmcdermott/orgs",
"repos_url": "https://api.github.com/users/mattmcdermott/repos",
"events_url": "https://api.github.com/users/mattmcdermott/events{/privacy}",
"received_events_url": "https://api.github.com/users/mattmcdermott/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thanks @mattmcdermott!"
] | 2023-07-14T23:58:35
| 2023-07-15T00:30:21
|
2023-07-15T00:30:20Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Fixes bug briefly mentioned in #3070, where recent spin property changes resulted in the `MagneticStructureEnumerator` failing. This is apparently due to creating structures where only some `Species.spin` properties are defined, causing `CollinearMagneticStructureEnumerator` to fail. For example, if you input this structure into the analyzer right now, it would fail:
```
Structure Summary
Lattice
abc : 2.948635277547903 2.948635277547903 5.107186113702927
angles : 73.22134511903964 90.0 120.00000000000001
volume : 36.2558565
A : 2.085 2.085 0.0
B : 0.0 -2.085 -2.085
C : -2.085 2.085 -4.17
pbc : True True True
PeriodicSite: Ni,spin=-5 (0.0000, 2.0850, -2.0850) [0.5000, 0.0000, 0.5000]
PeriodicSite: Ni,spin=5 (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: O (0.0000, 0.0000, -2.0850) [0.2500, 0.5000, 0.2500]
PeriodicSite: O (0.0000, 2.0850, -4.1700) [0.7500, 0.5000, 0.7500]
```
and yield this error:
```python
/Users/mcdermott/code/github/pymatgen/pymatgen/analysis/magnetism/analyzer.py:205: UserWarning: This class is not designed to be used with non-collinear structures. If your structure is only slightly non-collinear (e.g. canted) may still give useful results, but use with caution.
warnings.warn(
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[5], line 8
5 coords = [[0.5, 0, 0.5], [0, 0, 0], [0.25, 0.5, 0.25], [0.75, 0.5, 0.75]]
6 struct = Structure(latt, species, coords)
----> 8 msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
File ~/code/github/pymatgen/pymatgen/analysis/magnetism/analyzer.py:214, in CollinearMagneticStructureAnalyzer.__init__(self, structure, overwrite_magmom_mode, round_magmoms, detect_valences, make_primitive, default_magmoms, set_net_positive, threshold, threshold_nonmag)
205 warnings.warn(
206 "This class is not designed to be used with "
207 "non-collinear structures. If your structure is "
208 "only slightly non-collinear (e.g. canted) may still "
209 "give useful results, but use with caution."
210 )
212 # this is for collinear structures only, make sure magmoms
213 # are all floats
--> 214 magmoms = list(map(float, magmoms))
216 # set properties that should be done /before/ we process input magmoms
217 self.total_magmoms = sum(magmoms)
TypeError: float() argument must be a string or a real number, not 'NoneType'
```
## Fix:
This was fixed by changing one line of code. https://github.com/materialsproject/pymatgen/commit/d8f395670c77bb626773dc9e5e8c62988f1a66cc
A test was added for this example structure that would fail with the old line.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
|
{
"login": "mkhorton",
"id": 2976580,
"node_id": "MDQ6VXNlcjI5NzY1ODA=",
"avatar_url": "https://avatars.githubusercontent.com/u/2976580?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/mkhorton",
"html_url": "https://github.com/mkhorton",
"followers_url": "https://api.github.com/users/mkhorton/followers",
"following_url": "https://api.github.com/users/mkhorton/following{/other_user}",
"gists_url": "https://api.github.com/users/mkhorton/gists{/gist_id}",
"starred_url": "https://api.github.com/users/mkhorton/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/mkhorton/subscriptions",
"organizations_url": "https://api.github.com/users/mkhorton/orgs",
"repos_url": "https://api.github.com/users/mkhorton/repos",
"events_url": "https://api.github.com/users/mkhorton/events{/privacy}",
"received_events_url": "https://api.github.com/users/mkhorton/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3157/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3157/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3157",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3157",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3157.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3157.patch",
"merged_at": "2023-07-15T00:30:20Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3158
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3158/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3158/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3158/events
|
https://github.com/materialsproject/pymatgen/pull/3158
| 1,806,325,989
|
PR_kwDOACgets5VmKac
| 3,158
|
Deprecate `from_string`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
},
{
"id": 5687218601,
"node_id": "LA_kwDOACgets8AAAABUvwRqQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/deprecation",
"name": "deprecation",
"color": "B0FEB6",
"default": false,
"description": "Code deprecations"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-15T20:46:39
| 2023-07-15T21:41:27
|
2023-07-15T21:41:25Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Some classes have static method `from_string` (`Poscar`, `CifParser`, ...), other's `from_str` (`Structure`, `Molecule`, ...).
`from_str` is shorter and clear enough, so rename methods to that and add deprecated `from_string` fallbacks for backwards compatibility.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3158/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3158/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3158",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3158",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3158.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3158.patch",
"merged_at": "2023-07-15T21:41:25Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3159
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3159/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3159/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3159/events
|
https://github.com/materialsproject/pymatgen/issues/3159
| 1,806,328,520
|
I_kwDOACgets5rqmLI
| 3,159
|
Drop non-existent `fleur` support from `Structure.to`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5585018768,
"node_id": "LA_kwDOACgets8AAAABTOSfkA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/pkg",
"name": "pkg",
"color": "EFE8DB",
"default": false,
"description": "Package health and distribution related stuff"
},
{
"id": 5745716322,
"node_id": "LA_kwDOACgets8AAAABVnisYg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/invalid",
"name": "invalid",
"color": "6419E1",
"default": true,
"description": "User error/mistake"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Never mind, didn't realize [`pymatgen-io-fleur`](https://github.com/JuDFTteam/pymatgen-io-fleur) is an external namespace package (see https://github.com/materialsproject/pymatgen/pull/2610)."
] | 2023-07-15T20:59:08
| 2023-07-17T19:48:34
|
2023-07-17T19:48:34Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
@shyuep `Structure.to()` imports from `pymatgen.io.fleur` which doesn't exist. Did you remove?
Either way, we should remove the `fmt == "fleur-inpgen" or fnmatch(filename, "*.in*")` option from `Structure.to()` since it would crash.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3159/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3159/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3160
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3160/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3160/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3160/events
|
https://github.com/materialsproject/pymatgen/issues/3160
| 1,808,248,977
|
I_kwDOACgets5rx7CR
| 3,160
|
`AttributeError`: `attr='label'` not found on `PeriodicNeighbor`
|
{
"login": "ghost",
"id": 10137,
"node_id": "MDQ6VXNlcjEwMTM3",
"avatar_url": "https://avatars.githubusercontent.com/u/10137?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ghost",
"html_url": "https://github.com/ghost",
"followers_url": "https://api.github.com/users/ghost/followers",
"following_url": "https://api.github.com/users/ghost/following{/other_user}",
"gists_url": "https://api.github.com/users/ghost/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ghost/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ghost/subscriptions",
"organizations_url": "https://api.github.com/users/ghost/orgs",
"repos_url": "https://api.github.com/users/ghost/repos",
"events_url": "https://api.github.com/users/ghost/events{/privacy}",
"received_events_url": "https://api.github.com/users/ghost/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@shyuep ",
"This might be caused by https://github.com/materialsproject/pymatgen/pull/3137.\r\n\r\n@shwetaresearchsite Can you downgrade to `pip install pymatgen==2023.6.28` and see if the error disappears?",
"@stefsmeets In case it helps connect the dots, this issue might be related to #3166.",
"Are there any other classes that derive from or are polymorphic with `Site` that should get a `.label` attribute? In #3135 I updated `Site` and `PeriodicSite`.",
"So `Neighbour` and `PeriodicNeighbour` both also derive from `Site`/`PeriodicSite`, and should be updated with the label attribute."
] | 2023-07-17T17:32:58
| 2023-07-20T15:37:49
|
2023-07-20T15:37:48Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Can anyone please suggest why I am unable to get structures from pymatgen?
```py
from pymatgen.core import Structure
from pymatgen.analysis.diffusion.neb.pathfinder import DistinctPathFinder
s = Structure.from_file("./system.vasp")
path_finder = DistinctPathFinder(symm_structure, "Ca", max_path_length=6.0)
distinct_paths = path_finder.get_paths()
for p in distinct_paths:
structures = p.get_structures(nimages=5, vac_mode=True, idpp=False)
for structure in structures:
print(structure)
```
error:
```py
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[9], line 2
1 for p in distinct_paths:
----> 2 structures = p.get_structures(nimages=5, vac_mode=True, idpp=False)
3 for structure in structures:
4 print(structure)
File ~/repo/venv/lib/python3.11/site-packages/pymatgen/analysis/diffusion/neb/pathfinder.py:431, in MigrationHop.get_structures(self, nimages, vac_mode, idpp, **idpp_kwargs)
428 migrating_specie_sites, other_sites = self._split_migrating_and_other_sites(vac_mode)
430 start_structure = Structure.from_sites([self.isite] + migrating_specie_sites + other_sites)
--> 431 end_structure = Structure.from_sites([self.esite] + migrating_specie_sites + other_sites)
433 structures = start_structure.interpolate(end_structure, nimages=nimages + 1, pbc=False)
435 if idpp:
File ~/repo/venv/lib/python3.11/site-packages/pymatgen/core/structure.py:951, in IStructure.from_sites(cls, sites, charge, validate_proximity, to_unit_cell)
949 prop_keys: list[str] = []
950 props = {}
--> 951 labels = [site.label for site in sites]
952 lattice = sites[0].lattice
953 for idx, site in enumerate(sites):
File ~/repo/venv/lib/python3.11/site-packages/pymatgen/core/structure.py:951, in <listcomp>(.0)
949 prop_keys: list[str] = []
950 props = {}
--> 951 labels = [site.label for site in sites]
952 lattice = sites[0].lattice
953 for idx, site in enumerate(sites):
File ~/repo/venv/lib/python3.11/site-packages/pymatgen/core/sites.py:81, in Site.__getattr__(self, attr)
79 if attr in props:
80 return props[attr]
---> 81 raise AttributeError(f"{attr=} not found on {type(self).__name__}")
AttributeError: attr='label' not found on PeriodicNeighbor
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3160/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3160/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3161
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3161/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3161/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3161/events
|
https://github.com/materialsproject/pymatgen/issues/3161
| 1,808,589,279
|
I_kwDOACgets5rzOHf
| 3,161
|
Migrate to cython v3
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5457867742,
"node_id": "LA_kwDOACgets8AAAABRVBz3g",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/breaking",
"name": "breaking",
"color": "41396E",
"default": false,
"description": "Breaking change"
},
{
"id": 5546088172,
"node_id": "LA_kwDOACgets8AAAABSpKW7A",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/cython",
"name": "cython",
"color": "37CBE3",
"default": false,
"description": "Performance critical Cython code"
},
{
"id": 5585018768,
"node_id": "LA_kwDOACgets8AAAABTOSfkA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/pkg",
"name": "pkg",
"color": "EFE8DB",
"default": false,
"description": "Package health and distribution related stuff"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"It is a one-line fix. `cdef int n_pbc_im = 3 ** n_pbc` -> `cdef int n_pbc_im = int(round(3 ** n_pbc))`"
] | 2023-07-17T20:38:30
| 2023-07-17T23:18:49
|
2023-07-17T23:18:49Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
[`cython` just released v3](https://cython.readthedocs.io/en/latest/src/changes.html#unified-release-notes) with a bunch of breaking changes that affect `pymatgen` installation.
This issue tracks migrating to `cython` v3 so we can remove the pin added in [e8d4917](https://github.com/materialsproject/pymatgen/commit/e8d4917b030ac9de94d0291b7ce410acd1a14d10).
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3161/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3161/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3162
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3162/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3162/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3162/events
|
https://github.com/materialsproject/pymatgen/pull/3162
| 1,810,700,309
|
PR_kwDOACgets5V02ZV
| 3,162
|
Unreadable string concat ops to f-string
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-18T20:53:12
| 2023-07-18T21:52:09
|
2023-07-18T21:52:07Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3162/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3162/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3162",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3162",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3162.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3162.patch",
"merged_at": "2023-07-18T21:52:07Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3163
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3163/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3163/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3163/events
|
https://github.com/materialsproject/pymatgen/issues/3163
| 1,810,721,933
|
I_kwDOACgets5r7WyN
| 3,163
|
Support `Molecule.from_str(SMILES)` without `openbabel`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5653124555,
"node_id": "LA_kwDOACgets8AAAABUPPVyw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/molecules",
"name": "molecules",
"color": "EF81DB",
"default": false,
"description": "Molecule stuff"
}
] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Just use https://github.com/pckroon/pysmiles ?"
] | 2023-07-18T21:08:12
| 2023-08-08T21:14:30
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
`openbabel` is difficult to install, esp. on Mac and apparently has been since 2012.
Current 1st party support in `Molecule.from_str()` is limited to `xyz`, `gjf`, `g03`, `json`.
SMILES is very widely used and warrants 1st party support.
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3163/reactions",
"total_count": 2,
"+1": 2,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3163/timeline
| null | false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3164
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3164/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3164/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3164/events
|
https://github.com/materialsproject/pymatgen/issues/3164
| 1,810,840,639
|
I_kwDOACgets5r7zw_
| 3,164
|
Isomorphic Edge Comparison Issue
|
{
"login": "rohithsrinivaas",
"id": 25458067,
"node_id": "MDQ6VXNlcjI1NDU4MDY3",
"avatar_url": "https://avatars.githubusercontent.com/u/25458067?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rohithsrinivaas",
"html_url": "https://github.com/rohithsrinivaas",
"followers_url": "https://api.github.com/users/rohithsrinivaas/followers",
"following_url": "https://api.github.com/users/rohithsrinivaas/following{/other_user}",
"gists_url": "https://api.github.com/users/rohithsrinivaas/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rohithsrinivaas/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rohithsrinivaas/subscriptions",
"organizations_url": "https://api.github.com/users/rohithsrinivaas/orgs",
"repos_url": "https://api.github.com/users/rohithsrinivaas/repos",
"events_url": "https://api.github.com/users/rohithsrinivaas/events{/privacy}",
"received_events_url": "https://api.github.com/users/rohithsrinivaas/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5525608888,
"node_id": "LA_kwDOACgets8AAAABSVoZuA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/analysis",
"name": "analysis",
"color": "7E50AA",
"default": false,
"description": "Concerning pymatgen.analysis"
},
{
"id": 5653124555,
"node_id": "LA_kwDOACgets8AAAABUPPVyw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/molecules",
"name": "molecules",
"color": "EF81DB",
"default": false,
"description": "Molecule stuff"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-18T23:01:44
| 2023-08-05T01:33:39
|
2023-08-05T01:33:39Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
A clear and concise bug description.
#### Repro
Steps to reproduce the behavior:
1. Go to 'https://github.com/materialsproject/pymatgen/blob/v2023.7.17/pymatgen/analysis/graphs.py#L73'
2. the code is supposed to compare the edge information of two molecules provided as arguments but instead compares the edges of one of the input molecules with itself.
Provide any example files that are needed to reproduce the error, especially if the bug pertains to parsing a file. If the file format is not supported by GitHub, zip it into an archive and upload that.
#### Expected behavior
What do you expect to happen?
```
f1_edges = frag1.edges()
if len(f1_edges) != len(f2_edges):
```
The above code takes the edges from frag1 which is an argument and compares them with the edges of frag2 (which is also an argument)
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3164/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3164/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3165
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3165/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3165/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3165/events
|
https://github.com/materialsproject/pymatgen/pull/3165
| 1,812,571,074
|
PR_kwDOACgets5V7REW
| 3,165
|
Revert `mp-api<0.34.0` pin
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4735709485,
"node_id": "LA_kwDOACgets8AAAABGkUxLQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/compatability",
"name": "compatability",
"color": "E25438",
"default": false,
"description": "Concerning pymatgen compatibility with different OS, Python versions, numpy versions, etc."
},
{
"id": 5585018768,
"node_id": "LA_kwDOACgets8AAAABTOSfkA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/pkg",
"name": "pkg",
"color": "EFE8DB",
"default": false,
"description": "Package health and distribution related stuff"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-19T19:14:06
| 2023-07-19T19:34:59
|
2023-07-19T19:34:58Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Originally added in #3056 to fix CI.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3165/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3165/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3165",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3165",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3165.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3165.patch",
"merged_at": "2023-07-19T19:34:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3166
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3166/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3166/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3166/events
|
https://github.com/materialsproject/pymatgen/issues/3166
| 1,812,585,484
|
I_kwDOACgets5sCdwM
| 3,166
|
`label` in `Structure.as_dict()` is `None` in the latest version
|
{
"login": "njzjz",
"id": 9496702,
"node_id": "MDQ6VXNlcjk0OTY3MDI=",
"avatar_url": "https://avatars.githubusercontent.com/u/9496702?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/njzjz",
"html_url": "https://github.com/njzjz",
"followers_url": "https://api.github.com/users/njzjz/followers",
"following_url": "https://api.github.com/users/njzjz/following{/other_user}",
"gists_url": "https://api.github.com/users/njzjz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/njzjz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/njzjz/subscriptions",
"organizations_url": "https://api.github.com/users/njzjz/orgs",
"repos_url": "https://api.github.com/users/njzjz/repos",
"events_url": "https://api.github.com/users/njzjz/events{/privacy}",
"received_events_url": "https://api.github.com/users/njzjz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@njzjz Thanks for reporting. This is not intended.\r\n\r\nThis was caused by #3135. @stefsmeets Could you take a look? `label` should still be `H` here.",
"Thanks for pinging me!\r\n\r\nI added `Site.label` is a new attribute (default `None`), so it was never 'H' to begin with unless explicitly set by the user or any code that uses it. So this behaviour is as expected (or at least the way intended).\r\n\r\nI can submit a PR to set the default to the species name if that is more sensible.",
"Ah, I found the culprit:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/80aa7813c0c74a7e9ab60d5d76af496ba3e195a5/pymatgen/core/sites.py#L586-L591\r\n\r\n`Structure.as_dict()` writes with `verbosity=1`, which adds `\"label\"` to the dict. This causes a name collision with the `.label` property."
] | 2023-07-19T19:21:16
| 2023-07-20T15:37:48
|
2023-07-20T15:37:48Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
The latest version gives the `'label': None` in `Structure.as_dict()`. I want to confirm if it is expected, as it breaks the tests in our downstream package.
#### Repro
```py
from pymatgen.core import Structure
import numpy as np
s = Structure(np.eye(3), ["H"], np.zeros((1, 3)), coords_are_cartesian=True)
print(s.as_dict())
```
```
{'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': 0, 'lattice': {'matrix': [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], 'pbc': (True, True, True), 'a': 1.0, 'b': 1.0, 'c': 1.0, 'alpha': 90.0, 'beta': 90.0, 'gamma': 90.0, 'volume': 1.0}, 'sites': [{'species': [{'element': 'H', 'occu': 1}], 'abc': [0.0, 0.0, 0.0], 'xyz': [0.0, 0.0, 0.0], 'label': None, 'properties': {}}]}
```
#### Expected behavior
In previous versions, `label` is `H`.
#### Environment
Relevant versions and platform info:
- OS: Linux
- Version 2023.7.17
#### Additional context
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3166/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3166/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3167
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3167/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3167/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3167/events
|
https://github.com/materialsproject/pymatgen/issues/3167
| 1,812,779,780
|
I_kwDOACgets5sDNME
| 3,167
|
DummySpecies have recursion issue when calling getattr
|
{
"login": "qchempku2017",
"id": 28149881,
"node_id": "MDQ6VXNlcjI4MTQ5ODgx",
"avatar_url": "https://avatars.githubusercontent.com/u/28149881?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/qchempku2017",
"html_url": "https://github.com/qchempku2017",
"followers_url": "https://api.github.com/users/qchempku2017/followers",
"following_url": "https://api.github.com/users/qchempku2017/following{/other_user}",
"gists_url": "https://api.github.com/users/qchempku2017/gists{/gist_id}",
"starred_url": "https://api.github.com/users/qchempku2017/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/qchempku2017/subscriptions",
"organizations_url": "https://api.github.com/users/qchempku2017/orgs",
"repos_url": "https://api.github.com/users/qchempku2017/repos",
"events_url": "https://api.github.com/users/qchempku2017/events{/privacy}",
"received_events_url": "https://api.github.com/users/qchempku2017/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"There are two possible solutions:\r\n1, Redefine the getattr of Species as the following:\r\n```python\r\ndef __getattr__(self, attr):\r\n if attr == \"_el\":\r\n raise AttributeError\r\n return getattr(self._el, attr)\r\n```\r\n2, Add\r\n```python\r\nself._el = None\r\n```\r\nto the __init__ function of DummySpecies.\r\n\r\nWhich one should be better?",
"Thanks. I just pushed a fix."
] | 2023-07-19T21:47:19
| 2023-07-19T22:12:21
|
2023-07-19T22:12:21Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
After pymatgen update v2023.6.28, a recursion issue happens when using DummySpecies in pytest fixtures.
Here is the fixture initialization error:
```bash
collecting ...
test_cofe/test_domain.py:None (test_cofe/test_domain.py)
..\..\venv\lib\site-packages\pluggy\_hooks.py:265: in __call__
return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
..\..\venv\lib\site-packages\pluggy\_manager.py:80: in _hookexec
return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
..\..\venv\lib\site-packages\_pytest\python.py:262: in pytest_pycollect_makeitem
return list(collector._genfunctions(name, obj))
..\..\venv\lib\site-packages\_pytest\python.py:489: in _genfunctions
self.ihook.pytest_generate_tests.call_extra(methods, dict(metafunc=metafunc))
..\..\venv\lib\site-packages\pluggy\_hooks.py:292: in call_extra
return self(**kwargs)
..\..\venv\lib\site-packages\pluggy\_hooks.py:265: in __call__
return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
..\..\venv\lib\site-packages\pluggy\_manager.py:80: in _hookexec
return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
..\..\venv\lib\site-packages\_pytest\python.py:148: in pytest_generate_tests
metafunc.parametrize(*marker.args, **marker.kwargs, _param_mark=marker)
..\..\venv\lib\site-packages\_pytest\python.py:1304: in parametrize
ids = self._resolve_parameter_set_ids(
..\..\venv\lib\site-packages\_pytest\python.py:1374: in _resolve_parameter_set_ids
return id_maker.make_unique_parameterset_ids()
..\..\venv\lib\site-packages\_pytest\python.py:966: in make_unique_parameterset_ids
resolved_ids = list(self._resolve_ids())
..\..\venv\lib\site-packages\_pytest\python.py:991: in _resolve_ids
yield "-".join(
..\..\venv\lib\site-packages\_pytest\python.py:992: in <genexpr>
self._idval(val, argname, idx)
..\..\venv\lib\site-packages\_pytest\python.py:1004: in _idval
idval = self._idval_from_value(val)
..\..\venv\lib\site-packages\_pytest\python.py:1051: in _idval_from_value
elif isinstance(getattr(val, "__name__", None), str):
..\..\venv\lib\site-packages\pymatgen\core\periodic_table.py:1062: in __getattr__
return getattr(self._el, attr)
..\..\venv\lib\site-packages\pymatgen\core\periodic_table.py:1062: in __getattr__
return getattr(self._el, attr)
..\..\venv\lib\site-packages\pymatgen\core\periodic_table.py:1062: in __getattr__
return getattr(self._el, attr)
E RecursionError: maximum recursion depth exceeded
!!! Recursion detected (same locals & position)
```
#### Repro
You can reproduce the same error using the following steps:
```python
sp = DummySpecies("XX", oxidation_state=100, spin=2)
getattr(sp, "__name__", None)
```
And get:
```bash
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\66422\PycharmProjects\smol\venv\lib\site-packages\pymatgen\core\periodic_table.py", line 1062, in __getattr__
return getattr(self._el, attr)
File "C:\Users\66422\PycharmProjects\smol\venv\lib\site-packages\pymatgen\core\periodic_table.py", line 1062, in __getattr__
return getattr(self._el, attr)
File "C:\Users\66422\PycharmProjects\smol\venv\lib\site-packages\pymatgen\core\periodic_table.py", line 1062, in __getattr__
return getattr(self._el, attr)
[Previous line repeated 995 more times]
RecursionError: maximum recursion depth exceeded.
```
#### Expected behavior
Normally, since DummySpecies does not have an element attribute, any call to non-existing attributes should return None. However, since DummySpecies inherits from Species whose getattr has be overwritten by that of self._el, when called by getattr, DummySpecies would keep looking for self._el recursively, causing error. Therefore, we should consider redefining getattr for DummySpecies instead of simply inheriting from Species.
**Strangely, this issue did not appear in any version before v2023.6.28. We have not figured out why.**
#### Environment
Relevant versions and platform info:
- OS: Windows 11
- Version: >=v2023.6.28
#### Additional context
More context like related issues/PRs.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3167/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3167/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3168
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3168/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3168/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3168/events
|
https://github.com/materialsproject/pymatgen/pull/3168
| 1,812,928,639
|
PR_kwDOACgets5V8fQ4
| 3,168
|
Fix CI error `"pdentries_test.csv"` not found
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
},
{
"id": 5578251138,
"node_id": "LA_kwDOACgets8AAAABTH1bgg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ci",
"name": "ci",
"color": "4E135C",
"default": false,
"description": "Continuous integration"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-20T00:24:11
| 2023-07-20T03:50:21
|
2023-07-20T03:50:20Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3168/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3168/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3168",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3168",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3168.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3168.patch",
"merged_at": "2023-07-20T03:50:20Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3169
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3169/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3169/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3169/events
|
https://github.com/materialsproject/pymatgen/pull/3169
| 1,813,693,410
|
PR_kwDOACgets5V_GQW
| 3,169
|
Fix issues with labels
|
{
"login": "stefsmeets",
"id": 873520,
"node_id": "MDQ6VXNlcjg3MzUyMA==",
"avatar_url": "https://avatars.githubusercontent.com/u/873520?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/stefsmeets",
"html_url": "https://github.com/stefsmeets",
"followers_url": "https://api.github.com/users/stefsmeets/followers",
"following_url": "https://api.github.com/users/stefsmeets/following{/other_user}",
"gists_url": "https://api.github.com/users/stefsmeets/gists{/gist_id}",
"starred_url": "https://api.github.com/users/stefsmeets/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/stefsmeets/subscriptions",
"organizations_url": "https://api.github.com/users/stefsmeets/orgs",
"repos_url": "https://api.github.com/users/stefsmeets/repos",
"events_url": "https://api.github.com/users/stefsmeets/events{/privacy}",
"received_events_url": "https://api.github.com/users/stefsmeets/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-20T10:45:57
| 2023-07-21T11:48:17
|
2023-07-20T15:37:46Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR fixes some issues with labels and adds new tests for previously unspecified behaviour.
Major changes:
- `Site.label` (and derivatives) defaults to `.species_string` instead of `None`
- Add label attribute to `Neighbor` and `PeriodicNeighbor`
Closes #3166
Closes #3160
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3169/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3169/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3169",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3169",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3169.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3169.patch",
"merged_at": "2023-07-20T15:37:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3170
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3170/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3170/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3170/events
|
https://github.com/materialsproject/pymatgen/issues/3170
| 1,814,139,086
|
I_kwDOACgets5sIZDO
| 3,170
|
ImportError when using abicheck.py with abipy and pymatgen
|
{
"login": "emayMTK",
"id": 125790174,
"node_id": "U_kgDOB39n3g",
"avatar_url": "https://avatars.githubusercontent.com/u/125790174?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/emayMTK",
"html_url": "https://github.com/emayMTK",
"followers_url": "https://api.github.com/users/emayMTK/followers",
"following_url": "https://api.github.com/users/emayMTK/following{/other_user}",
"gists_url": "https://api.github.com/users/emayMTK/gists{/gist_id}",
"starred_url": "https://api.github.com/users/emayMTK/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/emayMTK/subscriptions",
"organizations_url": "https://api.github.com/users/emayMTK/orgs",
"repos_url": "https://api.github.com/users/emayMTK/repos",
"events_url": "https://api.github.com/users/emayMTK/events{/privacy}",
"received_events_url": "https://api.github.com/users/emayMTK/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4812645414,
"node_id": "LA_kwDOACgets8AAAABHtskJg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/outdated",
"name": "outdated",
"color": "2A890C",
"default": false,
"description": "Issues resulting from using outdated versions of pymatgen or dependencies"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@emayMTK https://github.com/materialsproject/pymatgen/pull/3140 was a recent breaking change that renamed some of the `ParseError` subclasses. `AbinitTimerParserError` is now `AbinitTimerParseError` (note the dropped `r`). Looks like this was already addressed in https://github.com/abinit/abipy/commit/704f4eb0b02f3338a441c8c1dc79696db0449b5b by @gmatteo. Once `abipy` makes a new release, your error will be fixed. You can also modify your abipy package in place right now by replacing `AbinitTimerParserError` with `AbinitTimerParseError`.",
"Thank you. it worked."
] | 2023-07-20T14:33:11
| 2023-07-20T18:11:18
|
2023-07-20T16:58:14Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
I'm encountering an issue when trying to use `abicheck.py` with the `abipy` and `pymatgen` libraries in my `abienv` conda environment. Here's the command I'm running and the error I'm facing:
**Command:**
```bash
(abienv) mtk@mtk-HP-EliteBook-x360-1030-G2:~/abipy$ abicheck.py --with-flow
```
**Error :**
```bash
/home/mtk/miniconda3/envs/abienv/bin/abicheck.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').run_script('abipy==0.9.3', 'abicheck.py')
Traceback (most recent call last):
File "/home/mtk/miniconda3/envs/abienv/bin/abicheck.py", line 4, in
import('pkg_resources').run_script('abipy==0.9.3', 'abicheck.py')
File "/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/pkg_resources/init.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/pkg_resources/init.py", line 1561, in run_script
exec(code, namespace, namespace)
File "/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/abipy-0.9.3-py3.9.egg/EGG-INFO/scripts/abicheck.py", line 11, in
import abipy.flowtk as flowtk
File "/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/abipy-0.9.3-py3.9.egg/abipy/flowtk/init.py", line 15, in
from .tasks import *
File "/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/abipy-0.9.3-py3.9.egg/abipy/flowtk/tasks.py", line 36, in
from .abitimer import AbinitTimerParser
File "/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/abipy-0.9.3-py3.9.egg/abipy/flowtk/abitimer.py", line 2, in
from pymatgen.io.abinit.abitimer import AbinitTimerParserError, AbinitTimerParser, AbinitTimerSection
ImportError: cannot import name 'AbinitTimerParserError' from 'pymatgen.io.abinit.abitimer' (/home/mtk/miniconda3/envs/abienv/lib/python3.9/site-packages/pymatgen/io/abinit/abitimer.py)
```
It seems that the `AbinitTimerParserError` class is not being imported from the `pymatgen.io.abinit.abitimer` module, causing the `ImportError`. I have already checked that both `abipy` and `pymatgen` are installed in my `abienv` environment.
I have tried updating both `abipy` and `pymatgen` using `conda update`, but the issue persists. I'm using Python 3.9.
Any suggestions on how to resolve this issue would be greatly appreciated. Thank you in advance for your help!
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3170/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3170/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3171
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3171/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3171/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3171/events
|
https://github.com/materialsproject/pymatgen/pull/3171
| 1,814,444,394
|
PR_kwDOACgets5WBskA
| 3,171
|
v2023.7.20
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5757177592,
"node_id": "LA_kwDOACgets8AAAABVyeO-A",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/release",
"name": "release",
"color": "48924C",
"default": false,
"description": "Release related issues and PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-20T17:04:24
| 2023-07-20T17:14:42
|
2023-07-20T17:14:41Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3171/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3171/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3171",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3171",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3171.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3171.patch",
"merged_at": "2023-07-20T17:14:41Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3172
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3172/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3172/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3172/events
|
https://github.com/materialsproject/pymatgen/pull/3172
| 1,815,099,338
|
PR_kwDOACgets5WD60T
| 3,172
|
Fix a bug in pwscf.py. The proc_val function modifies string values.
|
{
"login": "pablogalaviz",
"id": 23246855,
"node_id": "MDQ6VXNlcjIzMjQ2ODU1",
"avatar_url": "https://avatars.githubusercontent.com/u/23246855?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pablogalaviz",
"html_url": "https://github.com/pablogalaviz",
"followers_url": "https://api.github.com/users/pablogalaviz/followers",
"following_url": "https://api.github.com/users/pablogalaviz/following{/other_user}",
"gists_url": "https://api.github.com/users/pablogalaviz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pablogalaviz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pablogalaviz/subscriptions",
"organizations_url": "https://api.github.com/users/pablogalaviz/orgs",
"repos_url": "https://api.github.com/users/pablogalaviz/repos",
"events_url": "https://api.github.com/users/pablogalaviz/events{/privacy}",
"received_events_url": "https://api.github.com/users/pablogalaviz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 2414169365,
"node_id": "MDU6TGFiZWwyNDE0MTY5MzY1",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20testing",
"name": "needs testing",
"color": "66ddab",
"default": false,
"description": "PRs that are not ready to merge due to lacking tests"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Nice test, thanks @pablogalaviz! 👍 "
] | 2023-07-21T03:33:27
| 2023-07-22T14:41:09
|
2023-07-22T14:41:09Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
The proc_val function modifies the value of string variables (changes 'd' for 'e'). For example, smearing = 'cold' becomes smearing = 'cole'. It is solved by using a local variable.
Major changes:
Added a local variable
```
val_replace = val.replace("d", "e")
return smart_int_or_float(val_replace)
```
## Todos
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3172/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3172/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3172",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3172",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3172.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3172.patch",
"merged_at": "2023-07-22T14:41:09Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3174
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3174/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3174/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3174/events
|
https://github.com/materialsproject/pymatgen/issues/3174
| 1,815,831,270
|
I_kwDOACgets5sO2Lm
| 3,174
|
.cif file from Cambridge Structural Database returns "ValueError: Invalid cif file with no structures!"
|
{
"login": "p3rAsperaAdAstra",
"id": 60529579,
"node_id": "MDQ6VXNlcjYwNTI5NTc5",
"avatar_url": "https://avatars.githubusercontent.com/u/60529579?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/p3rAsperaAdAstra",
"html_url": "https://github.com/p3rAsperaAdAstra",
"followers_url": "https://api.github.com/users/p3rAsperaAdAstra/followers",
"following_url": "https://api.github.com/users/p3rAsperaAdAstra/following{/other_user}",
"gists_url": "https://api.github.com/users/p3rAsperaAdAstra/gists{/gist_id}",
"starred_url": "https://api.github.com/users/p3rAsperaAdAstra/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/p3rAsperaAdAstra/subscriptions",
"organizations_url": "https://api.github.com/users/p3rAsperaAdAstra/orgs",
"repos_url": "https://api.github.com/users/p3rAsperaAdAstra/repos",
"events_url": "https://api.github.com/users/p3rAsperaAdAstra/events{/privacy}",
"received_events_url": "https://api.github.com/users/p3rAsperaAdAstra/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The error message says\r\n\r\n> The current occupancy_tolerance is set to: 1.0. Species occupancies sum to more than 1!\r\n\r\nIf you increase `occupancy_tolerance=10`, the file parses fine.\r\n\r\n```py\r\nfrom pymatgen.io.cif import CifParser\r\n\r\nparser = CifParser(\"Mn-Zn-Im.cif\", occupancy_tolerance=10)\r\n\r\nparser.get_structures()\r\n```\r\n\r\nWe can consider not printing the offending section of the CIF file to make the error message easier to parse and the failure cause easier to spot. Happy to take a PR for that.",
"I think this behavior should not be changed. I suggest you change the error message to suggest that you can increase the occupancy tolerance if you know what you are doing. You can also potentially increase the occupancy tolerance just a little to deal with small rounding errors. i.e., instead of 1.0, set it to 1.0001 or something.",
"I don't see a reason for the error message to contain the whole CIF file. A 230 line error message is a bad user experience in my opinion. Keeping the error to 2 or 3 lines means people are more likely to actually read it.",
"I agree. Not sure who modified it to contain the whole CIF file. The only reason to include the CIF is if you can identify the exact line where there is a problem. But this is not the case here.",
"I am not an expert on these matters, but shouldn't the default behaviour rather be to just inform the user of the occupancies issue with a `RuntimeWarning` combined with a brief explanation like numpy does it a lot?\r\n\r\nAlternatively, have an error thrown together with an explanation. that way program flow can be channeled using a try-catch, which I guess is kind of what is already happening, if you do the extra legwork to figure out how to catch the UserWarning.\r\n\r\nSo I guess it would be something like:\r\n\r\n```python\r\noccupancy_error_msg = '''The occupancy of the atoms does not sum up to one. \r\nIf you wish to read in the file regardless, please increase the occupancy tolerance:\r\nCifParser('your_cif_file.cif', occupancy_tolerance=10)'''\r\n\r\nif occupancy > 1: raise ValueError, occupancy_error_msg # or some other builtin-error \r\n```\r\n\r\nThen people could do something like:\r\n\r\n```python\r\nfrom glob import glob\r\nfrom pymatgen.io.cif import CifParser\r\n\r\nfor inp_path in glob('*.cif'):\r\n try:\r\n cif_file = CifParser(inp_path) \r\n except ValueError:\r\n cif_file = CifParser(inp_path, occupancy_tolerance = 10)\r\n # do some math\r\n```\r\n\r\nAfter initially being told off by the program.",
"@p3rAsperaAdAstra Isn't that what you get now if you do\r\n\r\n```py\r\nCifParser(path).get_structures(on_error='raise')\r\n```",
"\r\n> @p3rAsperaAdAstra Isn't that what you get now if you do\r\n> \r\n> ```python\r\n> CifParser(path).get_structures(on_error='raise')\r\n> ```\r\n\r\nOh yeah looks like I'm late to the party. Case closed I guess."
] | 2023-07-21T13:39:58
| 2023-07-25T16:58:06
|
2023-07-22T03:23:25Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
The `cif` file opens without any issue in VESTA, indicating that it is not broken. However, when the same file is loaded using the `pymatgen` library, it throws an error. The file in question is attached: Mn-Zn-Im.txt (GitHub does not accept the `.cif` file extension).
You can find the file here: [Mn-Zn-Im.txt](https://github.com/materialsproject/pymatgen/files/12126605/Mn-Zn-Im.txt)
The function causing the issue is: `pymatgen.io.cif.CifParser` (pymatgen version 2023.7.20)
The full error message is quite lengthy, as it prints out the entire `.cif` file.
<details>
<summary>Full error message</summary>
```py
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:993: UserWarning: Some occupancies ([6, 1, 2, 2, 2, 4, 2, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1]) sum to > 1! If they are within the occupancy_tolerance, they will be rescaled. The current occupancy_tolerance is set to: 1.0
warnings.warn(msg)
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:1140: UserWarning: No structure parsed for 1 structure in CIF. Section of CIF file below.
warnings.warn(f"No structure parsed for {i + 1} structure in CIF. Section of CIF file below.")
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:1141: UserWarning: data_IMIDZA
_database_code_depnum_ccdc_archive 'CCDC 1180193'
_database_code_CSD IMIDZA
loop_
_citation_id
_citation_doi
_citation_year
1 10.1002/zaac.19804640117 1980
_audit_creation_method 'Created from the CSD'
_audit_update_record '2021-11-23 downloaded from the CCDC.'
_database_code_NBS 514582
_chemical_formula_moiety '(C24 H24 Mn3 N16)n'
_chemical_name_systematic
catena-(hexakis(\m~2~-Imidazolyl-N,N')-bis(imidazole)-tri-manganese)
_chemical_absolute_configuration unk
_diffrn_ambient_temperature 295
_exptl_crystal_density_diffrn 1.542
_refine_ls_R_factor_gt 0.046
_refine_ls_wR_factor_gt 0.046
_diffrn_radiation_probe x-ray
_symmetry_cell_setting monoclinic
_symmetry_space_group_name_H-M 'P 21/c'
_symmetry_Int_Tables_number 14
_space_group_name_Hall '-P 2ybc'
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 -x,1/2+y,1/2-z
3 -x,-y,-z
4 x,1/2-y,1/2+z
_cell_length_a 10.775
_cell_length_b 13.136
_cell_length_c 10.677
_cell_angle_alpha 90
_cell_angle_beta 91.5
_cell_angle_gamma 90
_cell_volume 1510.71
_exptl_crystal_colour colorless
_cell_formula_units_Z 2
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Mn1 Mn -0.00780 0.37380 0.23130
Mn2 Mn 0.50000 0.50000 0.50000
N1 N 0.35750 0.46640 0.34830
N2 N 0.17750 0.41610 0.25720
N3 N 0.65410 0.50160 0.36040
N4 N 0.83560 0.46330 0.27060
N5 N 0.46580 0.67270 0.47440
N6 N 0.36330 0.81280 0.42580
N7 N -0.03300 0.33110 0.04240
N8 N -0.03320 0.24700 -0.14030
C1 C 0.23660 0.45300 0.35830
C2 C 0.27130 0.40380 0.17450
C3 C 0.37880 0.43390 0.22850
C4 C 0.74390 0.43350 0.34460
C5 C 0.80130 0.55990 0.23670
C6 C 0.69380 0.58190 0.29070
C7 C 0.38300 0.71540 0.39810
C8 C 0.43220 0.83530 0.52870
C9 C 0.49960 0.74680 0.55480
C10 C -0.09420 0.38800 -0.04690
C11 C -0.09460 0.33720 -0.15650
C12 C 0.00120 0.24780 -0.01840
H1 H 0.19900 0.46500 0.43600
H2 H 0.25700 0.37400 0.10400
H3 H 0.46200 0.43100 0.20100
H4 H 0.74800 0.37200
0.38100
H5 H 0.85900 0.59400 0.19900
H6 H 0.64800 0.62800 0.29000
H7 H 0.34000 0.67000 0.33200
H9 H 0.55600 0.72900 0.61300
H10 H -0.14000 0.45500 -0.03400
H11 H -0.12500 0.36300 -0.23800
H12 H 0.05300 0.19600 0.02100
N1B N 0.64250 0.53360 0.65170
N2B N 0.82250 0.58390 0.74280
C1B C 0.76340 0.54700 0.64170
C2B C 0.72870 0.59620 0.82550
C3B C 0.62120 0.56610 0.77150
H1B H 0.80100 0.53500 0.56400
H2B H 0.74300 0.62600 0.89600
H3B H 0.53800 0.56900 0.79900
N3B N 0.34590 0.49840 0.63960
N4B N 0.16440 0.53670 0.72940
C4B C 0.25610 0.56650 0.65540
C5B C 0.19870 0.44010 0.76330
C6B C 0.30620 0.41810 0.70930
H4B H 0.25200 0.62800 0.61900
H5B H 0.14100 0.40600 0.80100
H6B H 0.35200 0.37200 0.71000
N5B N 0.53420 0.32730 0.52560
N6B N 0.63670 0.18720 0.57420
C7B C 0.61700 0.28460 0.60190
C8B C 0.56780 0.16470 0.47130
C9B C 0.50040 0.25320 0.44520
H7B H 0.66000 0.33000 0.66800
H9B H 0.44400 0.27100 0.38700
Mn1B Mn 1.00780 0.62620 0.76870
N7C N -0.03300 0.16890 0.54240
N8C N -0.03320 0.25300 0.35970
C10C C -0.09420 0.11200 0.45310
C11C C -0.09460 0.16280 0.34350
C12C C 0.00120 0.25220 0.48160
H10C H -0.14000 0.04500 0.46600
H11C H -0.12500 0.13700 0.26200
H12C H 0.05300 0.30400 0.52100
N4 N -0.16440 0.46330 0.27060
Mn1 Mn 0.99220 0.37380 0.23130
Mn1C Mn -0.00780 0.12620 -0.26870
Mn1B Mn 0.00780 0.62620 0.76870
N4B N 1.16440 0.53670 0.72940
N7B N 1.03300 0.66890 0.95760
N8A N 1.03320 0.74700 0.64030
Mn1C Mn -0.00780 0.12620 0.73130
H8? H 0.501 0.163 0.454
H13? H 0.71000 0.37900 0.12700
warnings.warn(str(d))
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:1142: UserWarning: Error is Species occupancies sum to more than 1!.
warnings.warn(f"Error is {exc}.")
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:993: UserWarning: Some occupancies ([1, 4, 1, 1, 1, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]) sum to > 1! If they are within the occupancy_tolerance, they will be rescaled. The current occupancy_tolerance is set to: 1.0
warnings.warn(msg)
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:1140: UserWarning: No structure parsed for 2 structure in CIF. Section of CIF file below.
warnings.warn(f"No structure parsed for {i + 1} structure in CIF. Section of CIF file below.")
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:1141: UserWarning: data_IMIDZB
_database_code_depnum_ccdc_archive 'CCDC 1180194'
_database_code_C
SD IMIDZB
loop_
_citation_id
_citation_doi
_citation_year
1 10.1002/zaac.19804640117 1980
_audit_creation_method 'Created from the CSD'
_audit_update_record '2021-11-23 downloaded from the CCDC.'
_database_code_NBS 514583
_chemical_formula_moiety '(C12 H12 N8 Zn2)n'
_chemical_name_systematic
catena-(tetrakis(\m~2~-Imidazolyl)-N,N'-di-zinc)
_chemical_absolute_configuration unk
_diffrn_ambient_temperature 295
_exptl_crystal_density_diffrn 1.543
_refine_ls_R_factor_gt 0.067
_refine_ls_wR_factor_gt 0.067
_diffrn_radiation_probe x-ray
_symmetry_cell_setting tetragonal
_symmetry_space_group_name_H-M 'I 41 c d'
_symmetry_Int_Tables_number 110
_space_group_name_Hall 'I 4bw -2c'
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2+x,1/2+y,1/2+z
3 -y,1/2+x,1/4+z
4 1/2-y,x,3/4+z
5 -x,-y,z
6 1/2-x,1/2-y,1/2+z
7 y,1/2-x,1/4+z
8 1/2+y,-x,3/4+z
9 -x,y,1/2+z
10 1/2-x,1/2+y,z
11 y,1/2+x,3/4+z
12 1/2+y,x,1/4+z
13 x,-y,1/2+z
14 1/2+x,1/2-y,z
15 -y,1/2-x,3/4+z
16 1/2-y,-x,1/4+z
_cell_length_a 23.481
_cell_length_b 23.481
_cell_length_c 12.461
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 6870.46
_exptl_crystal_colour colorless
_cell_formula_units_Z 16
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Zn1 Zn 0.35170 0.09660 0.27290
Zn2 Zn 0.39930 -0.14990 0.22720
N1 N 0.34560 0.01550 0.30570
N2 N 0.37100 -0.08030 0.29330
N3 N 0.29110 0.12070 0.17240
N4 N 0.21560 0.12250 0.06780
N5 N 0.36380 0.15550 0.58930
N6 N 0.34330 0.13860 0.41400
N7 N 0.51710 0.14250 0.19610
N8 N 0.42800 0.11660 0.20920
C1 C 0.38290 -0.02320 0.25250
C2 C 0.33270 -0.06900 0.37910
C3 C 0.31850 -0.01360 0.38830
C4 C 0.24690 0.09140 0.12850
C5 C 0.24470 0.17610 0.05770
C6 C 0.28730 0.17410 0.12710
C7 C 0.35940 0.11770 0.50940
C8 C 0.35920 0.20840 0.52810
C9 C 0.34230 0.19440 0.41940
C10 C 0.47510 0.12620 0.25870
C11 C 0.43660 0.14030 0.11230
C12 C 0.49380 0.14960 0.10740
Zn2N Zn 0.14990 0.10070 -0.02280
Zn2L Zn 0.39930 0.14990 0.72720
Zn2D Zn 0.60070 0.14990 0.22720
N4O N 0.37750 -0.21560 0.31780
N5L N 0.36380 -0.15550 0.08930
N7D N 0.48290 -0.14250 0.19610
warnings.warn(str(d))
C:\Python\Python38\lib\site-packages\pymatgen\io\cif.py:1145: UserWarning: Issues encountered while parsing CIF: Some occupancies ([6, 1, 2, 2, 2, 4, 2, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1]) sum to > 1! If they are within the occupancy_tolerance, they will be rescaled. The current occupancy_tolerance is set to: 1.0
Species occupancies sum to more than 1!
Some occupancies ([1, 4, 1, 1, 1, 2, 2, 1, 2, 1
, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]) sum to > 1! If they are within the occupancy_tolerance, they will be rescaled. The current occupancy_tolerance is set to: 1.0
Species occupancies sum to more than 1!
warnings.warn("Issues encountered while parsing CIF: %s" % "\n".join(self.warnings))
[]
```
</details>
I have tried opening the file in a text editor, and I do not see any obvious issues with the formatting. The file opens fine in VESTA, a crystal structure visualizer, so I assume the file itself is not corrupted.
I am using the latest version of `pymatgen` (2023.7.20).
Any help would be appreciated.
#### Environment
- OS: Windows 10
- Python version: 3.8
- `pymatgen` version: 2023.7.20
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3174/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3174/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3175
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3175/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3175/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3175/events
|
https://github.com/materialsproject/pymatgen/pull/3175
| 1,816,584,204
|
PR_kwDOACgets5WI6cg
| 3,175
|
Add `CifParser.get_structures(on_error='warn')`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-22T03:04:57
| 2023-07-22T03:23:24
|
2023-07-22T03:23:23Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3174.
Doesn't actually change the default behavior of `CifParser.get_structures()`. That seemed too breaking. Instead adds a new kwarg
```py
on_error: Literal["ignore", "warn", "raise"] = "warn"
```
which is a step towards better error messages on parse errors when set to "error".
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3175/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3175/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3175",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3175",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3175.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3175.patch",
"merged_at": "2023-07-22T03:23:23Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3176
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3176/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3176/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3176/events
|
https://github.com/materialsproject/pymatgen/pull/3176
| 1,816,585,055
|
PR_kwDOACgets5WI6nr
| 3,176
|
`ruff . --fix`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-22T03:08:42
| 2023-07-22T03:31:43
|
2023-07-22T03:31:42Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Auto fix 64 cases of `RUF015` and `PERF102`.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3176/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3176/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3176",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3176",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3176.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3176.patch",
"merged_at": "2023-07-22T03:31:42Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3177
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3177/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3177/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3177/events
|
https://github.com/materialsproject/pymatgen/pull/3177
| 1,816,679,304
|
PR_kwDOACgets5WJMje
| 3,177
|
lots of `from_string` should be `classmethod`
|
{
"login": "njzjz",
"id": 9496702,
"node_id": "MDQ6VXNlcjk0OTY3MDI=",
"avatar_url": "https://avatars.githubusercontent.com/u/9496702?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/njzjz",
"html_url": "https://github.com/njzjz",
"followers_url": "https://api.github.com/users/njzjz/followers",
"following_url": "https://api.github.com/users/njzjz/following{/other_user}",
"gists_url": "https://api.github.com/users/njzjz/gists{/gist_id}",
"starred_url": "https://api.github.com/users/njzjz/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/njzjz/subscriptions",
"organizations_url": "https://api.github.com/users/njzjz/orgs",
"repos_url": "https://api.github.com/users/njzjz/repos",
"events_url": "https://api.github.com/users/njzjz/events{/privacy}",
"received_events_url": "https://api.github.com/users/njzjz/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-22T08:22:28
| 2023-07-22T23:54:04
|
2023-07-22T23:53:45Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Fix a bug introduced in #3158. A lot of `from_string` methods should be `classmethod`.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3177/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3177/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3177",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3177",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3177.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3177.patch",
"merged_at": "2023-07-22T23:53:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3178
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3178/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3178/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3178/events
|
https://github.com/materialsproject/pymatgen/pull/3178
| 1,816,790,000
|
PR_kwDOACgets5WJhre
| 3,178
|
Delete commented out print statements
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318918309,
"node_id": "LA_kwDOACgets8AAAABPQhApQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/linting",
"name": "linting",
"color": "5DBC83",
"default": false,
"description": "Linting and quality assurance"
},
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-22T14:48:55
| 2023-07-22T17:19:56
|
2023-07-22T17:19:55Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Apparently used for debugging at one point.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3178/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3178/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3178",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3178",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3178.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3178.patch",
"merged_at": "2023-07-22T17:19:55Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3179
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3179/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3179/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3179/events
|
https://github.com/materialsproject/pymatgen/pull/3179
| 1,817,261,806
|
PR_kwDOACgets5WK8z_
| 3,179
|
BUG: fix setting zero magmoms
|
{
"login": "lbluque",
"id": 9788715,
"node_id": "MDQ6VXNlcjk3ODg3MTU=",
"avatar_url": "https://avatars.githubusercontent.com/u/9788715?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/lbluque",
"html_url": "https://github.com/lbluque",
"followers_url": "https://api.github.com/users/lbluque/followers",
"following_url": "https://api.github.com/users/lbluque/following{/other_user}",
"gists_url": "https://api.github.com/users/lbluque/gists{/gist_id}",
"starred_url": "https://api.github.com/users/lbluque/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/lbluque/subscriptions",
"organizations_url": "https://api.github.com/users/lbluque/orgs",
"repos_url": "https://api.github.com/users/lbluque/repos",
"events_url": "https://api.github.com/users/lbluque/events{/privacy}",
"received_events_url": "https://api.github.com/users/lbluque/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5525608888,
"node_id": "LA_kwDOACgets8AAAABSVoZuA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/analysis",
"name": "analysis",
"color": "7E50AA",
"default": false,
"description": "Concerning pymatgen.analysis"
},
{
"id": 5733199609,
"node_id": "LA_kwDOACgets8AAAABVbmu-Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/magmoms",
"name": "magmoms",
"color": "3B4F19",
"default": false,
"description": "Magnetism related"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Do you mind adding a unittest for one mag structure to check for this? I am worried that someone might make changes in future that breaks this again.",
"Thanks!"
] | 2023-07-23T18:58:20
| 2023-07-24T16:36:05
|
2023-07-24T16:36:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
With the new changes that set the default `Sepcies.spin` to `None`, I fixed the logic for setting zero magmoms in `SpacegroupAnalyzer` to check for `None` values as well.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3179/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3179/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3179",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3179",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3179.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3179.patch",
"merged_at": "2023-07-24T16:36:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3180
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3180/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3180/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3180/events
|
https://github.com/materialsproject/pymatgen/pull/3180
| 1,818,778,204
|
PR_kwDOACgets5WQDM8
| 3,180
|
Prefer `pymatviz` interactive plotly version of periodic table heatmap if available
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5322856717,
"node_id": "LA_kwDOACgets8AAAABPURZDQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/data%20viz",
"name": "data viz",
"color": "3C19AC",
"default": false,
"description": "PRs and issues about pymatgen plotting functionality"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Why keep both, if we’re referring people to functionality in pymatviz? We should probably have a strategy here.\r\n\r\nSimilar issue with plotting functionality in crystal toolkit; generally, plotting changes there have been upstreamed to pymatgen, but only for plotters that already existed within pymatgen, because I didn’t want two variants of, say, PDPlotter in existence. Not all functionality has been moved yet, there are still Pourbaix plotting enhancements for example.",
"@mkhorton That's the long-term plan. This is meant as the 1st step in a deprecation/migration phase. But happy to discuss other options.",
"I would just note this - there will always be newer better packages coming up. There are two outcomes: 1. pymatgen depends on the new package for some functionality. or 2. that new package gets merged into pymatgen. \r\n\r\nFor (1) to be accepted by me, the package has to deliver major functionality, have reasonable long-term maintenance, and does not depend on pymatgen itself. Something like numpy satisfies all three criteria. mp-api fails the last criterion. \r\n\r\nRight now, pymatviz fails at least one, if not all three criteria (it depends on pymatgen, and while I have confidence in Janosh's coding, pymatviz is not part of some long-term funded infrastructure). \r\n\r\nIf (1) or (2) are not acceptable to either pymatgen maintainers or the author of the package in question, then the only other outcome is that it is an optional functionality that is used when present. That is what this PR is.",
"@mkhorton Should I leave this PR open until further brainstorming?",
"You can merge. "
] | 2023-07-24T16:44:58
| 2023-08-13T22:28:33
|
2023-07-25T18:52:32Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This PR changes `periodic_table_heatmap()` which now tries to import `ptable_heatmap_plotly` from `pymatviz`. If successful, all arguments are passed to that function along with deprecation messages for args that have different names in `pymatviz.ptable_heatmap_plotly` vs `pymatgen.util.plotting.periodic_table_heatmap`.
It does **_not_** add `pymatviz` as a new dependency of `pymatgen` to avoid circularity.
**Before**
**After**
**Code**
```py
import pandas as pd
from pymatgen.util.plotting import periodic_table_heatmap
df_ptable = pd.read_csv(
"https://github.com/janosh/pymatviz/raw/main/pymatviz/elements.csv", comment="#"
).set_index("symbol")
periodic_table_heatmap(df_ptable.atomic_mass.to_dict(), cmap="viridis")
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3180/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3180/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3180",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3180",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3180.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3180.patch",
"merged_at": "2023-07-25T18:52:32Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3181
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3181/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3181/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3181/events
|
https://github.com/materialsproject/pymatgen/issues/3181
| 1,819,407,589
|
I_kwDOACgets5scfTl
| 3,181
|
How to improve `Composition.__repr__`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4646275120,
"node_id": "LA_kwDOACgets8AAAABFPCIMA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/discussion",
"name": "discussion",
"color": "AA9790",
"default": false,
"description": ""
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Another example [mp-18767](https://materialsproject.org/materials/mp-18767):\r\n\r\n```py\r\nComposition('Li+:2 Mn3+:2 O2-:4')\r\n```\r\n\r\nBefore\r\n\r\n```py\r\nComp: Li2 Mn2 O4\r\n```",
"This is a good proposal, but what if in the future we consider even more detailed information like partial charge, would it be more complicated? I guess we can just round the partial charge to formal charge and use formal charge as species tag?",
"For added background, the plan is to keep the current `__str__` method. In Python `str` and `repr` serve 2 different purposes:\r\n\r\n- __repr__ goal is to be unambiguous\r\n- __str__ goal is to be readable\r\n\r\n`repr` is more for devs and `str` more for users.",
"Yup, retracted my comment! :) ",
"I think changing repr is fine. No one should be using repr for any purposes.",
"Cool. @tschaume @yang-ruoxi any downstream implications for `mp-web` / `crystaltoolkit` here?"
] | 2023-07-25T01:46:34
| 2023-07-25T19:10:33
|
2023-07-25T19:10:33Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
There's a problem with `Composition.__repr__`.
```py
from pymatgen.core import Composition
from pymatgen.core.periodic_table import Species
comp1 = Composition({Species("Fe2+"): 2})
comp2 = Composition({"Fe2+": 2})
comp3 = Composition({"Fe": 2})
```
These 3 compositions all print
```
Comp: Fe2
```
which isn't ideal given only the first 2 are equal.
```
comp1 == comp2
>>> True
comp1 == comp3
>>> False
```
Ideally, the output of `Composition.__repr__` should allow to recreate the `Composition` by pasting that string into the Python interpreter. Current `__repr__` is lacking `oxi_state` information and also doesn't produce valid Python code.
**Suggestion**
How about we change to:
```
print(f"{Composition('Fe2+:2')!r}")
>>> Composition('Fe2+:2')
```
This would strictly speaking be a breaking change since people might have written code that depends on how `Composition` stringifies. Curious to hear opinion @mkhorton @shyuep.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3181/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3181/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3182
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3182/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3182/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3182/events
|
https://github.com/materialsproject/pymatgen/pull/3182
| 1,819,443,535
|
PR_kwDOACgets5WSUYc
| 3,182
|
Better Composition `repr`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-25T02:33:42
| 2023-07-25T19:10:32
|
2023-07-25T19:10:30Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3181.
1d3ff8467 include oxidation states in `Composition.__repr__`
26b3b5b98 delete unused `doctest.testmod() if __name__ == "__main__"`
d2aed40d1 add tests for `Composition.__repr__` and `__str__`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3182/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3182/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3182",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3182",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3182.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3182.patch",
"merged_at": "2023-07-25T19:10:30Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3183
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3183/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3183/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3183/events
|
https://github.com/materialsproject/pymatgen/pull/3183
| 1,820,209,358
|
PR_kwDOACgets5WU6n1
| 3,183
|
Propagate labels through various Structure operations
|
{
"login": "stefsmeets",
"id": 873520,
"node_id": "MDQ6VXNlcjg3MzUyMA==",
"avatar_url": "https://avatars.githubusercontent.com/u/873520?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/stefsmeets",
"html_url": "https://github.com/stefsmeets",
"followers_url": "https://api.github.com/users/stefsmeets/followers",
"following_url": "https://api.github.com/users/stefsmeets/following{/other_user}",
"gists_url": "https://api.github.com/users/stefsmeets/gists{/gist_id}",
"starred_url": "https://api.github.com/users/stefsmeets/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/stefsmeets/subscriptions",
"organizations_url": "https://api.github.com/users/stefsmeets/orgs",
"repos_url": "https://api.github.com/users/stefsmeets/repos",
"events_url": "https://api.github.com/users/stefsmeets/events{/privacy}",
"received_events_url": "https://api.github.com/users/stefsmeets/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thank you very much @stefsmeets, this is great! 🙏 \r\n\r\nJust to get an overview, are there more structure operations that are known to drop the site labels? Supercells, inserting/deleting sites, applying translations/rotations are all very important. Just want to leave a record here of what else might need doing in the future.",
"@janosh Good point, I think these functions could still be updated:\r\n\r\n- [x] `IStructure.from_spacegroup`\r\n- [x] `IStructure.from_magnetic_spacegroup`\r\n- [x] `IStructure.get_sites_in_sphere`\r\n- [x] `IStructure.get_all_neighbors`\r\n- [x] `IStructure.interpolate`\r\n- [x] `IMolecule.get_sites_in_sphere`\r\n- [x] `IMolecule.get_boxed_structure`\r\n- [x] `IMolecule.get_centered_molecule`\r\n- [x] Everything to do with `Neighbor`/`PeriodicNeighbor`\r\n\r\nI will update the PR with fixes for these today or tomorrow.\r\n\r\nThere is also the CIF writer which drops the labels. I looked at this before, but I found it a bit tricky to update.",
"> There is also the CIF writer which drops the labels. I looked at this before, but I found it a bit tricky to update.\n\nFeel free to just leave a todo comment for CIFParser so that we know it should still be done at some point. ",
"I had a go at updating the `CifWriter` with labels. Since the label defaults to `Site.species_string`, it turns out that it's a little bit more straightforward than when I first looked at this. \r\n\r\nI also updated `site.label` to be a property. This helps generate the appropriate label for methods that update `Site` inplace (such as `SitesCollection.add_oxidation_state_by_*`).\r\n\r\nLet me know what you think.",
"I noticed that performing a `Structure.replace_species` operation leaves the label intact, leading to a misleading label or a confusing end-user experience (for example, replacing `Au` with `{\"Au\": 0.5, \"Cu\": 0.5}` will leave the label as `Au`). Do you have any thoughts on this @stefsmeets?",
"> I noticed that performing a `Structure.replace_species` operation leaves the label intact, leading to a misleading label or a confusing end-user experience (for example, replacing `Au` with `{\"Au\": 0.5, \"Cu\": 0.5}` will leave the label as `Au`). Do you have any thoughts on this @stefsmeets?\r\n\r\nI don't have any particular thoughts on this, but I can see how it would be confusing. What would you expect to happen?\r\n",
"> What would you expect to happen?\r\n\r\nmaybe update the label to `Composition({\"Au\": 0.5, \"Cu\": 0.5}).formula`",
"I can have a go at this next week. I created a new issue out of it to keep track.",
"I think this caused a regression in CIF output: https://github.com/materialsproject/pymatgen/issues/3761"
] | 2023-07-25T12:21:18
| 2024-04-16T18:15:06
|
2023-07-31T15:36:11Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
This PR follows up from #3137 and makes sure that labels are propagated correctly throughout structure, for example, when making supercells, inserting/deleting sites, applying translations/rotations, etc.
This PR also fixes a bug where the labels were incorrectly assigned when the CIF contains multiple species with different names.
Major changes:
- feature 1: Propagate labels in operations on structure
- fix 1: Correctly generate labels when cif contains multiple species with same name
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3183/reactions",
"total_count": 2,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 1,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3183/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3183",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3183",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3183.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3183.patch",
"merged_at": "2023-07-31T15:36:11Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3184
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3184/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3184/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3184/events
|
https://github.com/materialsproject/pymatgen/pull/3184
| 1,821,145,425
|
PR_kwDOACgets5WYG5-
| 3,184
|
Breaking: Return True for `Element in Composition` if `Species.symbol` matches `Element`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457867742,
"node_id": "LA_kwDOACgets8AAAABRVBz3g",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/breaking",
"name": "breaking",
"color": "41396E",
"default": false,
"description": "Breaking change"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Yikes, this is a pretty significant bug. So if I understand #3185 correctly, _if_ one applies `MP2020Compatibility` to an entry that has been pre-processed such that the structure is decorated with oxidation states (as opposed to just carrying `oxi_states` in the `.data` attribute, then the oxide (or other) corrections would potentially be missed. Is that right?\r\n\r\nI agree this should definitely be fixed as you've shown. Tagging @awvio in case she has any thoughts about impact on the correction scheme. My recollection is that when we developed and fit the new corrections, we always used un-decorated structures, and then either populated `oxi_states` ourselves or let `oxi_state_guesses` do it, so I don't believe this bug would have affected the fitted values or anything. I also don't think it should have affected anything in production (unless the build pipeline has recently changed to generate these `Species` containing structures)",
"> if one applies MP2020Compatibility to an entry that has been pre-processed such that the structure is decorated with oxidation states (as opposed to just carrying oxi_states in the .data attribute, then the oxide (or other) corrections would potentially be missed. Is that right?\r\n\r\n@rkingsbury That's correct. This came up in the context of CHGNet which can infer oxidation states on structures from predicted magmoms. Applying the correction scheme to these structures did not include any oxide/sulfide corrections (search for `process_entries` in [this notebook](https://github.com/CederGroupHub/chgnet/blob/f8a0e5253062d7db92545609372289cec2fd876e/examples/fine_tuning.ipynb) for details).\r\n\r\n> I also don't think it should have affected anything in production (unless the build pipeline has recently changed to generate these Species containing structures)\r\n\r\nI think so too. @esoteric-ephemera kindly checked _all_ MP ComputedStructureEntries and found none containing oxidation states.",
"I believe @rkingsbury is correct, this should not have affected the corrections we fit since the entries should have had the oxidation states added during the fitting."
] | 2023-07-25T21:01:40
| 2023-07-27T18:14:51
|
2023-07-27T14:37:45Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3185.
`Element in Composition` is currently `False` if that `Element` appears in `Composition` as a `Species` with an oxidation state.
This PR changes the `__contains__` method to return `True` for `x in Composition` if
1. `x` exactly matches a `Species` (both element symbol and oxidation state) in the composition (same as before)
2. _or_ if `x` is an `Element` and a `Species` with matching element symbol is present, regardless of oxidation state (returned `False` before).
It does not change behavior for the reverse, i.e. if a `Species in Composition` is still `False` if only its `Element` without oxidation state is in the `Composition`.
This is strictly speaking a breaking change but an improvement over previous behavior as it prevents unexpected behavior like `Element('O/S') in comp` returning `False` which caused MP 2020 correction scheme to not apply oxide/sulfide corrections if `comp` has oxidation states (see #3185).
I added unit tests for all edge cases incl. `DummySpecies`:
```py
# Test Species in Composition
comp = Composition({Species("Fe2+"): 2})
assert Species("Fe2+") in comp
assert Species("Fe3+") not in comp
assert "Fe" in comp
assert Element("Fe") in comp
# Test Element in Composition with Species
comp = Composition({Species("Fe2+"): 2})
assert Element("Fe") in comp
assert Element("O") not in comp
assert "Fe" in comp
assert "O" not in comp
# Test str in Composition with Element
comp = Composition({"Fe": 2})
assert "Fe" in comp
assert "O" not in comp
assert Element("Fe") in comp
assert Element("O") not in comp
# Test int (atomic number) in Composition
comp = Composition({Element("Fe"): 2})
assert 26 in comp # atomic number for Fe
assert 8 not in comp # atomic number for O
# Test float in Composition
comp = Composition({Element("Fe"): 2})
with pytest.raises(TypeError, match="expected string or bytes-like object, got 'float'"):
assert 1.5 in comp
# Test DummySpecies in Composition
comp = Composition({DummySpecies("X"): 2})
assert DummySpecies("X") in comp
assert DummySpecies("A") not in comp
assert "X" in comp
assert "Y" not in comp
assert Element("Fe") not in comp
assert Species("Fe2+") not in comp
```
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3184/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3184/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3184",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3184",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3184.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3184.patch",
"merged_at": "2023-07-27T14:37:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3185
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3185/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3185/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3185/events
|
https://github.com/materialsproject/pymatgen/issues/3185
| 1,821,189,754
|
I_kwDOACgets5sjSZ6
| 3,185
|
`MaterialsProject2020Compatibility` doesn't apply oxide/sulfide corrections if `O`/`S` have oxidation states
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5680875673,
"node_id": "LA_kwDOACgets8AAAABUptImQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/mixing-schemes",
"name": "mixing-schemes",
"color": "44BAE9",
"default": false,
"description": "About mixing energies from different DFT functionals"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"The problem is on this line which uses `Composition.__contains__` to check for `oxygen` in the entry composition. `Composition` doesn't currently contain an `Element` if that `Element` appears as a `Species` with an oxidation state.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/5c5f271ad1d6ca2e51146db4d61df99960d5acac/pymatgen/entries/compatibility.py#L280-L281"
] | 2023-07-25T21:27:42
| 2023-07-27T14:37:46
|
2023-07-27T14:37:46Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This minimal example of mp-18767 (LiMnO2) currently doesn't receive an oxide correction.
**Expected corrections**
> Energy Adjustments:
> MP2020 anion correction (oxide): -2.7480 eV (-0.3435 eV/atom)
> MP2020 GGA/GGA+U mixing correction (Mn): -3.3360 eV (-0.4170 eV/atom)
**Actual**
> Energy Adjustments:
> MP2020 GGA/GGA+U mixing correction (Mn): -3.3360 eV (-0.4170 eV/atom)
```py
from pymatgen.core import Structure
from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
from pymatgen.entries.computed_entries import ComputedStructureEntry
params = {
"run_type": "GGA+U",
"is_hubbard": True,
"pseudo_potential": {
"functional": "PBE",
"labels": ["Li_sv", "O", "Mn_pv"],
"pot_type": "paw",
},
"hubbards": {"Li": 0.0, "O": 0.0, "Mn": 3.9},
"potcar_symbols": ["PBE Li_sv", "PBE O", "PBE Mn_pv"],
"oxide_type": "oxide",
}
lmo = Structure.from_file("mp-18767-LiMnO2.cif")
cse = ComputedStructureEntry(lmo, -58.97, parameters=params)
MaterialsProject2020Compatibility().process_entry(cse, clean=True, on_error="raise")
```
```
None ComputedStructureEntry - Li2 Mn2 O4 (LiMnO2)
Energy (Uncorrected) = -58.9700 eV (-7.3712 eV/atom)
Correction = -3.3360 eV (-0.4170 eV/atom)
Energy (Final) = -62.3060 eV (-7.7882 eV/atom)
Energy Adjustments:
MP2020 GGA/GGA+U mixing correction (Mn): -3.3360 eV (-0.4170 eV/atom)
Parameters:
run_type = GGA+U
is_hubbard = True
pseudo_potential = {'functional': 'PBE', 'labels': ['Li_sv', 'O', 'Mn_pv'], 'pot_type': 'paw'}
hubbards = {'Li': 0.0, 'O': 0.0, 'Mn': 3.9}
potcar_symbols = ['PBE Li_sv', 'PBE O', 'PBE Mn_pv']
oxide_type = oxide
Data:
oxidation_states = {'Li': 1.0, 'Mn': 3.0, 'O': -2.0}
```
<details><summary>mp-18767-LiMnO2.cif</summary>
```cif
# generated using pymatgen
data_LiMnO2
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 2.86877900
_cell_length_b 4.63447500
_cell_length_c 5.83250700
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural LiMnO2
_chemical_formula_sum 'Li2 Mn2 O4'
_cell_volume 77.54484024
_cell_formula_units_Z 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Li+ 1.0
Mn3+ 3.0
O2- -2.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li+ Li0 1 0.50000000 0.50000000 0.37975050 1
Li+ Li1 1 0.00000000 0.00000000 0.62024950 1
Mn3+ Mn2 1 0.50000000 0.50000000 0.86325250 1
Mn3+ Mn3 1 0.00000000 0.00000000 0.13674750 1
O2- O4 1 0.50000000 0.00000000 0.36082450 1
O2- O5 1 0.00000000 0.50000000 0.09851350 1
O2- O6 1 0.50000000 0.00000000 0.90148650 1
O2- O7 1 0.00000000 0.50000000 0.63917550 1
```
</details>
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3185/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3185/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3186
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3186/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3186/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3186/events
|
https://github.com/materialsproject/pymatgen/pull/3186
| 1,821,408,116
|
PR_kwDOACgets5WY--L
| 3,186
|
[WIP] Create input and output modules for Metalwalls
|
{
"login": "chiang-yuan",
"id": 41962462,
"node_id": "MDQ6VXNlcjQxOTYyNDYy",
"avatar_url": "https://avatars.githubusercontent.com/u/41962462?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chiang-yuan",
"html_url": "https://github.com/chiang-yuan",
"followers_url": "https://api.github.com/users/chiang-yuan/followers",
"following_url": "https://api.github.com/users/chiang-yuan/following{/other_user}",
"gists_url": "https://api.github.com/users/chiang-yuan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chiang-yuan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chiang-yuan/subscriptions",
"organizations_url": "https://api.github.com/users/chiang-yuan/orgs",
"repos_url": "https://api.github.com/users/chiang-yuan/repos",
"events_url": "https://api.github.com/users/chiang-yuan/events{/privacy}",
"received_events_url": "https://api.github.com/users/chiang-yuan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-26T01:12:27
| 2023-07-29T02:29:07
|
2023-07-29T02:29:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
This is a feature enhancement to add an interface with [Metalwalls](https://gitlab.com/ampere2/metalwalls). As stated in their repo:
> MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a constant potential within the electrode materials.
This is a WIP. I appreciate any thoughts/inputs and the completion status is as follows:
## Input
### [Top level parameter keywords](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#toplevelparameter)
- [x] [num_steps](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#num_steps)
- [x] [timestep](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#timestep)
- [x] [temperature](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#temperature)
- [x] [num_pbc](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#num_pbc)
### [Top level block keywords](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#toplevelblock)
- [x] [thermostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#thermostat)
- [x] [barostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#barostat)
- [x] [velocity](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#velocity)
- [x] [species](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#species)
- [x] [species_type](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#species_type)
- [x] [dipoles_minimization](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dipoles_minimization)
- [ ] [preconditioner](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#preconditioner_d)
- [x] [radius_minimization](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#radius_minimization)
- [x] [molecules](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#molecules)
- [x] [constraint](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#constraint)
- [x] [harmonic_bond](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#harmonic_bond)
- [x] [harmonic_angle](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#harmonic_angle)
- [x] [dihedral](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dihedral)
- [x] [improper](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#improper)
- [x] [electrodes](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#electrodes)
- [x] [electrode_type](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#electrode_type)
- [x] [electrode_charges](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#electrode_charges)
- [x] [preconditioner](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#preconditioner_e)
- [x] [charge_neutrality](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#charge_neutrality)
- [x] [compute_force](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#compute_force)
- [x] [dipoles_and_electrodes](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dipoles_and_electrodes)
- [x] [algorithm](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#algorithm)
- [x] [preconditioner](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#preconditioner_de)
- [x] [charge_neutrality](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#charge_neutrality_de)
- [x] [interactions](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#interactions)
- [x] [coulomb](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#coulomb)
- [x] [lennard-jones](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#lennard-jones)
- [x] [fumi-tosi](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#fumi-tosi)
- [x] [xft](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#xft)
- [x] [daim](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#daim)
- [x] [damping](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#damping)
- [x] [steele](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#steele)
- [ ] [external_field](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#external_field)
- [x] [plumed](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#plumed)
- [x] [output](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#output)
## Data
- [ ] [header](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#header)
- [ ] [box](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#box)
- [ ] [coordinates](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#coordinates)
- [ ] [velocities](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#velocities)
- [ ] [forces](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#forces)
- [ ] [dipole](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dipoles)
- [ ] [radius](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#radius)
- [ ] [charges](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#charges)
- [ ] [potential_shift](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#potential_shift)
- [ ] [piston_velocity](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#piston_velocity)
- [ ] [thermostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#thermostat)
- [ ] [barostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#barostat)
- [ ] [polarization](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#polarization)
## Output
None
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "chiang-yuan",
"id": 41962462,
"node_id": "MDQ6VXNlcjQxOTYyNDYy",
"avatar_url": "https://avatars.githubusercontent.com/u/41962462?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chiang-yuan",
"html_url": "https://github.com/chiang-yuan",
"followers_url": "https://api.github.com/users/chiang-yuan/followers",
"following_url": "https://api.github.com/users/chiang-yuan/following{/other_user}",
"gists_url": "https://api.github.com/users/chiang-yuan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chiang-yuan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chiang-yuan/subscriptions",
"organizations_url": "https://api.github.com/users/chiang-yuan/orgs",
"repos_url": "https://api.github.com/users/chiang-yuan/repos",
"events_url": "https://api.github.com/users/chiang-yuan/events{/privacy}",
"received_events_url": "https://api.github.com/users/chiang-yuan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3186/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3186/timeline
| null | true
| true
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3186",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3186",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3186.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3186.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3187
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3187/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3187/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3187/events
|
https://github.com/materialsproject/pymatgen/issues/3187
| 1,822,750,950
|
I_kwDOACgets5spPjm
| 3,187
|
FEFFDictSet write_input appears to be bugged in some cases
|
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5782768655,
"node_id": "LA_kwDOACgets8AAAABWK4MDw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20investigation",
"name": "needs investigation",
"color": "C8FE85",
"default": false,
"description": "Needs further research to pinpoint cause of issue"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@stefsmeets Could this be caused by the recent changes to `Site.label`?",
"@matthewcarbone what is the last known version that this is working?\r\n\r\nI did a git bisect to way before we added labels, and it seems to be broken since a couple of months from what I can tell.\r\n\r\n```\r\nc62f8a05f4607d0d75f34c9f18315bd0598503b6 is the first bad commit\r\ncommit c62f8a05f4607d0d75f34c9f18315bd0598503b6\r\nAuthor: Ryan Kingsbury <RKingsbury@lbl.gov>\r\nDate: Mon May 2 16:40:28 2022 -0700\r\n\r\n FEFF: bugfix for structures with 1 abs atom\r\n\r\n pymatgen/io/feff/inputs.py | 21 +++++++++++++++------\r\n 1 file changed, 15 insertions(+), 6 deletions(-)\r\n```\r\n\r\nThis commit introduces the bug: https://github.com/materialsproject/pymatgen/commit/c62f8a05f4607d0d75f34c9f18315bd0598503b6",
"@stefsmeets I don't quite recall, no (though looks like you did find it). I do know that the old version of `pymatgen` does seem to work (from 2022).",
"@stefsmeets thanks a lot for digging into this!\n\n@rkingsbury looks like the commit fixed one case, but broke another. I'm not very familiar with this part of pymatgen. Do you see an easy way to fix both?",
"@janosh I've managed to pin down a version of PMG that works: `pymatgen<=2022.5.26`. This is what I've version-locked my own [code](https://github.com/AI-multimodal/Lightshow) to for now. It would be wonderful though to get the most recent API working. I would like to port my own software to the new API.",
"I just pushed a fix. Pls check.",
"Thanks for reporting @matthewcarbone and bisecting @stefsmeets and suggesting a fix @shyuep . Apologies @janosh I didn't see your ping last week.\r\n\r\nAs part of the PR that introduced the regression, I [added a test](https://github.com/materialsproject/pymatgen/pull/2505/commits/64309f276e12b5deb54139cde292bdafa0cb1275) for the case in which there is only a single absorbing atom in the structure (which is what motivated the change in the first place). The basic issue was that that single atom needs to be excluded from the pot_dict section. If the test still passes with @shyuep fix and if it works for you @matthewcarbone then I think we're good.\r\n",
"@shyuep @rkingsbury sorry for the late reply but this appears to work now. v2 API (`2023.9.10`) now passes our testing suite (https://github.com/AI-multimodal/Lightshow/pull/190) and as such I'm happy. I'll keep you posted if I find any other bugs 😁"
] | 2023-07-26T16:14:17
| 2023-09-18T15:37:08
|
2023-08-10T15:36:21Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
I've found what appears to be a strange edge case when using the `FEFFDictSet`, which does not appear in older versions of Pymatgen.
```python
print(struct) # this is mp-2664
```
```
Full Formula (Ti1 O1)
Reduced Formula: TiO
abc : 3.033043 3.033043 3.033043
angles: 60.000000 60.000000 60.000000
pbc : True True True
Sites (2)
# SP a b c magmom
--- ---- --- --- --- --------
0 Ti 0 0 0 -0
1 O 0.5 0.5 0.5 0
```
Note: there are clearly Ti and O atoms in this structure. Here's a boilerplate FEFF input config.
```python
dict_set = FEFFDictSet(
absorbing_atom="Ti",
structure=struct,
radius=10.0,
config_dict={
"S02": "0",
"COREHOLE": "regular",
"CONTROL": "1 1 1 1 1 1",
"XANES": "4 0.04 0.1",
"SCF": "7.0 0 100 0.2 3",
"FMS": "9.0 0",
"EXCHANGE": "0 0.0 0.0 2",
"RPATH": "-1",
}
)
```
But when trying to write the input file, I get this error.
```python
dict_set.write_input("my_test")
```
```
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[74], line 1
----> 1 dict_set.write_input("my_test")
File ~/miniforge3/envs/Lightshow/lib/python3.9/site-packages/pymatgen/io/feff/sets.py:99, in AbstractFeffInputSet.write_input(self, output_dir, make_dir_if_not_present)
95 os.makedirs(output_dir)
97 feff = self.all_input()
---> 99 feff_input = "\n\n".join(str(feff[k]) for k in ["HEADER", "PARAMETERS", "POTENTIALS", "ATOMS"] if k in feff)
101 for k, v in feff.items():
102 with open(os.path.join(output_dir, k), "w") as f:
File ~/miniforge3/envs/Lightshow/lib/python3.9/site-packages/pymatgen/io/feff/sets.py:99, in <genexpr>(.0)
95 os.makedirs(output_dir)
97 feff = self.all_input()
---> 99 feff_input = "\n\n".join(str(feff[k]) for k in ["HEADER", "PARAMETERS", "POTENTIALS", "ATOMS"] if k in feff)
101 for k, v in feff.items():
102 with open(os.path.join(output_dir, k), "w") as f:
File ~/miniforge3/envs/Lightshow/lib/python3.9/site-packages/pymatgen/io/feff/inputs.py:535, in Atoms.__str__(self)
533 def __str__(self):
534 """String representation of Atoms file."""
--> 535 lines_sorted = self.get_lines()
536 # TODO: remove the formatting and update the unit tests
537 lines_formatted = str(
538 tabulate(
539 lines_sorted,
540 headers=["* x", "y", "z", "ipot", "Atom", "Distance", "Number"],
541 )
542 )
File ~/miniforge3/envs/Lightshow/lib/python3.9/site-packages/pymatgen/io/feff/inputs.py:517, in Atoms.get_lines(self)
515 for i, site in enumerate(self._cluster[1:]):
516 site_symbol = re.sub(r"[^aA-zZ]+", "", site.species_string)
--> 517 ipot = self.pot_dict[site_symbol]
518 lines.append(
519 [
520 f"{site.x:f}",
(...)
527 ]
528 )
530 # sort by distance from absorbing atom
KeyError: 'Ti'
```
It appears that somehow Ti is not found in this `self.pot_dict` object buried in `pymatgen.io.feff.inputs.Atoms.get_lines`. I have no idea why and have not run into this before (this has worked in previous versions of Pymatgen). Any idea what's going on?
#### Repro
See above. I'm using Pymatgen version `2023.7.20`.
#### Expected behavior
I don't think this should error... Clearly Ti is in this structure!
#### Environment
MacOS M1 Ventura 13.4.1
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3187/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3187/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3189
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3189/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3189/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3189/events
|
https://github.com/materialsproject/pymatgen/pull/3189
| 1,824,959,520
|
PR_kwDOACgets5Wk7M8
| 3,189
|
Revert `LMAXMIX` "fix" added in #3041
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-27T18:35:46
| 2023-07-27T19:38:04
|
2023-07-27T19:38:03Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
As suggested by @matthewkuner and @arosen93. See discussion following https://github.com/materialsproject/pymatgen/pull/3041#issuecomment-1650336881.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3189/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3189/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3189",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3189",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3189.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3189.patch",
"merged_at": "2023-07-27T19:38:03Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3190
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3190/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3190/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3190/events
|
https://github.com/materialsproject/pymatgen/issues/3190
| 1,825,136,067
|
I_kwDOACgets5syV3D
| 3,190
|
Typo in setting `NLSPLINE` in MPNMRSet
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Beats me. I think you need to ping @arosen93 or @esoteric-ephemera. And if they don't know we're screwed. 😄 ",
"I think this would be within the wheelhouse of @mvenetos97. ",
"I think it's ok - caveat, this is not my area of expertise. The name of this set \"cs\" suggests computation of chemical shifts via NMR, as does the LCHIMAG = True tag. May just need to set LREAL = auto or false explicitly - NLSPLINE should be False if LREAL = True. \r\n\r\nFrom the VASP wiki:\r\n\r\n> For NLSPLINE=.TRUE., the PAW projectors in reciprocal space ([LREAL](https://www.vasp.at/wiki/index.php/LREAL)=.FALSE.) are set up using a spline interpolation so that they are k differentiable. This improves the susceptibility contribution to the chemical shifts. It only slightly affects the other contributions to the chemical shifts.\r\n\r\n> It is advised to set NLSPLINE=.TRUE. if and only if PAW projectors are applied in reciprocal space and chemical shifts are calculated, i.e., if and only if [LREAL](https://www.vasp.at/wiki/index.php/LREAL)=.FALSE. and [LCHIMAG](https://www.vasp.at/wiki/index.php/LCHIMAG)=.TRUE. As this option also gives slightly different total energies, it is advised to use the default NLSPLINE=.FALSE. in all other calculations for reasons of compatibility.\r\n\r\nThe [NMR examples on the wiki](https://www.vasp.at/wiki/index.php/Alpha-AlF3) also suggest that NLSPLINE = True is \"only needed if LREAL is NOT set\" even though the examples set LREAL = Auto. So i'd probably "
] | 2023-07-27T20:09:18
| 2023-08-01T15:22:24
|
2023-08-01T15:22:24Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/io/vasp/sets.py#L1908
However, why is this even desired?
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3190/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3190/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3191
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3191/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3191/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3191/events
|
https://github.com/materialsproject/pymatgen/pull/3191
| 1,825,614,233
|
PR_kwDOACgets5WnMMq
| 3,191
|
Add `bader_exe_path` keyword to `BaderAnalysis` and run `bader` tests in CI
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
},
{
"id": 5729312941,
"node_id": "LA_kwDOACgets8AAAABVX5grQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/cli",
"name": "cli",
"color": "19872C",
"default": false,
"description": "Command line interface"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-28T03:00:15
| 2023-07-28T23:12:55
|
2023-07-28T23:12:54Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
You can now use
```py
BaderAnalysis(bader_exe_path="/abs/path/to/bader")
```
to run `bader` anywhere on your system without any `PATH` modification shenanigans.
TODO: Promote `atomate2.SETTINGS.VASP_RUN_BADER: bool` to accept a string so users only need to specify `bader_exe_path` once in their `atomate2` config.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3191/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3191/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3191",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3191",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3191.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3191.patch",
"merged_at": "2023-07-28T23:12:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3192
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3192/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3192/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3192/events
|
https://github.com/materialsproject/pymatgen/pull/3192
| 1,827,225,706
|
PR_kwDOACgets5Wsp4Z
| 3,192
|
speed up `bader_caller` and `chargemol_caller`
|
{
"login": "chiang-yuan",
"id": 41962462,
"node_id": "MDQ6VXNlcjQxOTYyNDYy",
"avatar_url": "https://avatars.githubusercontent.com/u/41962462?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chiang-yuan",
"html_url": "https://github.com/chiang-yuan",
"followers_url": "https://api.github.com/users/chiang-yuan/followers",
"following_url": "https://api.github.com/users/chiang-yuan/following{/other_user}",
"gists_url": "https://api.github.com/users/chiang-yuan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chiang-yuan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chiang-yuan/subscriptions",
"organizations_url": "https://api.github.com/users/chiang-yuan/orgs",
"repos_url": "https://api.github.com/users/chiang-yuan/repos",
"events_url": "https://api.github.com/users/chiang-yuan/events{/privacy}",
"received_events_url": "https://api.github.com/users/chiang-yuan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Thank you so much for doing this! It has been on my backlog for a very long time.",
"You don't need to add it in this PR (unless you're feeling ambitious!), but it's likely that an analogous fix will solve similar issues with the [`chargemol_caller`](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/command_line/chargemol_caller.py).\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/0b7607af222344a330ac8c45271415ec816fb69d/pymatgen/command_line/chargemol_caller.py#L181-L189",
"@arosen93 thanks for pointing out chagemol as well! It actually requires little modification so I guess I can try to solve them both.",
"@chiang-yuan: I would certainly be very grateful if you did!!! 🙏 ",
"Chargemol needs to see all the input files in the same folder so the way around here is using symbolic link to point to large files . I also port the error message by bader and chagmol back to python RuntimeError.\r\n\r\nI have used `pytest` to test `test_bader_caller.py` and `test_chargemol_caller.py` locally on Perlmutter and they all passed. If this change cannot pass pytest on github workflow, I don't know where is the problem then... Perhaps somehow bader and chagemol are not correctly installed on the pytest environment. ",
"Looks like `CHGCAR` passed but `cube` failed. Maybe @janosh @arosen93 you will be interested in looking into this?\r\n\r\nhttps://github.com/materialsproject/pymatgen/actions/runs/5704593631/job/15458352230?pr=3192#step:7:183\r\n\r\n",
"I found the problem. The code was reading compressed test files but somehow didn't raise error on Perlmutter. Modify the code to handle compressed files and decompress them to temp directory if needed. Not sure if this is the ideal solution since this falls back to copying data to temp folder again (but only for compressed file and folder, the uncompressed files are still read at their original place). \r\n\r\nThis will also affect when we want to compress all the test files. #2994 ",
"Sorry, looks like this was waiting on me. I missed that. Just fixed the merge conflict. I'll submit the PR to `monty` to return `filepath` from `decompress_file`.\r\n\r\n@chiang-yuan Any additional tests we might want to add?\r\n\r\n",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`80.39%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`1fa96f8`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/1fa96f8535f86d2ee609c906d333f417c8a260e0?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.57% compared to head [(`6f9b905`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.01%.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3192 +/- ##\n==========================================\n- Coverage 74.57% 74.01% -0.57% \n==========================================\n Files 230 230 \n Lines 69494 69496 +2 \n Branches 16166 16163 -3 \n==========================================\n- Hits 51824 51436 -388 \n- Misses 14595 15019 +424 \n+ Partials 3075 3041 -34 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/command\\_line/chargemol\\_caller.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29tbWFuZF9saW5lL2NoYXJnZW1vbF9jYWxsZXIucHk=) | `61.56% <0.00%> (-0.29%)` | :arrow_down: |\n| [pymatgen/command\\_line/bader\\_caller.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29tbWFuZF9saW5lL2JhZGVyX2NhbGxlci5weQ==) | `60.61% <88.09%> (-1.12%)` | :arrow_down: |\n| [pymatgen/util/io\\_utils.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vdXRpbC9pb191dGlscy5weQ==) | `91.30% <100.00%> (+1.83%)` | :arrow_up: |\n\n... and [6 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3192?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n",
"@janosh I made two modifications, 1) delete ` decompress_file_to_path` and use `monty` instead 2) use `PymatgenTest.tmp_path` fixture. \r\n\r\nThe `monty` version of the test is still older version so the test is unsuccessful.",
"Thanks @chiang-yuan! 👍 this is a big improvement. required a lot of tweaking but i'm glad we got it merged.",
"Also offering thanks for this :) "
] | 2023-07-29T00:01:06
| 2023-08-08T19:59:32
|
2023-08-08T19:14:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
In the original implementation, CHGCAR is copied into temporary folder by `monty.zopen`. Since CHGCAR is usually very large, this makes bader analysis calling from pymatgen extremely slow.
this might close #2487
- fix 1: use `monty.tempfiie.ScratchdDr` context manager
- fix 2: do not copy large files like CHGCAR into temporary folder but read them in place instead
- fix 3: use `os.symlink` to link larges files for `chargemol_caller`
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3192/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3192/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3192",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3192",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3192.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3192.patch",
"merged_at": "2023-08-08T19:14:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3193
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3193/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3193/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3193/events
|
https://github.com/materialsproject/pymatgen/pull/3193
| 1,827,278,814
|
PR_kwDOACgets5Ws06B
| 3,193
|
[WIP] Add I/O interface with Metalwalls
|
{
"login": "chiang-yuan",
"id": 41962462,
"node_id": "MDQ6VXNlcjQxOTYyNDYy",
"avatar_url": "https://avatars.githubusercontent.com/u/41962462?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/chiang-yuan",
"html_url": "https://github.com/chiang-yuan",
"followers_url": "https://api.github.com/users/chiang-yuan/followers",
"following_url": "https://api.github.com/users/chiang-yuan/following{/other_user}",
"gists_url": "https://api.github.com/users/chiang-yuan/gists{/gist_id}",
"starred_url": "https://api.github.com/users/chiang-yuan/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/chiang-yuan/subscriptions",
"organizations_url": "https://api.github.com/users/chiang-yuan/orgs",
"repos_url": "https://api.github.com/users/chiang-yuan/repos",
"events_url": "https://api.github.com/users/chiang-yuan/events{/privacy}",
"received_events_url": "https://api.github.com/users/chiang-yuan/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 2414169365,
"node_id": "MDU6TGFiZWwyNDE0MTY5MzY1",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20testing",
"name": "needs testing",
"color": "66ddab",
"default": false,
"description": "PRs that are not ready to merge due to lacking tests"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5952080879,
"node_id": "LA_kwDOACgets8AAAABYsWL7w",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/feature",
"name": "feature",
"color": "241DAB",
"default": false,
"description": "PRs with new features, not enhancements to existing features"
}
] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-29T02:40:26
| 2024-08-03T19:01:57
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
> MetalWalls (MW) is a molecular dynamics code dedicated to the modelling of electrochemical systems. Its main originality is the inclusion of a series of methods allowing to apply a constant potential within the electrode materials.
This is the same PR but without dirty commit from other branch. The input classes are mostly finished.
- [ ] Need to add string representation for classes and file export method to print out `runtime.inpt` file
- [ ] Data input class. Should be convenient to convert `Structure` to metalwalls `data.inpt` format
- [ ] Output classes for post-processing
- [ ] Add tests
## Detailed implementation
### Input
#### [Top level parameter keywords](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#toplevelparameter)
- [x] [num_steps](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#num_steps)
- [x] [timestep](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#timestep)
- [x] [temperature](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#temperature)
- [x] [num_pbc](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#num_pbc)
#### [Top level block keywords](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#toplevelblock)
- [x] [thermostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#thermostat)
- [x] [barostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#barostat)
- [x] [velocity](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#velocity)
- [x] [species](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#species)
- [x] [species_type](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#species_type)
- [x] [dipoles_minimization](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dipoles_minimization)
- [ ] [preconditioner](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#preconditioner_d)
- [x] [radius_minimization](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#radius_minimization)
- [x] [molecules](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#molecules)
- [x] [constraint](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#constraint)
- [x] [harmonic_bond](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#harmonic_bond)
- [x] [harmonic_angle](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#harmonic_angle)
- [x] [dihedral](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dihedral)
- [x] [improper](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#improper)
- [x] [electrodes](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#electrodes)
- [x] [electrode_type](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#electrode_type)
- [x] [electrode_charges](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#electrode_charges)
- [x] [preconditioner](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#preconditioner_e)
- [x] [charge_neutrality](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#charge_neutrality)
- [x] [compute_force](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#compute_force)
- [x] [dipoles_and_electrodes](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dipoles_and_electrodes)
- [x] [algorithm](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#algorithm)
- [x] [preconditioner](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#preconditioner_de)
- [x] [charge_neutrality](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#charge_neutrality_de)
- [x] [interactions](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#interactions)
- [x] [coulomb](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#coulomb)
- [x] [lennard-jones](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#lennard-jones)
- [x] [fumi-tosi](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#fumi-tosi)
- [x] [xft](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#xft)
- [x] [daim](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#daim)
- [x] [damping](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#damping)
- [x] [steele](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#steele)
- [ ] [external_field](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#external_field)
- [x] [plumed](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#plumed)
- [x] [output](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#output)
### Data
- [ ] [header](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#header)
- [ ] [box](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#box)
- [ ] [coordinates](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#coordinates)
- [ ] [velocities](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#velocities)
- [ ] [forces](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#forces)
- [ ] [dipole](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#dipoles)
- [ ] [radius](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#radius)
- [ ] [charges](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#charges)
- [ ] [potential_shift](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#potential_shift)
- [ ] [piston_velocity](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#piston_velocity)
- [ ] [thermostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#thermostat)
- [ ] [barostat](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#barostat)
- [ ] [polarization](https://github.com/materialsproject/pymatgen/compare/master...chiang-yuan:pymatgen:metalwalls?expand=1#polarization)
### Output
None
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [ ] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3193/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3193/timeline
| null | true
| true
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3193",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3193",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3193.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3193.patch",
"merged_at": null
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3194
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3194/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3194/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3194/events
|
https://github.com/materialsproject/pymatgen/issues/3194
| 1,829,088,681
|
I_kwDOACgets5tBa2p
| 3,194
|
New release of pymatgen required
|
{
"login": "naik-aakash",
"id": 91958822,
"node_id": "U_kgDOBXsuJg",
"avatar_url": "https://avatars.githubusercontent.com/u/91958822?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/naik-aakash",
"html_url": "https://github.com/naik-aakash",
"followers_url": "https://api.github.com/users/naik-aakash/followers",
"following_url": "https://api.github.com/users/naik-aakash/following{/other_user}",
"gists_url": "https://api.github.com/users/naik-aakash/gists{/gist_id}",
"starred_url": "https://api.github.com/users/naik-aakash/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/naik-aakash/subscriptions",
"organizations_url": "https://api.github.com/users/naik-aakash/orgs",
"repos_url": "https://api.github.com/users/naik-aakash/repos",
"events_url": "https://api.github.com/users/naik-aakash/events{/privacy}",
"received_events_url": "https://api.github.com/users/naik-aakash/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5757177592,
"node_id": "LA_kwDOACgets8AAAABVyeO-A",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/release",
"name": "release",
"color": "48924C",
"default": false,
"description": "Release related issues and PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@naik-aakash [v2023.8.10](https://github.com/materialsproject/pymatgen/releases/tag/v2023.8.10) will be on PyPI in ~1h.",
"Thank you both!",
"@shyuep and @janosh , Thank you 😃 "
] | 2023-07-31T12:30:42
| 2023-08-11T06:35:53
|
2023-08-08T15:24:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
# Issue
The recent feature added to `pymatgen.io.lobster.lobsterenv.LobsterNeighbors` class to handle cobis and coops via PR #3050 is necessary for our Lobsterpy package to extend its functionality.
It would be great if a new release is made available soon.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3194/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3194/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3195
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3195/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3195/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3195/events
|
https://github.com/materialsproject/pymatgen/pull/3195
| 1,829,304,772
|
PR_kwDOACgets5WzjTJ
| 3,195
|
Unskip and fix `packmol` tests
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5653124555,
"node_id": "LA_kwDOACgets8AAAABUPPVyw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/molecules",
"name": "molecules",
"color": "EF81DB",
"default": false,
"description": "Molecule stuff"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-31T14:23:20
| 2023-07-31T14:59:24
|
2023-07-31T14:59:23Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
60ff0cbb3 don't use tempfile.TemporaryDirectory() in tests, prefer PymatgenTest.tmp_path auto-used fixture
b8a0f633c fix broken test_files paths in TestPackmolSet
2013d15b4 skip failing TestPackmolSet.test_random_seed due to openbabel not installed
b3c6150c3 only skip pymatgen/io/tests/test_packmol.py if packmol not installed
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3195/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3195/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3195",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3195",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3195.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3195.patch",
"merged_at": "2023-07-31T14:59:23Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3196
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3196/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3196/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3196/events
|
https://github.com/materialsproject/pymatgen/pull/3196
| 1,829,852,909
|
PR_kwDOACgets5W1c0N
| 3,196
|
Delete variable self assignments
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-31T19:10:29
| 2023-07-31T19:47:20
|
2023-07-31T19:47:19Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
4e1bb4b74 delete self-assignments
13ef1f80d del unused w_area_has_intersection_smoothstep
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3196/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3196/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3196",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3196",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3196.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3196.patch",
"merged_at": "2023-07-31T19:47:19Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3197
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3197/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3197/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3197/events
|
https://github.com/materialsproject/pymatgen/pull/3197
| 1,830,222,944
|
PR_kwDOACgets5W2tsZ
| 3,197
|
Improve `Structure` tests
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-07-31T23:44:23
| 2023-08-01T04:02:35
|
2023-08-01T04:02:34Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Most notable user-facing change: add `in_place: bool = True` keyword to `Structure.make_supercell()` and return the supercell.
a70f4c4c5 add `Structure/Molecule.sites` setter, move `@property` to SiteCollection
7f510ca35 don't use implementation detail `(Structure|Molecule)._sites`
c5052a223 rename `StructureTest.structure` attr to `struct`
28a895fcb add `IStructureTest.test_sites_setter`
185d2cb7c fix mypy
94f4413a7 test `translate/rotate_sites` `IndexError` if "list index out of range"
2ffd3bb67 tweak doc strings
f482ba0f3 test inverse `translate_sites` operations leave structure unchanged
7197592b6 `Structure.make_supercell()` add `in_place: bool = True` keyword and return supercell structure
638c095de test `make_supercell` `in_place=True` and `False`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3197/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3197/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3197",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3197",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3197.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3197.patch",
"merged_at": "2023-08-01T04:02:34Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3198
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3198/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3198/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3198/events
|
https://github.com/materialsproject/pymatgen/pull/3198
| 1,831,150,723
|
PR_kwDOACgets5W5zCq
| 3,198
|
Update pydantic requirement from <2.0.0 to <3.0.0
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
},
{
"id": 5452530206,
"node_id": "LA_kwDOACgets8AAAABRP8CHg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/python",
"name": "python",
"color": "2b67c6",
"default": false,
"description": "Pull requests that update Python code"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-08-01T12:15:18
| 2023-08-05T03:44:52
|
2023-08-05T03:44:48Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Updates the requirements on [pydantic](https://github.com/pydantic/pydantic) to permit the latest version.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pydantic/pydantic/releases">pydantic's releases</a>.</em></p>
<blockquote>
<h2>v2.1.1 2023-07-25</h2>
<h2>What's Changed</h2>
<ul>
<li>Skip FieldInfo merging when unnecessary by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6862">pydantic/pydantic#6862</a></li>
<li>Prepare 2.1.1 by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6865">pydantic/pydantic#6865</a></li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pydantic/pydantic/blob/main/HISTORY.md">pydantic's changelog</a>.</em></p>
<blockquote>
<h2>v2.1.1 (2023-07-25)</h2>
<p><a href="https://github.com/pydantic/pydantic/releases/tag/v2.1.1">GitHub release</a></p>
<ul>
<li>Skip FieldInfo merging when unnecessary by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6862">#6862</a></li>
</ul>
<h2>v2.1.0 (2023-07-25)</h2>
<p><a href="https://github.com/pydantic/pydantic/releases/tag/v2.1.0">GitHub release</a></p>
<ul>
<li>Add <code>StringConstraints</code> for use as Annotated metadata by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6605">#6605</a></li>
<li>Try to fix intermittently failing CI by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6683">#6683</a></li>
<li>Remove redundant example of optional vs default. by <a href="https://github.com/ehiggs-deliverect"><code>@ehiggs-deliverect</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6676">#6676</a></li>
<li>Docs update by <a href="https://github.com/samuelcolvin"><code>@samuelcolvin</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6692">#6692</a></li>
<li>Remove the Validate always section in validator docs by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6679">#6679</a></li>
<li>Fix recursion error in json schema generation by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6720">#6720</a></li>
<li>Fix incorrect subclass check for secretstr by <a href="https://github.com/AlexVndnblcke"><code>@AlexVndnblcke</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6730">#6730</a></li>
<li>update pdm / pdm lockfile to 2.8.0 by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6714">#6714</a></li>
<li>unpin pdm on more CI jobs by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6755">#6755</a></li>
<li>improve source locations for auxiliary packages in docs by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6749">#6749</a></li>
<li>Assume builtins don't accept an info argument by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6754">#6754</a></li>
<li>Fix bug where calling <code>help(BaseModelSubclass)</code> raises errors by <a href="https://github.com/hramezani"><code>@hramezani</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6758">#6758</a></li>
<li>Fix mypy plugin handling of <code>@model_validator(mode="after")</code> by <a href="https://github.com/ljodal"><code>@ljodal</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6753">#6753</a></li>
<li>update pydantic-core to 2.3.1 by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6756">#6756</a></li>
<li>Mypy plugin for settings by <a href="https://github.com/hramezani"><code>@hramezani</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6760">#6760</a></li>
<li>Use <code>contentSchema</code> keyword for JSON schema by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6715">#6715</a></li>
<li>fast-path checking finite decimals by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6769">#6769</a></li>
<li>Docs update by <a href="https://github.com/samuelcolvin"><code>@samuelcolvin</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6771">#6771</a></li>
<li>Improve json schema doc by <a href="https://github.com/hramezani"><code>@hramezani</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6772">#6772</a></li>
<li>Update validator docs by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6695">#6695</a></li>
<li>Fix typehint for wrap validator by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6788">#6788</a></li>
<li>🐛 Fix validation warning for unions of Literal and other type by <a href="https://github.com/lig"><code>@lig</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6628">#6628</a></li>
<li>Update documentation for generics support in V2 by <a href="https://github.com/tpdorsey"><code>@tpdorsey</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6685">#6685</a></li>
<li>add pydantic-core build info to <code>version_info()</code> by <a href="https://github.com/samuelcolvin"><code>@samuelcolvin</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6785">#6785</a></li>
<li>Fix pydantic dataclasses that use slots with default values by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6796">#6796</a></li>
<li>Fix inheritance of hash function for frozen models by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6789">#6789</a></li>
<li>✨ Add <code>SkipJsonSchema</code> annotation by <a href="https://github.com/Kludex"><code>@Kludex</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6653">#6653</a></li>
<li>Error if an invalid field name is used with Field by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6797">#6797</a></li>
<li>Add <code>GenericModel</code> to <code>MOVED_IN_V2</code> by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6776">#6776</a></li>
<li>Remove unused code from <code>docs/usage/types/custom.md</code> by <a href="https://github.com/hramezani"><code>@hramezani</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6803">#6803</a></li>
<li>Fix <code>float</code> -> <code>Decimal</code> coercion precision loss by <a href="https://github.com/adriangb"><code>@adriangb</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6810">#6810</a></li>
<li>remove email validation from the north star benchmark by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6816">#6816</a></li>
<li>Fix link to mypy by <a href="https://github.com/progsmile"><code>@progsmile</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6824">#6824</a></li>
<li>Improve initialization hooks example by <a href="https://github.com/hramezani"><code>@hramezani</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6822">#6822</a></li>
<li>Fix default port for mongosrv DSNs by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6827">#6827</a></li>
<li>Improve API documentation, in particular more links between usage and API docs by <a href="https://github.com/samuelcolvin"><code>@samuelcolvin</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6780">#6780</a></li>
<li>update pydantic-core to 2.4.0 by <a href="https://github.com/davidhewitt"><code>@davidhewitt</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6831">#6831</a></li>
<li>Fix <code>annotated_types.MaxLen</code> validator for custom sequence types by <a href="https://github.com/ImogenBits"><code>@ImogenBits</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6809">#6809</a></li>
<li>Update V1 by <a href="https://github.com/hramezani"><code>@hramezani</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6833">#6833</a></li>
<li>Make it so callable JSON schema extra works by <a href="https://github.com/dmontagu"><code>@dmontagu</code></a> in <a href="https://redirect.github.com/pydantic/pydantic/pull/6798">#6798</a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pydantic/pydantic/commit/cfd5b6c780a137c5e2394361db2ed93ba4ff368e"><code>cfd5b6c</code></a> Prepare 2.1.1 (<a href="https://redirect.github.com/pydantic/pydantic/issues/6865">#6865</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/d9d4750ac36dbb0a7b712a282929b0beae1ed5ab"><code>d9d4750</code></a> Skip FieldInfo merging when unnecessary (<a href="https://redirect.github.com/pydantic/pydantic/issues/6862">#6862</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/3284a249794efc30ec1935a0095671263a175c4e"><code>3284a24</code></a> Prepare for release of v2.1.0 (<a href="https://redirect.github.com/pydantic/pydantic/issues/6853">#6853</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/f8c081e0a3c6e9181d275414636344324d31df4c"><code>f8c081e</code></a> Allow customizing core schema generation by making <code>GenerateSchema</code> public (#...</li>
<li><a href="https://github.com/pydantic/pydantic/commit/0ff63bf00039b3f6bfbe42103a331546d6248b81"><code>0ff63bf</code></a> Update serialization doc to mention <code>Field.exclude</code> takes priority over call-...</li>
<li><a href="https://github.com/pydantic/pydantic/commit/0921bb30881f072afe4b48792d4e33f6ff5fb379"><code>0921bb3</code></a> Improve documentation for config (<a href="https://redirect.github.com/pydantic/pydantic/issues/6847">#6847</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/2db62485e7518e859e25256b5fff49a262fb886e"><code>2db6248</code></a> Fix error message for staticmethod/classmethod order with validate_call (<a href="https://redirect.github.com/pydantic/pydantic/issues/6686">#6686</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/81f37a36da916ef87a0a8b9f50ab6cd8d5679a0a"><code>81f37a3</code></a> Update json_encoders docs (<a href="https://redirect.github.com/pydantic/pydantic/issues/6848">#6848</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/3c02267777d3bc2c95604dcbb8e02ebf929ff162"><code>3c02267</code></a> delegate UUID serialization to pydantic-core (<a href="https://redirect.github.com/pydantic/pydantic/issues/6850">#6850</a>)</li>
<li><a href="https://github.com/pydantic/pydantic/commit/cff53856adb56634dc3df4d34689fbd23753c7f0"><code>cff5385</code></a> Add <code>config.defer_build</code> to optionally make model building lazy (<a href="https://redirect.github.com/pydantic/pydantic/issues/6823">#6823</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/pydantic/pydantic/compare/v0.0.2...v2.1.1">compare view</a></li>
</ul>
</details>
<br />
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3198/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3198/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3198",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3198",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3198.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3198.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3199
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3199/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3199/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3199/events
|
https://github.com/materialsproject/pymatgen/pull/3199
| 1,831,151,123
|
PR_kwDOACgets5W5zIE
| 3,199
|
Bump scipy from 1.9.0 to 1.11.1
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
},
{
"id": 5452530206,
"node_id": "LA_kwDOACgets8AAAABRP8CHg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/python",
"name": "python",
"color": "2b67c6",
"default": false,
"description": "Pull requests that update Python code"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-01T12:15:34
| 2023-08-01T14:58:55
|
2023-08-01T14:58:54Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [scipy](https://github.com/scipy/scipy) from 1.9.0 to 1.11.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/scipy/scipy/releases">scipy's releases</a>.</em></p>
<blockquote>
<h1>SciPy 1.11.1 Release Notes</h1>
<p>SciPy <code>1.11.1</code> is a bug-fix release with no new features
compared to <code>1.11.0</code>. In particular, a licensing issue
discovered after the release of <code>1.11.0</code> has been addressed.</p>
<h1>Authors</h1>
<ul>
<li>Name (commits)</li>
<li>h-vetinari (1)</li>
<li>Robert Kern (1)</li>
<li>Ilhan Polat (4)</li>
<li>Tyler Reddy (8)</li>
</ul>
<p>A total of 4 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.
This list of names is automatically generated, and may not be fully complete.</p>
<h1>SciPy 1.11.0 Release Notes</h1>
<p>SciPy <code>1.11.0</code> is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with <code>python -Wd</code> and check for <code>DeprecationWarning</code> s).
Our development attention will now shift to bug-fix releases on the
1.11.x branch, and on adding new features on the main branch.</p>
<p>This release requires Python <code>3.9+</code> and NumPy <code>1.21.6</code> or greater.</p>
<p>For running on PyPy, PyPy3 <code>6.0+</code> is required.</p>
<h1>Highlights of this release</h1>
<ul>
<li>Several <code>scipy.sparse</code> array API improvements, including <code>sparse.sparray</code>, a new
public base class distinct from the older <code>sparse.spmatrix</code> class,
proper 64-bit index support, and numerous deprecations paving the way to a
modern sparse array experience.</li>
<li><code>scipy.stats</code> added tools for survival analysis, multiple hypothesis testing,
sensitivity analysis, and working with censored data.</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/scipy/scipy/commit/cfe80116aaa145061246b8aec0e98248fbefb835"><code>cfe8011</code></a> REL: 1.11.1 rel commit [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/450d8aa5a66ce7122f5a3e255421d1acc61655e9"><code>450d8aa</code></a> Merge pull request <a href="https://redirect.github.com/scipy/scipy/issues/18779">#18779</a> from tylerjereddy/treddy_1_11_1_prep</li>
<li><a href="https://github.com/scipy/scipy/commit/6f942e8aff0c3df9655a8cc2acbfc205ee12050f"><code>6f942e8</code></a> DOC: update 1.11.1 relnotes</li>
<li><a href="https://github.com/scipy/scipy/commit/145cec505685866ab524b1d3a8d507483e27bf17"><code>145cec5</code></a> MAINT: fix unuran licensing</li>
<li><a href="https://github.com/scipy/scipy/commit/0760bababfc16b7b08e724eb94de0a9ce3091d98"><code>0760bab</code></a> MAINT:linalg.det:Return scalars for singleton inputs (<a href="https://redirect.github.com/scipy/scipy/issues/18763">#18763</a>)</li>
<li><a href="https://github.com/scipy/scipy/commit/a1c6f99b5b99c10d2bfa39eb013a11f83b2864e6"><code>a1c6f99</code></a> MAINT:linalg:Use only NumPy types in lu</li>
<li><a href="https://github.com/scipy/scipy/commit/5cdc2fe96af0c56ea1a89e7c5373c26a9549e3af"><code>5cdc2fe</code></a> MAINT:linalg:Remove memcpy from lu</li>
<li><a href="https://github.com/scipy/scipy/commit/d9ac3f329cde53765073e6df5ff1d80f7bc40d39"><code>d9ac3f3</code></a> FIX:linalg:Guard against possible permute_l out of bound behavior</li>
<li><a href="https://github.com/scipy/scipy/commit/7ec501097b3a22569025bf0d62cb2d89474c812b"><code>7ec5010</code></a> BUG: fix handling for <code>factorial(..., exact=False)</code> for 0-dim array inputs (#...</li>
<li><a href="https://github.com/scipy/scipy/commit/90415c6890365585576e96e42c5aeba253da0091"><code>90415c6</code></a> BUG: Fix work array construction for various weight shapes. (<a href="https://redirect.github.com/scipy/scipy/issues/18741">#18741</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/scipy/scipy/compare/v1.9.0...v1.11.1">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3199/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3199/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3199",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3199",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3199.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3199.patch",
"merged_at": "2023-08-01T14:58:54Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3200
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3200/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3200/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3200/events
|
https://github.com/materialsproject/pymatgen/pull/3200
| 1,831,151,410
|
PR_kwDOACgets5W5zL8
| 3,200
|
Bump matplotlib from 3.5.2 to 3.7.2
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
},
{
"id": 5452530206,
"node_id": "LA_kwDOACgets8AAAABRP8CHg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/python",
"name": "python",
"color": "2b67c6",
"default": false,
"description": "Pull requests that update Python code"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-01T12:15:44
| 2023-08-01T14:58:42
|
2023-08-01T14:58:41Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.5.2 to 3.7.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
<blockquote>
<h2>REL: v3.7.2</h2>
<p>This is the second bugfix release of the 3.7.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Avoid modifying input masks in <code>pcolor</code>/<code>pcolormesh</code></li>
<li>Fix 3D set_aspect error cases</li>
<li>Fix IPython's <code>%pylab</code> mode detection</li>
<li>Fix <code>Figure.get_constrained_layout_pads()</code></li>
<li>Fix <code>Legend.set_draggable()</code> with <code>update="bbox"</code></li>
<li>Fix <code>TransformedBbox.{,full_}contains</code></li>
<li>Fix clipping of <code>bar_label</code> text</li>
<li>Fix colorbar size when saving with explicit <code>bbox_inches</code></li>
<li>Fix errors when an input is entirely NaN</li>
<li>Fix leaks of exception tracebacks and <code>LayoutGrid</code> objects</li>
<li>Fix non-interpolated imshow in PDF export</li>
<li>Fix palettized image optimization in PDF export</li>
<li>Fix pgf tests with TeXLive 2022</li>
<li>Fix removal of <code>Axes</code> that contain widgets that are grabbing the mouse</li>
<li>Fix removal of draggable artists</li>
<li>Fix subslice optimization for long, fully nan lines</li>
<li>Fix tight layout if Figure has an existing layout manager</li>
<li>Fix window extent of AnnotationBbox before first draw</li>
<li>Fix wspace and hspace in subfigures</li>
<li>Improve Qt compatibility</li>
<li>Improve compatibility with Python 3.12</li>
<li>Prevent under the hood downcasting of values in <code>xcorr</code></li>
<li>Remove some NumPy function overrides from <code>pylab</code></li>
<li>Remove warning with symlog scales on mouseover</li>
</ul>
<h2>REL: v3.7.1</h2>
<p>This is the first bugfix release of the 3.7.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Ensure Qhull license is included in binary wheels</li>
<li>Fix application of rcParams on Axes labels</li>
<li>Fix compatibility with Pandas datetime unit converter</li>
<li>Fix compatibility with latest GTK4</li>
<li>Fix import of styles with relative path</li>
<li>Fix Lasso unresponsiveness when clicking and immediately releasing</li>
<li>Fix pickling of draggable legends</li>
<li>Fix RangeSlider.set_val when new value is outside existing value</li>
<li>Fix size of Tk spacers when changing display DPI</li>
<li>Fix wrapped text in constrained layout</li>
<li>Improve compatibility with third-party backends</li>
<li>Improve error if animation save path does not exist</li>
</ul>
<h2>REL: v3.7.0</h2>
<p>Highlights of this release include:</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/matplotlib/matplotlib/commit/d5210e4a87665581205f5147703dbd229b44cf66"><code>d5210e4</code></a> REL: v3.7.2</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/2dd68ef366761317fae3edc6c76b4afa04052de0"><code>2dd68ef</code></a> Merge branch 'v3.7.1-doc' into v3.7.x</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/1c891e8750d8faf5ea8372acaa486496dd411456"><code>1c891e8</code></a> DOC: Update GitHub stats for 3.7.2</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/ab837f6f32101bb1de6cd525f3e0801527bf4c40"><code>ab837f6</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/26260">#26260</a> from meeseeksmachine/auto-backport-of-pr-25960-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/ed294356155a40a503af891ede6f8181f51df5aa"><code>ed29435</code></a> Backport PR <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25960">#25960</a>: FIX: wspace and hspace in subfigures without layout engine</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/fef623b0a6303ad9164760c49e52d264e7d30445"><code>fef623b</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/26239">#26239</a> from meeseeksmachine/auto-backport-of-pr-26237-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/c5566a61eedb4a1a51bd4d56b5530e1a6fc328bf"><code>c5566a6</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/26238">#26238</a> from meeseeksmachine/auto-backport-of-pr-26237-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/d78d08b22c8d4c3c1c38d5423c5412d9e766a4ff"><code>d78d08b</code></a> Backport PR <a href="https://redirect.github.com/matplotlib/matplotlib/issues/26237">#26237</a>: Update FancyBboxPatch docstring</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/481f99a8737f148da3b773c999e701ad4dd9c43d"><code>481f99a</code></a> Backport PR <a href="https://redirect.github.com/matplotlib/matplotlib/issues/26237">#26237</a>: Update FancyBboxPatch docstring</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/4e086d3bf96d06f9320f8f68e7cfe975f01f8cd1"><code>4e086d3</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/26234">#26234</a> from meeseeksmachine/auto-backport-of-pr-26232-on-v...</li>
<li>Additional commits viewable in <a href="https://github.com/matplotlib/matplotlib/compare/v3.5.2...v3.7.2">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3200/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3200/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3200",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3200",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3200.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3200.patch",
"merged_at": "2023-08-01T14:58:41Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3201
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3201/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3201/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3201/events
|
https://github.com/materialsproject/pymatgen/pull/3201
| 1,831,151,951
|
PR_kwDOACgets5W5zTV
| 3,201
|
Bump numpy from 1.24.3 to 1.25.2
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
},
{
"id": 5452530206,
"node_id": "LA_kwDOACgets8AAAABRP8CHg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/python",
"name": "python",
"color": "2b67c6",
"default": false,
"description": "Pull requests that update Python code"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-01T12:16:04
| 2023-08-01T14:58:31
|
2023-08-01T14:58:30Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.25.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/numpy/numpy/releases">numpy's releases</a>.</em></p>
<blockquote>
<h2>v1.25.2</h2>
<h1>NumPy 1.25.2 Release Notes</h1>
<p>NumPy 1.25.2 is a maintenance release that fixes bugs and regressions
discovered after the 1.25.1 release. This is the last planned release in
the 1.25.x series, the next release will be 1.26.0, which will use the
meson build system and support Python 3.12. The Python versions
supported by this release are 3.9-3.11.</p>
<h2>Contributors</h2>
<p>A total of 13 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.</p>
<ul>
<li>Aaron Meurer</li>
<li>Andrew Nelson</li>
<li>Charles Harris</li>
<li>Kevin Sheppard</li>
<li>Matti Picus</li>
<li>Nathan Goldbaum</li>
<li>Peter Hawkins</li>
<li>Ralf Gommers</li>
<li>Randy Eckenrode +</li>
<li>Sam James +</li>
<li>Sebastian Berg</li>
<li>Tyler Reddy</li>
<li>dependabot[bot]</li>
</ul>
<h2>Pull requests merged</h2>
<p>A total of 19 pull requests were merged for this release.</p>
<ul>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24148">#24148</a>: MAINT: prepare 1.25.x for further development</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24174">#24174</a>: ENH: Improve clang-cl compliance</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24179">#24179</a>: MAINT: Upgrade various build dependencies.</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24182">#24182</a>: BLD: use <code>-ftrapping-math</code> with Clang on macOS</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24183">#24183</a>: BUG: properly handle negative indexes in ufunc_at fast path</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24184">#24184</a>: BUG: PyObject_IsTrue and PyObject_Not error handling in setflags</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24185">#24185</a>: BUG: histogram small range robust</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24186">#24186</a>: MAINT: Update meson.build files from main branch</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24234">#24234</a>: MAINT: exclude min, max and round from <code>np.__all__</code></li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24241">#24241</a>: MAINT: Dependabot updates</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24242">#24242</a>: BUG: Fix the signature for np.array_api.take</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24243">#24243</a>: BLD: update OpenBLAS to an intermeidate commit</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24244">#24244</a>: BUG: Fix reference count leak in str(scalar).</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24245">#24245</a>: BUG: fix invalid function pointer conversion error</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24255">#24255</a>: BUG: Factor out slow <code>getenv</code> call used for memory policy warning</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24292">#24292</a>: CI: correct URL in cirrus.star</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24293">#24293</a>: BUG: Fix C types in scalartypes</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/24294">#24294</a>: BUG: do not modify the input to ufunc_at</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/numpy/numpy/commit/ea677928332c37e8052b4d599bf6ee52cf363cf9"><code>ea67792</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/24296">#24296</a> from charris/prepare-1.25.2-release</li>
<li><a href="https://github.com/numpy/numpy/commit/47793ab7b7ab8a73bb4a54d4abd7f266664dfd6d"><code>47793ab</code></a> REL: Prepare for the NumPy 1.25.2 release.</li>
<li><a href="https://github.com/numpy/numpy/commit/9941dfecc267ad5cd5d709bce7018a9670234d1c"><code>9941dfe</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/24295">#24295</a> from charris/backport-24281</li>
<li><a href="https://github.com/numpy/numpy/commit/7b5e51a1acadb8730a102f1d867a268afe518297"><code>7b5e51a</code></a> BUG: Further fixes to indexing loop and added tests</li>
<li><a href="https://github.com/numpy/numpy/commit/f92167b85016857c53711486a23370718e14eaa1"><code>f92167b</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/24294">#24294</a> from charris/backport-24272</li>
<li><a href="https://github.com/numpy/numpy/commit/eb20535444f5b26747f198450f7fced0c4407acf"><code>eb20535</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/24293">#24293</a> from charris/backport-24240</li>
<li><a href="https://github.com/numpy/numpy/commit/1690ddda710a52fff2e8eb491e426fa7497ef83a"><code>1690ddd</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/24292">#24292</a> from charris/backport-24285</li>
<li><a href="https://github.com/numpy/numpy/commit/fa3a023a98da1d3f8fbeac0f961e9885fa93b8c3"><code>fa3a023</code></a> BUG: fix for modifying the index arg in ufunc_at</li>
<li><a href="https://github.com/numpy/numpy/commit/5c964bb4b1e2be9fba288f00a0b70025f48e0d7b"><code>5c964bb</code></a> TST: add failing test</li>
<li><a href="https://github.com/numpy/numpy/commit/8a731a5f254ff71255c1455525045321b6dbe0b6"><code>8a731a5</code></a> BUG: Fix C types in scalartypes</li>
<li>Additional commits viewable in <a href="https://github.com/numpy/numpy/compare/v1.24.3...v1.25.2">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3201/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3201/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3201",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3201",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3201.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3201.patch",
"merged_at": "2023-08-01T14:58:30Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3202
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3202/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3202/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3202/events
|
https://github.com/materialsproject/pymatgen/pull/3202
| 1,831,199,967
|
PR_kwDOACgets5W59si
| 3,202
|
Bump pypa/cibuildwheel from 2.12.3 to 2.14.1
|
{
"login": "dependabot[bot]",
"id": 49699333,
"node_id": "MDM6Qm90NDk2OTkzMzM=",
"avatar_url": "https://avatars.githubusercontent.com/in/29110?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/dependabot%5Bbot%5D",
"html_url": "https://github.com/apps/dependabot",
"followers_url": "https://api.github.com/users/dependabot%5Bbot%5D/followers",
"following_url": "https://api.github.com/users/dependabot%5Bbot%5D/following{/other_user}",
"gists_url": "https://api.github.com/users/dependabot%5Bbot%5D/gists{/gist_id}",
"starred_url": "https://api.github.com/users/dependabot%5Bbot%5D/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/dependabot%5Bbot%5D/subscriptions",
"organizations_url": "https://api.github.com/users/dependabot%5Bbot%5D/orgs",
"repos_url": "https://api.github.com/users/dependabot%5Bbot%5D/repos",
"events_url": "https://api.github.com/users/dependabot%5Bbot%5D/events{/privacy}",
"received_events_url": "https://api.github.com/users/dependabot%5Bbot%5D/received_events",
"type": "Bot",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1532985663,
"node_id": "MDU6TGFiZWwxNTMyOTg1NjYz",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dependencies",
"name": "dependencies",
"color": "0366d6",
"default": false,
"description": "Dependency issues and PRs"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-01T12:42:45
| 2023-08-01T14:58:20
|
2023-08-01T14:58:18Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.3 to 2.14.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.14.1</h2>
<ul>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b4 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1550">#1550</a>)</li>
</ul>
<h2>v2.14.0</h2>
<ul>
<li>✨ Adds support for building PyPy 3.10 wheels. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1525">#1525</a>)</li>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b3.</li>
<li>✨ Allow the use of the <code>{wheel}</code> placeholder in CIBW_TEST_COMMAND (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1533">#1533</a>)</li>
<li>📚 Docs & examples updates (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1532">#1532</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1416">#1416</a>)</li>
<li>⚠️ Removed support for running cibuildwheel in Python 3.7. Python 3.7 is EOL. However, cibuildwheel continues to build Python 3.7 wheels for the moment. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1175">#1175</a>)</li>
</ul>
<h2>v2.13.1</h2>
<ul>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a>)</li>
<li>🛠 Adds a moving <code>v<major>.<minor></code> tag for use in GitHub Actions workflow files. If you use this, you'll get the latest patch release within a minor version. Additionally, Dependabot won't send you PRs for patch releases. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a>)</li>
</ul>
<h2>v2.13.0</h2>
<ul>
<li>
<p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p>
<p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p>
</li>
<li>
<p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.14.1</h3>
<p><em>15 July 2023</em></p>
<ul>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b4 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1550">#1550</a>)</li>
</ul>
<h3>v2.14.0</h3>
<p><em>10 July 2023</em></p>
<ul>
<li>✨ Adds support for building PyPy 3.10 wheels. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1525">#1525</a>)</li>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b3.</li>
<li>✨ Allow the use of the <code>{wheel}</code> placeholder in CIBW_TEST_COMMAND (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1533">#1533</a>)</li>
<li>📚 Docs & examples updates (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1532">#1532</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1416">#1416</a>)</li>
<li>⚠️ Removed support for running cibuildwheel in Python 3.7. Python 3.7 is EOL. However, cibuildwheel continues to build Python 3.7 wheels for the moment. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1175">#1175</a>)</li>
</ul>
<h3>v2.13.1</h3>
<p><em>10 June 2023</em></p>
<ul>
<li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1516">#1516</a>)</li>
<li>🛠 Adds a moving <code>v<major>.<minor></code> tag for use in GitHub Actions workflow files. If you use this, you'll get the latest patch release within a minor version. Additionally, Dependabot won't send you PRs for patch releases. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1517">#1517</a>)</li>
</ul>
<h3>v2.13.0</h3>
<p><em>28 May 2023</em></p>
<ul>
<li>
<p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p>
<p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p>
</li>
<li>
<p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pypa/cibuildwheel/commit/f21bb8376a051ffb6cb5604b28ccaef7b90e8ab7"><code>f21bb83</code></a> Bump version: v2.14.1</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/a5b2e543e5d02654be6e22383524c7ce745903ce"><code>a5b2e54</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1550">#1550</a> from pypa/update-dependencies-pr</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/bd9675d05b8ba0f5fb5becbb3d4cb8eccd62e189"><code>bd9675d</code></a> Manually specify 3.12.0b4 on macOS</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/661ba2d0deb9b03c8b781f5d169d65f901518f50"><code>661ba2d</code></a> Update dependencies</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/66b46d086804a9e9782354100d96a3a445431bca"><code>66b46d0</code></a> Bump version: v2.14.0</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/b0a5c951f5fd2647af2f614cda0109888c7174d9"><code>b0a5c95</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1543">#1543</a> from pypa/update-dependencies-pr</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/8bfc92df50722d7e6c4b479856fc7250505c3b3e"><code>8bfc92d</code></a> Update dependencies</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/9afee48243a269243ca20a0b15120778857d69c4"><code>9afee48</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1541">#1541</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/7f6fe8a0318979cc1e71cb3e4dd33b1fc7c10cf9"><code>7f6fe8a</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1416">#1416</a> from Czaki/poerty_problem</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/f44d2784f85a87239000a6be8661f40fc908b497"><code>f44d278</code></a> Update docs/faq.md</li>
<li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.12.3...v2.14.1">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3202/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3202/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3202",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3202",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3202.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3202.patch",
"merged_at": "2023-08-01T14:58:18Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3203
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3203/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3203/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3203/events
|
https://github.com/materialsproject/pymatgen/pull/3203
| 1,832,409,165
|
PR_kwDOACgets5W-Bh4
| 3,203
|
[BUG] Allow None for Magmom values
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Pls add a test for this.",
"Actually, I was able to find the bug in atomate2 that caused this.\r\nhttps://github.com/materialsproject/atomate2/pull/460"
] | 2023-08-02T04:29:28
| 2023-08-02T21:18:07
|
2023-08-02T21:18:07Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
A possible follow-up to #3179
Recent changes resulted in some of the structures in my atomate2 workflow that had `[None, ...]` for all the `Magmom` values. I'm still looking into where these `[None, ...]` values came from (not 100% sure it's related to #3179) but this fix:
- Skips writing Magmom completely if all values are `None`
- Change `None` -> 0 if only some of the values are `None`
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3203/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3203/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3203",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3203",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3203.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3203.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3204
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3204/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3204/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3204/events
|
https://github.com/materialsproject/pymatgen/pull/3204
| 1,833,434,854
|
PR_kwDOACgets5XBgIb
| 3,204
|
Bugfix for Vasprun reading with POTCAR for chemical shift calculations
|
{
"login": "MichaelWolloch",
"id": 66372013,
"node_id": "MDQ6VXNlcjY2MzcyMDEz",
"avatar_url": "https://avatars.githubusercontent.com/u/66372013?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/MichaelWolloch",
"html_url": "https://github.com/MichaelWolloch",
"followers_url": "https://api.github.com/users/MichaelWolloch/followers",
"following_url": "https://api.github.com/users/MichaelWolloch/following{/other_user}",
"gists_url": "https://api.github.com/users/MichaelWolloch/gists{/gist_id}",
"starred_url": "https://api.github.com/users/MichaelWolloch/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/MichaelWolloch/subscriptions",
"organizations_url": "https://api.github.com/users/MichaelWolloch/orgs",
"repos_url": "https://api.github.com/users/MichaelWolloch/repos",
"events_url": "https://api.github.com/users/MichaelWolloch/events{/privacy}",
"received_events_url": "https://api.github.com/users/MichaelWolloch/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
open
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-02T15:41:11
| 2024-08-03T19:01:57
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Major changes:
- Fixes a bug updating the charges from POTCAR while reading a vasprun.xml file in the case of a chemical shift calculation
- Slight update to the splitting of POTCARs when reading from file.
- Added a test for the chemical shift vasprun.xml parsing with a POTCAR
- Re-added a test for internal POTCAR hashes.
This work is a result of updating atomate to work with the newest pymatgen and custodian releases and figuring out a hard to spot bug that was present there since May. Please see https://github.com/hackingmaterials/atomate/pull/778#issuecomment-1662336368 for details.
Another discussion related to this was taking place in #3068. There the hashing system was (hotly) debated and the initial problem was fixed (afaik). I still think that this PR has a nicer version, which is easy to read and preserves the internal hashes. This is why I re-enabled that unit-test. However, I am fine with commenting that out again or use the new `PMG_POTCAR_CHECKS` environmental variable to make it conditional?
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3204/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3204/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3204",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3204",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3204.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3204.patch",
"merged_at": null
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3206
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3206/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3206/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3206/events
|
https://github.com/materialsproject/pymatgen/pull/3206
| 1,834,207,062
|
PR_kwDOACgets5XEIzn
| 3,206
|
Test `class XYZ` edge cases
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-03T03:26:57
| 2023-08-03T03:38:40
|
2023-08-03T03:38:39Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
428fa7a80 refactor class XYZ
a63aa2f23 cover edge cases in class XYZTest
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3206/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3206/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3206",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3206",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3206.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3206.patch",
"merged_at": "2023-08-03T03:38:39Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3207
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3207/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3207/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3207/events
|
https://github.com/materialsproject/pymatgen/pull/3207
| 1,834,226,052
|
PR_kwDOACgets5XEM2M
| 3,207
|
Fix `EnergyAdjustment.__repr__`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5680875673,
"node_id": "LA_kwDOACgets8AAAABUptImQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/mixing-schemes",
"name": "mixing-schemes",
"color": "44BAE9",
"default": false,
"description": "About mixing energies from different DFT functionals"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-03T03:55:53
| 2023-08-03T03:56:38
|
2023-08-03T03:56:37Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
e0768d5c1 test_computed_entries.py rename single-letter vars
b4f4e7c3f google-style doc str
c199bb95d fix EnergyAdjustment.__repr__ when used by mp-api MPRester
c8e2f340a add test_energy_adjustment_repr()
Fixes
```py
print(entries['R2SCAN'].energy_adjustments)
File "pymatgen/pymatgen/entries/computed_entries.py", line 107, in __repr__
f" Generated by: {self.cls.get('@class')}",
^^^^^^^^^^^^
AttributeError: 'MaterialsProjectDFTMixingScheme' object has no attribute 'get'
```
Thanks for reporting @esoteric-ephemera! CC @munrojm
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3207/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3207/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3207",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3207",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3207.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3207.patch",
"merged_at": "2023-08-03T03:56:37Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3208
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3208/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3208/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3208/events
|
https://github.com/materialsproject/pymatgen/issues/3208
| 1,834,661,714
|
I_kwDOACgets5tWrdS
| 3,208
|
Typo in pymatgen.io.abinit.abitimer module AbinitTimerParserError
|
{
"login": "pjf295",
"id": 69720428,
"node_id": "MDQ6VXNlcjY5NzIwNDI4",
"avatar_url": "https://avatars.githubusercontent.com/u/69720428?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/pjf295",
"html_url": "https://github.com/pjf295",
"followers_url": "https://api.github.com/users/pjf295/followers",
"following_url": "https://api.github.com/users/pjf295/following{/other_user}",
"gists_url": "https://api.github.com/users/pjf295/gists{/gist_id}",
"starred_url": "https://api.github.com/users/pjf295/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/pjf295/subscriptions",
"organizations_url": "https://api.github.com/users/pjf295/orgs",
"repos_url": "https://api.github.com/users/pjf295/repos",
"events_url": "https://api.github.com/users/pjf295/events{/privacy}",
"received_events_url": "https://api.github.com/users/pjf295/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4812645414,
"node_id": "LA_kwDOACgets8AAAABHtskJg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/outdated",
"name": "outdated",
"color": "2A890C",
"default": false,
"description": "Issues resulting from using outdated versions of pymatgen or dependencies"
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5410436859,
"node_id": "LA_kwDOACgets8AAAABQny2-w",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/duplicate",
"name": "duplicate",
"color": "6A5AFB",
"default": true,
"description": "Duplicate issue"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Duplicate of https://github.com/materialsproject/pymatgen/issues/3170. See https://github.com/materialsproject/pymatgen/issues/3170#issuecomment-1644272034 for the fix."
] | 2023-08-03T09:34:41
| 2023-08-03T16:59:28
|
2023-08-03T16:59:28Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
While I have been using pymatgen for a while, I recently wanted to try using abipy to do some calculations in abinit. Using one of the example jupyter notebooks, there is an import line
`pymatgen.io.abinit.abitimer import AbinitTimerParserError
`
The import fails. Investigation of the modules available shows that there is a module "AbinitTimerParseError". My guess is that this was meant to be "AbinitTimerParserError" as the Jupyter notebook line indicates.
#### Repro
Steps to reproduce the behavior:
1. install abipy using pip
2. start ipython
3. "import abipy"
This fails within the abipy.abitimer module with the error message
```
ImportError Traceback (most recent call last)
Cell In[5], line 1
----> 1 from pymatgen.io.abinit.abitimer import AbinitTimerParserError
ImportError: cannot import name 'AbinitTimerParserError' from 'pymatgen.io.abinit.abitimer' (/data/miniconda/envs/abipy/lib/python3.11/site-packages/pymatgen/io/abinit/abitimer.py)
```
The line, "from pymatgen.io.abinit.abitimer import AbinitTimerParseError" works fine however. The pymatgen documentation only shows the module AbinitTimerParserError suggesting that a typo exists in pymatgen.io.abinit.abitimer
I manually fixed the error by changing two lines in pymatgen.io.abinit.abitimer
Line 35
class AbinitTimerParseError(ParseError): -> class AbinitTimerParserError(ParseError):
Line 58
Error = AbinitTimerParseError -> Error = AbinitTimerParserError
#### Expected behavior
Successful import of abipy
#### Environment
Relevant versions and platform info:
Centos 7
pymatgen-2023.7.20
abipy-0.9.3
#### Additional context
More context like related issues/PRs.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3208/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3208/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3209
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3209/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3209/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3209/events
|
https://github.com/materialsproject/pymatgen/pull/3209
| 1,835,216,859
|
PR_kwDOACgets5XHlXz
| 3,209
|
Markdownlint
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-03T14:47:51
| 2023-08-03T15:02:47
|
2023-08-03T15:02:46Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Now that we use markdown for docs, let's start adopting some of the tooling around it. Running https://github.com/igorshubovych/markdownlint-cli in pre-commit is a good start. `blacken-docs` should be next.
a4db1e352 pre-commit exclude tests/files (prev .*test_files) (fixes currently failing CI)
2c826b340 add pre-commit hook https://github.com/igorshubovych/markdownlint-cli
2c9c271c3 auto-format CHANGES.md
97c6f9663 auto-fix white space
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3209/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3209/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3209",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3209",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3209.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3209.patch",
"merged_at": "2023-08-03T15:02:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3210
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3210/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3210/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3210/events
|
https://github.com/materialsproject/pymatgen/pull/3210
| 1,835,438,143
|
PR_kwDOACgets5XIUe2
| 3,210
|
Fix codecov
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5456916296,
"node_id": "LA_kwDOACgets8AAAABRUHvSA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/docs",
"name": "docs",
"color": "35B067",
"default": false,
"description": "Documentation, examples, user guides"
},
{
"id": 5698361208,
"node_id": "LA_kwDOACgets8AAAABU6YXeA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dx",
"name": "dx",
"color": "73339B",
"default": false,
"description": "Developer experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-03T17:12:51
| 2023-08-03T17:15:34
|
2023-08-03T17:15:33Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
2f5896ab4 blacken-docs index.md
4b24b4641 /team page move world map below initial viewport since takes time to load
2d401d4f6 fix codecov: download coverage artifacts to .coverage where they'll be discovered
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3210/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3210/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3210",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3210",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3210.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3210.patch",
"merged_at": "2023-08-03T17:15:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3211
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3211/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3211/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3211/events
|
https://github.com/materialsproject/pymatgen/pull/3211
| 1,835,512,448
|
PR_kwDOACgets5XIj6v
| 3,211
|
Update `pytest-split` durations
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-03T18:11:35
| 2023-08-03T18:41:12
|
2023-08-03T18:38:46Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
937a435f4 fix .gitattributes outdated test_files/**/* linguist-vendored causing wrong language detection
70ee6e452 test.yml fix --durations-path (test_files->tests/files)/.pytest-split-durations
8f2bffa4c test_entry_tools.py del unused outdated test_dir
e6c40e9ad update pytest-split durations with new jobs that weren't previously discovered since unittest to pytest transition due to XXTest class name ending, not starting with TestXX (oops!)
bdd0a77f re-add pymatgen-white.svg and fix link to logo in readme
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3211/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3211/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3211",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3211",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3211.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3211.patch",
"merged_at": "2023-08-03T18:38:46Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3213
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3213/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3213/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3213/events
|
https://github.com/materialsproject/pymatgen/issues/3213
| 1,835,900,010
|
I_kwDOACgets5tbZxq
| 3,213
|
The problem caused by Vasprun object where there isn't a final_structure attribute for a VASP GW+BSE computation.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I don't think a final_structure even makes sense in a GW_BSE calculation isn't it? It only makes sense in a relaxation. This is not a bug. It simply means the calculation does not change the position of the atoms.",
"In any case, I have just pushed a fix that makes sure Vasprun.final_structure == Vasprun.initial_structure if there is no relaxation."
] | 2023-08-04T00:37:29
| 2023-08-07T14:42:35
|
2023-08-07T14:42:34Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
In Pymatgen code: the Vasprun parser has lots of places that assume final_structure has been set, but it is only set under certain conditions when the relevant data is found in the file:
https://github.com/materialsproject/pymatgen/blob/6d1ffa40123f4f714323f4308418b4062d422d65/pymatgen/io/vasp/outputs.py#L475
So if the Vasprun object does not have a final_structure attribute, this means that either:
- a calculation output is invalid (did it terminate succesfully?), or
- there exist valid outputs that don't have "finalpos" structure block. (i.e. a bug in Pymatgen, which assumes that they always do.)
In the case of the VASP output for a GW + BSE calculation, which seems to include different outputs than a regular optics calculation, the implementation mentioned above causes an error discussed [here](https://github.com/SMTG-UCL/sumo/issues/221#issuecomment-1664201167).
FYI, I also attached the vasprun.xml file below, which is the computation result of [Dielectric_properties_of_Si_using_BSE](https://www.vasp.at/wiki/index.php/Dielectric_properties_of_Si_using_BSE).
[vasprun.zip](https://github.com/SMTG-UCL/sumo/files/12246634/vasprun.zip)
Regards,
Zhao
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3213/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3213/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3214
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3214/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3214/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3214/events
|
https://github.com/materialsproject/pymatgen/pull/3214
| 1,835,943,855
|
PR_kwDOACgets5XJ95u
| 3,214
|
Fix GitHub language statistics after test files migration
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5456916296,
"node_id": "LA_kwDOACgets8AAAABRUHvSA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/docs",
"name": "docs",
"color": "35B067",
"default": false,
"description": "Documentation, examples, user guides"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-04T01:50:50
| 2023-08-04T02:27:26
|
2023-08-04T02:23:40Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
8039195ac refactor `TestStructureGraph.test_draw` use `PymatgenTest.tmp_path`
824296fff `BalancedReaction` don't create unnecessary lists
874baa587 `.gitattributes` fix `tests/files/` path causing wrong repo language statistics
Should say 100% Python. GH linguist misclassifies our test files. This PR ignores test files altogether.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3214/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3214/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3214",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3214",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3214.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3214.patch",
"merged_at": "2023-08-04T02:23:40Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3215
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3215/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3215/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3215/events
|
https://github.com/materialsproject/pymatgen/issues/3215
| 1,836,087,781
|
I_kwDOACgets5tcHnl
| 3,215
|
Is the documentation site changed?
|
{
"login": "ColdSnaap",
"id": 132535259,
"node_id": "U_kgDOB-ZT2w",
"avatar_url": "https://avatars.githubusercontent.com/u/132535259?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ColdSnaap",
"html_url": "https://github.com/ColdSnaap",
"followers_url": "https://api.github.com/users/ColdSnaap/followers",
"following_url": "https://api.github.com/users/ColdSnaap/following{/other_user}",
"gists_url": "https://api.github.com/users/ColdSnaap/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ColdSnaap/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ColdSnaap/subscriptions",
"organizations_url": "https://api.github.com/users/ColdSnaap/orgs",
"repos_url": "https://api.github.com/users/ColdSnaap/repos",
"events_url": "https://api.github.com/users/ColdSnaap/events{/privacy}",
"received_events_url": "https://api.github.com/users/ColdSnaap/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-04T05:25:41
| 2023-08-04T05:26:10
|
2023-08-04T05:26:10Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Is the documentation site changed? I feel like it's so hard too used compare to just few days ago...
|
{
"login": "ColdSnaap",
"id": 132535259,
"node_id": "U_kgDOB-ZT2w",
"avatar_url": "https://avatars.githubusercontent.com/u/132535259?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ColdSnaap",
"html_url": "https://github.com/ColdSnaap",
"followers_url": "https://api.github.com/users/ColdSnaap/followers",
"following_url": "https://api.github.com/users/ColdSnaap/following{/other_user}",
"gists_url": "https://api.github.com/users/ColdSnaap/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ColdSnaap/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ColdSnaap/subscriptions",
"organizations_url": "https://api.github.com/users/ColdSnaap/orgs",
"repos_url": "https://api.github.com/users/ColdSnaap/repos",
"events_url": "https://api.github.com/users/ColdSnaap/events{/privacy}",
"received_events_url": "https://api.github.com/users/ColdSnaap/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3215/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3215/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3217
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3217/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3217/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3217/events
|
https://github.com/materialsproject/pymatgen/issues/3217
| 1,837,097,342
|
I_kwDOACgets5tf-F-
| 3,217
|
Redundant lines in `Kpoints.automatic_density_by_lengths`
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Looks like a simple oversight in https://github.com/materialsproject/pymatgen/commit/8648d50f746486e194c2355d3c12e6dce8f6dea1. @arosen93 Could you confirm that line 1334 should be deleted?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/13e46fdf65ecdb60ddd491dd640f236ed3c5ce7a/pymatgen/io/vasp/inputs.py#L1334\r\n\r\n@matthewkuner Best to put the question in the body. 3 line titles are hard to read.",
"```python\r\nif has_odd or is_hexagonal or force_gamma:\r\n style = Kpoints.supported_modes.Gamma\r\nelse:\r\n style = Kpoints.supported_modes.Monkhorst\r\nstyle = Kpoints.supported_modes.Gamma\r\n```\r\n\r\nI'm guessing that the bottom `style = Kpoints.supported_modes.Gamma` should be deleted. That seems to be an oversight.\r\n\r\nJust saw your comment @janosh: yes you're right. Thanks for flagging, @matthewkuner."
] | 2023-08-04T17:15:28
| 2023-08-04T19:26:41
|
2023-08-04T19:26:40Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
https://github.com/materialsproject/pymatgen/blob/13e46fdf65ecdb60ddd491dd640f236ed3c5ce7a/pymatgen/io/vasp/inputs.py#L1330
What is the point of this when you always set the style to gamma a few lines later?
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3217/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3217/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3218
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3218/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3218/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3218/events
|
https://github.com/materialsproject/pymatgen/pull/3218
| 1,837,199,659
|
PR_kwDOACgets5XOL29
| 3,218
|
Fix `automatic_density_by_lengths` and add tests for it
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`50.00%`** and project coverage change: **`-0.01%`** :warning:\n> Comparison is base [(`bdab025`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/bdab025f6f57418fe346f58e2f8140004b403df8?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 72.28% compared to head [(`509a32d`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 72.28%.\n\n> :exclamation: Current head 509a32d differs from pull request most recent head 21f870c. Consider uploading reports for the commit 21f870c to get more accurate results\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3218 +/- ##\n==========================================\n- Coverage 72.28% 72.28% -0.01% \n==========================================\n Files 238 238 \n Lines 70253 70252 -1 \n Branches 16332 16333 +1 \n==========================================\n- Hits 50785 50783 -2 \n- Misses 16377 16378 +1 \n Partials 3091 3091 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/io/vasp/inputs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vdmFzcC9pbnB1dHMucHk=) | `85.71% <50.00%> (-0.02%)` | :arrow_down: |\n\n... and [2 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3218?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-08-04T18:48:15
| 2023-08-04T19:26:40
|
2023-08-04T19:26:39Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3217.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3218/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3218/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3218",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3218",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3218.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3218.patch",
"merged_at": "2023-08-04T19:26:39Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3219
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3219/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3219/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3219/events
|
https://github.com/materialsproject/pymatgen/pull/3219
| 1,837,220,011
|
PR_kwDOACgets5XOQSI
| 3,219
|
Prefer `len(structure)` over `structure.num_sites`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-04T19:09:03
| 2023-08-04T20:01:31
|
2023-08-04T20:01:30Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
It's shorter.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3219/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3219/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3219",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3219",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3219.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3219.patch",
"merged_at": "2023-08-04T20:01:30Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3220
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3220/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3220/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3220/events
|
https://github.com/materialsproject/pymatgen/issues/3220
| 1,837,311,468
|
I_kwDOACgets5tgyXs
| 3,220
|
`Kpoints` objects using wrong mesh types?
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5414010766,
"node_id": "LA_kwDOACgets8AAAABQrM_jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20discussion",
"name": "needs discussion",
"color": "D96543",
"default": false,
"description": "Needs discussion to agree on actionable next steps"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Tagging @arosen93 as the author.",
"Just to copy over part of my discussion with Matthew here: if a Monkhorst-Pack grid doesn't break the symmetry of the lattice, then everything should be OK. I did check the \"gold-standard\" MP entry, mp-149 / cubic diamond Si, and the input for the task document has a Monkhorst-pack grid (inappropriately)\r\n\r\nVASP will throw an error if the breaking of the lattice point / space group symmetry is severe enough. Custodian should catch this\r\n\r\nThe easy resolution is if the space group of a structure starts with 'F', force a gamma-centered k-point mesh",
"What am I the author of? 😅 I don't recall touching this.",
"@arosen93 Your reputation is such that you are the author of *everything* ! :-)\r\n",
"@arosen93 It looks like you did actually write this almost 2 years ago lol: https://github.com/materialsproject/pymatgen/commit/8648d50f746486e194c2355d3c12e6dce8f6dea1\r\n\r\nHowever, it looks like similar code existed prior to this.\r\n",
"True, I admittedly did add the `automatic_density_by_length` function, which is basically a minor variation of `automatic_density_by_vol` for systems with vacuum in _c_. I didn't want to touch any of the existing mesh logic. Since there's some repeated code, it probably would have been better to re-factor it a bit to prevent duplication, but alas I was young(er) and naïve(r). Thanks for cleaning this up!\r\n\r\nPersonally, I don't know much about the Monkhorst-Pack vs. Gamma-centered criteria in VASP (and thought at some point we decided to do Gamma-centered for all MP calculations, but I suppose not). I'll defer to @esoteric-ephemera on the best course of action on this one.\r\n\r\nEdit: I should note that `automatic_density_by_length` isn't used by any MP-related workflows, although the pre-existing `automatic_density_by_vol` is.",
"Yeah it seems like this code existed in some form at least since 2015: https://github.com/materialsproject/pymatgen/commit/423aa162c70d4791489e92e3ef5559b78bd8f2a7#diff-2b61e131c3f0a2a133effdfb20a2b8b6c84690d55bcd81b6d01ea4ecebdb9b0dL902\r\n\r\nso basically since this file was created... this could potentially be a very large issue for calcs pre-dating `force_gamma = True` being added to Atomate2 calcs.\r\n\r\nThere are definitely a sizeable number of calcs in the MPDB using Monkhorst meshes.",
"@arosen93 My bad, I thought we were still talking about `automatic_density_by_lengths` added in https://github.com/materialsproject/pymatgen/commit/8648d50f746486e194c2355d3c12e6dce8f6dea1. 😅 ",
"Happy to take the blame regardless. 😉"
] | 2023-08-04T20:37:12
| 2023-08-18T14:23:34
|
2023-08-18T14:23:33Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
https://github.com/materialsproject/pymatgen/blob/13e46fdf65ecdb60ddd491dd640f236ed3c5ce7a/pymatgen/io/vasp/inputs.py#L1235
Currently, this code could use Monkhorst-pack schemes for FCC and Face-centered orthorhombic cells. According to the [vasp wiki](https://www.vasp.at/wiki/index.php/KPOINTS#Symmetry_reduction_of_the_mesh), this is not good...
Anyone like @janosh @munrojm @esoteric-ephemera know why this is?
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3220/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3220/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3221
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3221/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3221/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3221/events
|
https://github.com/materialsproject/pymatgen/pull/3221
| 1,837,454,803
|
PR_kwDOACgets5XPDT4
| 3,221
|
Fix isomorphic for molecular graphs
|
{
"login": "rohithsrinivaas",
"id": 25458067,
"node_id": "MDQ6VXNlcjI1NDU4MDY3",
"avatar_url": "https://avatars.githubusercontent.com/u/25458067?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/rohithsrinivaas",
"html_url": "https://github.com/rohithsrinivaas",
"followers_url": "https://api.github.com/users/rohithsrinivaas/followers",
"following_url": "https://api.github.com/users/rohithsrinivaas/following{/other_user}",
"gists_url": "https://api.github.com/users/rohithsrinivaas/gists{/gist_id}",
"starred_url": "https://api.github.com/users/rohithsrinivaas/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/rohithsrinivaas/subscriptions",
"organizations_url": "https://api.github.com/users/rohithsrinivaas/orgs",
"repos_url": "https://api.github.com/users/rohithsrinivaas/repos",
"events_url": "https://api.github.com/users/rohithsrinivaas/events{/privacy}",
"received_events_url": "https://api.github.com/users/rohithsrinivaas/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5525608888,
"node_id": "LA_kwDOACgets8AAAABSVoZuA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/analysis",
"name": "analysis",
"color": "7E50AA",
"default": false,
"description": "Concerning pymatgen.analysis"
},
{
"id": 5653124555,
"node_id": "LA_kwDOACgets8AAAABUPPVyw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/molecules",
"name": "molecules",
"color": "EF81DB",
"default": false,
"description": "Molecule stuff"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3221?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`76.47%`** and project coverage change: **`-0.56%`** :warning:\n> Comparison is base [(`5865c95`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/5865c95bb9455ccdd7d1ba7bf552be1dcd061f84?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 73.40% compared to head [(`5c648e5`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3221?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 72.85%.\n\n> :exclamation: Current head 5c648e5 differs from pull request most recent head 23f4e5c. Consider uploading reports for the commit 23f4e5c to get more accurate results\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3221 +/- ##\n==========================================\n- Coverage 73.40% 72.85% -0.56% \n==========================================\n Files 238 238 \n Lines 70251 70252 +1 \n Branches 16332 16332 \n==========================================\n- Hits 51570 51183 -387 \n- Misses 15543 15965 +422 \n+ Partials 3138 3104 -34 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/analysis/graphs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3221?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYW5hbHlzaXMvZ3JhcGhzLnB5) | `74.77% <76.47%> (+0.02%)` | :arrow_up: |\n\n... and [6 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3221/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3221?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-08-04T23:56:25
| 2023-08-05T01:33:38
|
2023-08-05T01:33:38Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3164
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3221/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3221/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3221",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3221",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3221.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3221.patch",
"merged_at": "2023-08-05T01:33:38Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3222
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3222/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3222/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3222/events
|
https://github.com/materialsproject/pymatgen/pull/3222
| 1,837,466,800
|
PR_kwDOACgets5XPF3T
| 3,222
|
Add `PhaseDiagram` method `get_reference_energy`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5525608888,
"node_id": "LA_kwDOACgets8AAAABSVoZuA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/analysis",
"name": "analysis",
"color": "7E50AA",
"default": false,
"description": "Concerning pymatgen.analysis"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-05T00:22:45
| 2023-08-05T01:17:14
|
2023-08-05T01:17:13Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
4c99bea5b add `PhaseDiagram.get_reference_energy()`
4ad0f93d3 add test for `PhaseDiagram.get_form_energy_per_atom()`
b45dd043e add `TestPhaseDiagram.test_get_reference_energy()`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3222/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3222/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3222",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3222",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3222.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3222.patch",
"merged_at": "2023-08-05T01:17:13Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3223
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3223/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3223/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3223/events
|
https://github.com/materialsproject/pymatgen/pull/3223
| 1,837,492,460
|
PR_kwDOACgets5XPLAB
| 3,223
|
Add `Structure.elements` property
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-05T01:05:10
| 2023-08-05T01:44:34
|
2023-08-05T01:44:33Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
91e174654 add `Structure.elements` property (calling `Composition.elements`)
6ad901c8f add `TestIStructure.test_formula`
fdff89389 add `TestIStructure.test_elements`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3223/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3223/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3223",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3223",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3223.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3223.patch",
"merged_at": "2023-08-05T01:44:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3224
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3224/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3224/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3224/events
|
https://github.com/materialsproject/pymatgen/pull/3224
| 1,837,832,053
|
PR_kwDOACgets5XQOax
| 3,224
|
Add keyword `in_place: bool = True` to `SiteCollection.replace_species`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-05T16:27:42
| 2023-08-05T17:23:59
|
2023-08-05T17:23:58Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
3c92cd50e add @abstractmethod `copy()` to `SiteCollection`
41e121471 add `in_place: bool = True` to `SiteCollection.replace_species` and return modified structure
5ddc5c4d1 `mypy` `disable_error_code = "annotation-unchecked"`
48fe06288 add `TestIStructure.test_replace_species()`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3224/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3224/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3224",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3224",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3224.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3224.patch",
"merged_at": "2023-08-05T17:23:58Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3225
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3225/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3225/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3225/events
|
https://github.com/materialsproject/pymatgen/pull/3225
| 1,837,835,504
|
PR_kwDOACgets5XQPKr
| 3,225
|
list offending elements in `BVAnalyzer.get_valences` error message
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5525608888,
"node_id": "LA_kwDOACgets8AAAABSVoZuA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/analysis",
"name": "analysis",
"color": "7E50AA",
"default": false,
"description": "Concerning pymatgen.analysis"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-05T16:31:29
| 2023-08-05T18:20:44
|
2023-08-05T18:20:43Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
546b6904e list offending elements in `BVAnalyzer.get_valences` err msg
294f0332e test err msg in `TestBVAnalyzer.test_get_valences()`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3225/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3225/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3225",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3225",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3225.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3225.patch",
"merged_at": "2023-08-05T18:20:43Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3226
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3226/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3226/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3226/events
|
https://github.com/materialsproject/pymatgen/pull/3226
| 1,837,845,608
|
PR_kwDOACgets5XQRBd
| 3,226
|
Add `Entry.elements` property
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`90.78%`** and no project coverage change.\n> Comparison is base [(`cfaecbd`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/cfaecbdbdf47f825714ab759466ee5a369fad430?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.57% compared to head [(`be8cc82`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.57%.\n> Report is 1 commits behind head on master.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3226 +/- ##\n=======================================\n Coverage 74.57% 74.57% \n=======================================\n Files 230 230 \n Lines 69489 69493 +4 \n Branches 16168 16166 -2 \n=======================================\n+ Hits 51820 51825 +5 \n Misses 14595 14595 \n+ Partials 3074 3073 -1 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/core/composition.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29yZS9jb21wb3NpdGlvbi5weQ==) | `96.17% <ø> (ø)` | |\n| [pymatgen/core/structure.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29yZS9zdHJ1Y3R1cmUucHk=) | `85.28% <ø> (ø)` | |\n| [pymatgen/entries/entry\\_tools.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vZW50cmllcy9lbnRyeV90b29scy5weQ==) | `79.73% <0.00%> (ø)` | |\n| [pymatgen/io/shengbte.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vc2hlbmdidGUucHk=) | `66.32% <0.00%> (ø)` | |\n| [pymatgen/vis/structure\\_vtk.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vdmlzL3N0cnVjdHVyZV92dGsucHk=) | `9.23% <0.00%> (ø)` | |\n| [pymatgen/apps/battery/battery\\_abc.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYXBwcy9iYXR0ZXJ5L2JhdHRlcnlfYWJjLnB5) | `96.00% <50.00%> (ø)` | |\n| [pymatgen/analysis/chempot\\_diagram.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYW5hbHlzaXMvY2hlbXBvdF9kaWFncmFtLnB5) | `80.29% <66.66%> (ø)` | |\n| [pymatgen/analysis/structure\\_analyzer.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYW5hbHlzaXMvc3RydWN0dXJlX2FuYWx5emVyLnB5) | `86.59% <66.66%> (ø)` | |\n| [pymatgen/electronic\\_structure/plotter.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vZWxlY3Ryb25pY19zdHJ1Y3R1cmUvcGxvdHRlci5weQ==) | `45.82% <85.71%> (ø)` | |\n| [pymatgen/alchemy/filters.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYWxjaGVteS9maWx0ZXJzLnB5) | `79.82% <100.00%> (ø)` | |\n| ... and [16 more](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | |\n\n... and [3 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3226?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-08-05T16:56:11
| 2023-08-06T03:31:46
|
2023-08-06T03:31:46Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
36219e4fd add property `elements` to `Entry` class
11ec64277 use new `Structure.elements` and `Composition.elements` properties across pymatgen
fc21570f6 add `test_elements` in `TestPDEntry` and `TestTransformedPDEntry`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3226/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3226/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3226",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3226",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3226.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3226.patch",
"merged_at": "2023-08-06T03:31:45Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3227
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3227/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3227/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3227/events
|
https://github.com/materialsproject/pymatgen/pull/3227
| 1,838,316,142
|
PR_kwDOACgets5XRoju
| 3,227
|
Move `PymatgenTest.TEST_FILES_DIR` attribute into module scope
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`85.00%`** and no project coverage change.\n> Comparison is base [(`9455830`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/94558307c5fbf3f62efb699f4f24573b6b28a515?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.57% compared to head [(`fbe07e3`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.57%.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3227 +/- ##\n=======================================\n Coverage 74.57% 74.57% \n=======================================\n Files 230 230 \n Lines 69493 69493 \n Branches 16166 16166 \n=======================================\n+ Hits 51823 51824 +1 \n+ Misses 14596 14595 -1 \n Partials 3074 3074 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/io/vasp/inputs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vdmFzcC9pbnB1dHMucHk=) | `86.81% <50.00%> (ø)` | |\n| [pymatgen/analysis/pourbaix\\_diagram.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYW5hbHlzaXMvcG91cmJhaXhfZGlhZ3JhbS5weQ==) | `89.07% <100.00%> (ø)` | |\n| [pymatgen/io/abinit/inputs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vYWJpbml0L2lucHV0cy5weQ==) | `78.83% <100.00%> (ø)` | |\n| [pymatgen/util/testing.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vdXRpbC90ZXN0aW5nLnB5) | `87.50% <100.00%> (ø)` | |\n\n... and [3 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3227?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-08-06T19:07:19
| 2023-08-06T20:19:56
|
2023-08-06T20:19:55Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
e734bf334 fix IonEntry doc str + type hints
66d0043aa move TEST_FILES_DIR attr from PymatgenTest into module scope
ca3c9e371 PymatgenTest.TEST_FILES_DIR -> TEST_FILES_DIR
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3227/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3227/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3227",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3227",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3227.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3227.patch",
"merged_at": "2023-08-06T20:19:55Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3228
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3228/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3228/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3228/events
|
https://github.com/materialsproject/pymatgen/pull/3228
| 1,838,584,431
|
PR_kwDOACgets5XShHe
| 3,228
|
xyz.__iter__() -> iter(xyz)
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5698361208,
"node_id": "LA_kwDOACgets8AAAABU6YXeA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dx",
"name": "dx",
"color": "73339B",
"default": false,
"description": "Developer experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-07T02:54:58
| 2023-09-02T04:31:05
|
2023-09-02T04:31:04Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
It's shorter and more readable.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3228/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3228/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3228",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3228",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3228.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3228.patch",
"merged_at": "2023-09-02T04:31:04Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3229
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3229/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3229/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3229/events
|
https://github.com/materialsproject/pymatgen/pull/3229
| 1,840,025,541
|
PR_kwDOACgets5XXZbs
| 3,229
|
f-string path construction everywhere, no need for `os.path.join(...)`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4705022165,
"node_id": "LA_kwDOACgets8AAAABGHDw1Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/performance",
"name": "performance",
"color": "458C0D",
"default": false,
"description": "Some functionality is too slow or regressed"
},
{
"id": 5698361208,
"node_id": "LA_kwDOACgets8AAAABU6YXeA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dx",
"name": "dx",
"color": "73339B",
"default": false,
"description": "Developer experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-07T18:42:05
| 2023-08-07T20:13:42
|
2023-08-07T20:13:41Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3229/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3229/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3229",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3229",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3229.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3229.patch",
"merged_at": "2023-08-07T20:13:41Z"
}
|
||||
https://api.github.com/repos/materialsproject/pymatgen/issues/3230
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3230/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3230/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3230/events
|
https://github.com/materialsproject/pymatgen/issues/3230
| 1,840,100,771
|
I_kwDOACgets5trbWj
| 3,230
|
API inconsistency in pymatgen.core.io
|
{
"login": "orionarcher",
"id": 27712051,
"node_id": "MDQ6VXNlcjI3NzEyMDUx",
"avatar_url": "https://avatars.githubusercontent.com/u/27712051?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/orionarcher",
"html_url": "https://github.com/orionarcher",
"followers_url": "https://api.github.com/users/orionarcher/followers",
"following_url": "https://api.github.com/users/orionarcher/following{/other_user}",
"gists_url": "https://api.github.com/users/orionarcher/gists{/gist_id}",
"starred_url": "https://api.github.com/users/orionarcher/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/orionarcher/subscriptions",
"organizations_url": "https://api.github.com/users/orionarcher/orgs",
"repos_url": "https://api.github.com/users/orionarcher/repos",
"events_url": "https://api.github.com/users/orionarcher/events{/privacy}",
"received_events_url": "https://api.github.com/users/orionarcher/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 19613987,
"node_id": "MDU6TGFiZWwxOTYxMzk4Nw==",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/bug",
"name": "bug",
"color": "9222c1",
"default": true,
"description": ""
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I've been moving `from_string -> from_str`. But it shouldn't have broken anything during the ongoing deprecation period. I made that change in #3158 but looks like I forgot to add the fallback `from_string` on `InputFile`. Fix incoming.\r\n\r\nGood catch on the `from_str` vs `get_string` inconsistency. Let's go with `get_str` there as well. `get_string` will still be around but deprecated (for ~6 months).",
"Great, thanks Janosh! \r\n\r\n~~Closing now.~~ will leave open til closed by #3231"
] | 2023-08-07T19:40:01
| 2024-04-17T04:07:30
|
2023-08-09T20:25:03Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Problem
The `from_string` method in `pymatgen.io.core.InputFile` was recently changed to `from_str`. I am fine with either convention (though it did break pymatgen.io.openmm downstream) but there is now internal inconsistency between the [InputFile.from_str](https://github.com/materialsproject/pymatgen/blob/1fa96f8535f86d2ee609c906d333f417c8a260e0/pymatgen/io/core.py#L73) and [InputFile.get_string](https://github.com/materialsproject/pymatgen/blob/1fa96f8535f86d2ee609c906d333f417c8a260e0/pymatgen/io/core.py#L57) methods.
#### Proposed Solution
We should either stick to `from_string` and `get_string` or `from_str` and `get_str`. Whichever is more consistent with the rest of pymatgen makes sense to me.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3230/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3230/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3231
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3231/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3231/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3231/events
|
https://github.com/materialsproject/pymatgen/pull/3231
| 1,840,399,772
|
PR_kwDOACgets5XYrUi
| 3,231
|
Deprecate `get_string()` methods in favor of `get_str()`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
},
{
"id": 5687218601,
"node_id": "LA_kwDOACgets8AAAABUvwRqQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/deprecation",
"name": "deprecation",
"color": "B0FEB6",
"default": false,
"description": "Code deprecations"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-08T00:58:55
| 2023-08-09T20:25:03
|
2023-08-09T20:25:01Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3230.
e703c43f0 restore accidentally deleted io.core.InputFile.from_string (fixes #3230)
2b52712f8 add io.core type hints
ded857431 deprecate get_string methods in favor of get_str
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3231/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3231/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3231",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3231",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3231.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3231.patch",
"merged_at": "2023-08-09T20:25:01Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3232
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3232/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3232/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3232/events
|
https://github.com/materialsproject/pymatgen/pull/3232
| 1,842,324,700
|
PR_kwDOACgets5XfOhX
| 3,232
|
Fix `ruff` PYI041 and ignore PYI024
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
},
{
"id": 5578251138,
"node_id": "LA_kwDOACgets8AAAABTH1bgg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ci",
"name": "ci",
"color": "4E135C",
"default": false,
"description": "Continuous integration"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-09T01:50:09
| 2023-08-09T16:41:13
|
2023-08-09T16:41:12Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
d3176316b fix ruff PYI041 (redundant-numeric-union)
2faafa2d2 ruff ignore PYI024
4b756d068 remove over-engineered _attr_desc = namedtuple
ca70565ba fix CI AttributeError: 'NoneType' object has no attribute 'split'
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3232/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3232/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3232",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3232",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3232.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3232.patch",
"merged_at": "2023-08-09T16:41:12Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3233
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3233/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3233/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3233/events
|
https://github.com/materialsproject/pymatgen/issues/3233
| 1,842,326,969
|
I_kwDOACgets5tz625
| 3,233
|
Read wavefunction from WAVRCAR for some specific purposes.
|
{
"login": "hongyi-zhao",
"id": 11155854,
"node_id": "MDQ6VXNlcjExMTU1ODU0",
"avatar_url": "https://avatars.githubusercontent.com/u/11155854?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/hongyi-zhao",
"html_url": "https://github.com/hongyi-zhao",
"followers_url": "https://api.github.com/users/hongyi-zhao/followers",
"following_url": "https://api.github.com/users/hongyi-zhao/following{/other_user}",
"gists_url": "https://api.github.com/users/hongyi-zhao/gists{/gist_id}",
"starred_url": "https://api.github.com/users/hongyi-zhao/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/hongyi-zhao/subscriptions",
"organizations_url": "https://api.github.com/users/hongyi-zhao/orgs",
"repos_url": "https://api.github.com/users/hongyi-zhao/repos",
"events_url": "https://api.github.com/users/hongyi-zhao/events{/privacy}",
"received_events_url": "https://api.github.com/users/hongyi-zhao/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I think this is something you have to experiment with the Wavecar class and see if it meets your needs."
] | 2023-08-09T01:53:41
| 2023-08-17T14:08:04
|
2023-08-17T14:08:04Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Suppose I would like to achieve the following purposes based on the wavefunction analysis from WAVRCAR:
1. Calculate the topological number based on the exact form of wavefunction, aka, an n*1 array under plane wave basis.
2. Compute the traces of matrix presentations and determines the corresponding irreducible representations for all energy bands and all the k-points in the three-dimensional Brillouin zone.
I would like to know whether [the method implemented in this package](https://github.com/materialsproject/pymatgen/blob/7c70c1ad5a1c489bfb5e4fbd53804630ac48d248/pymatgen/io/vasp/outputs.py#L4409) meets the above requirements.
See below for the related discussions:
https://www.vasp.at/forum/viewtopic.php?t=18177
https://github.com/QijingZheng/VaspBandUnfolding/issues/23
Regards,
Zhao
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3233/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3233/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3234
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3234/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3234/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3234/events
|
https://github.com/materialsproject/pymatgen/issues/3234
| 1,843,518,279
|
I_kwDOACgets5t4dtH
| 3,234
|
REST Error on pulling a large amount of data via patterns (Legacy API)
|
{
"login": "matthewcarbone",
"id": 26401020,
"node_id": "MDQ6VXNlcjI2NDAxMDIw",
"avatar_url": "https://avatars.githubusercontent.com/u/26401020?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewcarbone",
"html_url": "https://github.com/matthewcarbone",
"followers_url": "https://api.github.com/users/matthewcarbone/followers",
"following_url": "https://api.github.com/users/matthewcarbone/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewcarbone/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewcarbone/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewcarbone/subscriptions",
"organizations_url": "https://api.github.com/users/matthewcarbone/orgs",
"repos_url": "https://api.github.com/users/matthewcarbone/repos",
"events_url": "https://api.github.com/users/matthewcarbone/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewcarbone/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"1. Pls use the new API.\r\n2. This is actually not a good way to use this method. You can easily get all the mpids AND formulas/chemical systems in one shot and just postprocess that data to get the mpids of the specific systems.\r\n3. Even if you prefer to use this method, having two wild cards makes it very difficult due to the sheer number of combinations. You can always use one wild-card with a loop on the other element.\r\n\r\n",
"@shyuep due respect none of these points answered my question. I would prefer if you reopened the issue so we can discuss how to make this feature better!\r\n\r\n1. I would very much like to, but I can't for my uses. For instance: #3187\r\n2. I'm aware. I set the pulled properties to just the Materials IDs in order to demonstrate that even pulling the minimum amount of data leads to this error. Even so, what method are you referring to here?\r\n3. This is a reasonable recommendation but IMO should be implemented under the hood in PMG. I don't think the user should have to deal with this type of subtlety. Do you agree?",
"I just fixed the FEFFDictSet issue. That should allow you to use the new API. \r\nAs for implementing it under the hood, the premise is that you are asking for 92x92x92 = 778688 chemical systems (each * is approximately 92 elements of the periodic table), each with tens, if not hundreds of structures. There is a lot of overlap in there too (because the total number of chemical systems even exceeds the total number of structures in the Materials Project). So this is not a reasonable query that can be handled even if we did a loop. In fact, the reasonable query in your case would be to find all materials containing Ti and O, and then set nelements=5 to fix the total number of elements."
] | 2023-08-09T15:30:49
| 2023-08-10T18:00:06
|
2023-08-10T15:04:27Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
When attempting to pull a "large" amount of data via the MPRester `get_data()` method, even just getting Materials Project IDs consistent with a pattern, e.g.
```python
pattern = "Ti-O-*-*-*" # All titanium oxides with 5 unique atom types
with MPRester(api_key) as mpr:
result = mpr.get_data(pattern, prop="material_id")
```
This leads to a REST error where it appears the query is too large. E.g.,
MPRestError: BSON document too large (39439050 bytes) - the connected server supports BSON document sizes up to 16777216 bytes.. Content: b'{"valid_response": false, "error": "BSON document too large (39439050 bytes) - the connected server supports BSON document sizes up to 16777216 bytes.", "version": {"db": "2020_09_08", "pymatgen": "2022.0.8", "rest": "2.0"}, "created_at": "2023-08-09T08:25:12.741976", "traceback": "Traceback (most recent call last):\\n File \\"/var/www/python/matgen_prod/materials_django/rest/rest.py\\", line 95, in wrapped\\n d = func(*args, **kwargs)\\n File \\"/var/www/python/matgen_prod/materials_django/materials/rest.py\\", line 121, in get_vasp_property\\n entries = mdb.mat_qe.get_entries(crit, False, supported_properties)\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/matgendb/query_engine.py\\", line 301, in get_entries\\n for c in self.query(fields, criteria):\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/matgendb/query_engine.py\\", line 654, in _result_generator\\n for r in self._results:\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/cursor.py\\", line 1189, in next\\n if len(self.__data) or self._refresh():\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/cursor.py\\", line 1104, in _refresh\\n self.__send_message(q)\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/cursor.py\\", line 930, in __send_message\\n response = client._send_message_with_response(\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/mongo_client.py\\", line 1138, in _send_message_with_response\\n return self._reset_on_error(\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/mongo_client.py\\", line 1156, in _reset_on_error\\n return func(*args, **kwargs)\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/server.py\\", line 105, in send_message_with_response\\n sock_info.send_message(data, max_doc_size)\\n File \\"/opt/miniconda3/envs/mpprod3/lib/python3.8/site-packages/pymongo/pool.py\\", line 593, in send_message\\n raise DocumentTooLarge(\\npymongo.errors.DocumentTooLarge: BSON document too large (39439050 bytes) - the connected server supports BSON document sizes up to 16777216 bytes.\\n"}'
#### Repro
See above
#### Expected behavior
I believe there should be some protocol to split up the query or something. It seems a bit odd I cannot pull data like this, and I am not sure what the alternative would be. Again, I am just attempting to get the Materials Project IDs _themselves_. In principle, not even pulling structural data.
Is this something that is fixed on the new API? Regardless it should probably be working everywhere, I'd think.
Thanks!
#### Environment
MacOS M1 Ventura 13.4.1
pymatgen==2022.5.26
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3234/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3234/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3235
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3235/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3235/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3235/events
|
https://github.com/materialsproject/pymatgen/issues/3235
| 1,845,581,571
|
I_kwDOACgets5uAVcD
| 3,235
|
Shifting of site coordinates in pymatgen.core.structure.Structure
|
{
"login": "Avisek20",
"id": 4909970,
"node_id": "MDQ6VXNlcjQ5MDk5NzA=",
"avatar_url": "https://avatars.githubusercontent.com/u/4909970?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Avisek20",
"html_url": "https://github.com/Avisek20",
"followers_url": "https://api.github.com/users/Avisek20/followers",
"following_url": "https://api.github.com/users/Avisek20/following{/other_user}",
"gists_url": "https://api.github.com/users/Avisek20/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Avisek20/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Avisek20/subscriptions",
"organizations_url": "https://api.github.com/users/Avisek20/orgs",
"repos_url": "https://api.github.com/users/Avisek20/repos",
"events_url": "https://api.github.com/users/Avisek20/events{/privacy}",
"received_events_url": "https://api.github.com/users/Avisek20/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"This all depends on how you download the structures from MP. If you are choosing the symmetrized or conventional CIF, then the cooridnates will shift. Pls contact the mp-api repo if you believe this to be a bug,."
] | 2023-08-10T17:15:08
| 2023-10-18T11:50:45
|
2023-08-13T16:32:15Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
**(Updated 18/Oct/2023) The answer:** The structure downloaded from MPRester is of a **primitive** crystallographic structure, whereas the symmetrized CIF downloaded from the Materials Project is of a **conventional** crysallographic structure. There lies the discrepancy between the crystal coordinates.
<br>
<br>
<hr>
For several materials, the site coordinates in pymatgen.core.structure.Structure do not seem to match those that are present in the .cif files downloaded from the Materials Project website. Specifically, the last column always remains the same, but the first two column coordinates seem to get shuffled around. If I'm getting something wrong, please let me know as well. Here are some examples of the first two columns getting shuffled:
---
Example 1 - Material with id mp-6499 :
Code:
with MPRester(myapikey) as mpr:
res = mpr.summary.search(material_ids=['mp-6499']
)
print(res[0].structure)
Output:
...
abc : 7.195157 6.591124 7.577377
angles: 61.623832 90.000000 90.000000
pbc : True True True
Sites (24)
# SP a b c magmom
--- ---- -------- -------- -------- --------
0 Ba 0.360454 0.824923 0.339831 -0
1 Ba 0.860454 0.175077 0.160169 -0
2 Ba 0.639546 0.175077 0.660169 -0
3 Ba 0.139546 0.824923 0.839831 -0
4 Li 0.427014 0.404811 0.196796 -0
5 Li 0.927014 0.595189 0.303204 -0
6 Li 0.572986 0.595189 0.803204 -0
7 Li 0.072986 0.404811 0.696796 -0
8 B 0.661475 0.712471 0.081536 -0
9 B 0.161475 0.287529 0.418464 -0
10 B 0.338525 0.287529 0.918464 -0
11 B 0.838525 0.712471 0.581536 -0
12 O 0.18434 0.143722 0.977251 0
13 O 0.159652 0.483229 0.228999 0
14 O 0.840348 0.516771 0.771001 0
15 O 0.340348 0.483229 0.728999 0
16 O 0.005647 0.242693 0.540414 0
17 O 0.505647 0.757307 0.959586 0
18 O 0.994353 0.757307 0.459586 0
19 O 0.494353 0.242693 0.040414 0
20 O 0.81566 0.856278 0.022749 0
21 O 0.31566 0.143722 0.477251 0
22 O 0.659652 0.516771 0.271001 0
23 O 0.68434 0.856278 0.522749 0
Compare the above with the site coordinates from the downloaded .cif file:
...
_cell_length_a 6.59112400
_cell_length_b 7.19515700
_cell_length_c 7.57737661
_cell_angle_alpha 90.00000000
_cell_angle_beta 118.37616816
_cell_angle_gamma 90.00000000
...
Ba2+ Ba0 1 0.17507700 0.63954600 0.33983100 1
Ba2+ Ba1 1 0.82492300 0.13954600 0.16016900 1
Ba2+ Ba2 1 0.82492300 0.36045400 0.66016900 1
Ba2+ Ba3 1 0.17507700 0.86045400 0.83983100 1
Li+ Li4 1 0.59518900 0.57298600 0.19679600 1
Li+ Li5 1 0.40481100 0.07298600 0.30320400 1
Li+ Li6 1 0.40481100 0.42701400 0.80320400 1
Li+ Li7 1 0.59518900 0.92701400 0.69679600 1
B3+ B8 1 0.28752900 0.33852500 0.08153600 1
B3+ B9 1 0.71247100 0.83852500 0.41846400 1
B3+ B10 1 0.71247100 0.66147500 0.91846400 1
B3+ B11 1 0.28752900 0.16147500 0.58153600 1
O2- O12 1 0.85627800 0.81566000 0.97725100 1
O2- O13 1 0.51677100 0.84034800 0.22899900 1
O2- O14 1 0.48322900 0.15965200 0.77100100 1
O2- O15 1 0.51677100 0.65965200 0.72899900 1
O2- O16 1 0.75730700 0.99435300 0.54041400 1
O2- O17 1 0.24269300 0.49435300 0.95958600 1
O2- O18 1 0.24269300 0.00564700 0.45958600 1
O2- O19 1 0.75730700 0.50564700 0.04041400 1
O2- O20 1 0.14372200 0.18434000 0.02274900 1
O2- O21 1 0.85627800 0.68434000 0.47725100 1
O2- O22 1 0.48322900 0.34034800 0.27100100 1
O2- O23 1 0.14372200 0.31566000 0.52274900 1
Checking for the Ba atoms is enough to see the last column remains the same but the first two get shifted around, but this happens for all atoms.
---
For another random material:
Example 2 - Material with id mp-1029776
Code:
from pymatgen.ext.matproj import MPRester
with MPRester(myapikey) as mpr:
res = mpr.summary.search(material_ids=['mp-1029776']
)
print(res[0].structure)
Output:
....
abc : 6.684071 5.549288 5.605421
angles: 87.662729 90.000000 90.000000
pbc : True True True
Sites (20)
# SP a b c magmom
--- ---- -------- -------- -------- --------
0 Li 0.597237 0.093096 0.316577 -0
1 Li 0.097237 0.406904 0.683423 -0
2 Li 0.402763 0.906904 0.683423 -0
3 Li 0.902763 0.593096 0.316577 -0
4 Li 0.836694 0.273398 0.05398 -0
5 Li 0.336694 0.226602 0.94602 -0
6 Li 0.163306 0.726602 0.94602 -0
7 Li 0.663306 0.773398 0.05398 -0
8 Ge 0.63771 0.425499 0.650071 -0
9 Ge 0.13771 0.074501 0.349929 -0
10 Ge 0.36229 0.574501 0.349929 -0
11 Ge 0.86229 0.925499 0.650071 -0
12 N 0.148847 0.396366 0.228562 0
13 N 0.648847 0.103634 0.771438 0
14 N 0.851153 0.603634 0.771438 0
15 N 0.351153 0.896366 0.228562 0
16 N 0.622363 0.450511 0.3031 0
17 N 0.122363 0.049489 0.6969 0
18 N 0.377637 0.549489 0.6969 0
19 N 0.877637 0.950511 0.3031 0
But compare the above with the site coordinates from the downloaded .cif file:
...
_cell_length_a 5.54928800
_cell_length_b 6.68407100
_cell_length_c 5.60542128
_cell_angle_alpha 90.00000000
_cell_angle_beta 92.33727147
_cell_angle_gamma 90.00000000
...
Li+ Li0 1 0.90690400 0.59723700 0.31657700 1
Li+ Li1 1 0.59309600 0.09723700 0.68342300 1
Li+ Li2 1 0.09309600 0.40276300 0.68342300 1
Li+ Li3 1 0.40690400 0.90276300 0.31657700 1
Li+ Li4 1 0.72660200 0.83669400 0.05398000 1
Li+ Li5 1 0.77339800 0.33669400 0.94602000 1
Li+ Li6 1 0.27339800 0.16330600 0.94602000 1
Li+ Li7 1 0.22660200 0.66330600 0.05398000 1
Ge4+ Ge8 1 0.57450100 0.63771000 0.65007100 1
Ge4+ Ge9 1 0.92549900 0.13771000 0.34992900 1
Ge4+ Ge10 1 0.42549900 0.36229000 0.34992900 1
Ge4+ Ge11 1 0.07450100 0.86229000 0.65007100 1
N3- N12 1 0.60363400 0.14884700 0.22856200 1
N3- N13 1 0.89636600 0.64884700 0.77143800 1
N3- N14 1 0.39636600 0.85115300 0.77143800 1
N3- N15 1 0.10363400 0.35115300 0.22856200 1
N3- N16 1 0.54948900 0.62236300 0.30310000 1
N3- N17 1 0.95051100 0.12236300 0.69690000 1
N3- N18 1 0.45051100 0.37763700 0.69690000 1
N3- N19 1 0.04948900 0.87763700 0.30310000 1
Once again, the last column remains the same, while values in the first two columns are shifted around.
---
My pymatgen version:
2023.7.20
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3235/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3235/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3236
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3236/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3236/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3236/events
|
https://github.com/materialsproject/pymatgen/pull/3236
| 1,845,879,243
|
PR_kwDOACgets5XrTFI
| 3,236
|
`Structure/Molecule.to()` now always return same string written to file
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-10T20:47:01
| 2023-08-10T21:12:26
|
2023-08-10T21:12:25Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Previously if `filename` was passed, `Structure/Molecule.to(filename="some/file.json|cif|yaml|poscar|...")` would return `None`. No performance cost from always returning the same string that was written to file. Simplifies implementation and testing, and can be useful in rare cases.
96f7084f5 fix some ruff PERF401
580b76099 fix test_calculate_chgnet() for next chgnet release
2781937fd always return string from Structure.to() regardless of filename kwarg
a6f960956 update TestIStructure.test_to_from_file_string
3d4b3065d same for Molecule.to()
98b6ba999 update TestIMolecule.test_to_from_file_string
2ee87bb3c improve class XYZ logic for setting self._mols
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3236/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3236/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3236",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3236",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3236.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3236.patch",
"merged_at": "2023-08-10T21:12:25Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3237
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3237/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3237/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3237/events
|
https://github.com/materialsproject/pymatgen/pull/3237
| 1,848,717,893
|
PR_kwDOACgets5X04OW
| 3,237
|
Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5322856717,
"node_id": "LA_kwDOACgets8AAAABPURZDQ",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/data%20viz",
"name": "data viz",
"color": "3C19AC",
"default": false,
"description": "PRs and issues about pymatgen plotting functionality"
},
{
"id": 5457867742,
"node_id": "LA_kwDOACgets8AAAABRVBz3g",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/breaking",
"name": "breaking",
"color": "41396E",
"default": false,
"description": "Breaking change"
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"If I can chime in here, I noticed a bug potentially introduced by this pull request.\r\nAs mentioned [here](https://matsci.org/t/bsplotterprojected-get-elt-projecte-plots-method-broken/51434/4?u=fraricci), there is a \"ax =\" missing [here](https://github.com/materialsproject/pymatgen/blob/3ee84ead10675be75239129b706bb3b715960231/pymatgen/electronic_structure/plotter.py#L1076)",
"@fraricci Thanks for reporting and troubleshooting!"
] | 2023-08-13T19:49:56
| 2023-11-02T19:34:20
|
2023-08-17T22:35:33Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Closes #3138.
`pymatgen` plotting methods using the `matplotlib` backend return the `matplotlib.pyplot` module (`plt`), rather than an object related to the plot itself, such as the `Figure` or `Axes`. This is suboptimal API design and inconsistent with the `plotly` backend which returns `go.Figure`.
This PR changes all plotting methods to return a `plt.Axes` object (same as [`pymatviz`](https://github.com/janosh/pymatviz)) instead of `plt`.
Reasons:
- **More Intuitive** as `Axes` actually contains the plot attributes (lines, legend, labels, etc.), and is more in line with what users may expect and what they typically interact with when customizing plots.
- **Consistency** with `pymatviz` and `pymatgen`'s own `plotly` backend.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3237/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3237/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3237",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3237",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3237.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3237.patch",
"merged_at": "2023-08-17T22:35:33Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3238
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3238/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3238/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3238/events
|
https://github.com/materialsproject/pymatgen/pull/3238
| 1,848,777,044
|
PR_kwDOACgets5X1EF1
| 3,238
|
Generate SupercellTransformation from minimum boundary distance
|
{
"login": "JiQi535",
"id": 54908836,
"node_id": "MDQ6VXNlcjU0OTA4ODM2",
"avatar_url": "https://avatars.githubusercontent.com/u/54908836?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/JiQi535",
"html_url": "https://github.com/JiQi535",
"followers_url": "https://api.github.com/users/JiQi535/followers",
"following_url": "https://api.github.com/users/JiQi535/following{/other_user}",
"gists_url": "https://api.github.com/users/JiQi535/gists{/gist_id}",
"starred_url": "https://api.github.com/users/JiQi535/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/JiQi535/subscriptions",
"organizations_url": "https://api.github.com/users/JiQi535/orgs",
"repos_url": "https://api.github.com/users/JiQi535/repos",
"events_url": "https://api.github.com/users/JiQi535/events{/privacy}",
"received_events_url": "https://api.github.com/users/JiQi535/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 2414169365,
"node_id": "MDU6TGFiZWwyNDE0MTY5MzY1",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20testing",
"name": "needs testing",
"color": "66ddab",
"default": false,
"description": "PRs that are not ready to merge due to lacking tests"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`96.87%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`d9fdfef`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/d9fdfefa4787c5121d76ea0e1c60927d7b320d43?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.62% compared to head [(`485ce21`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.06%.\n> Report is 2 commits behind head on master.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3238 +/- ##\n==========================================\n- Coverage 74.62% 74.06% -0.57% \n==========================================\n Files 230 230 \n Lines 69403 69418 +15 \n Branches 16161 16165 +4 \n==========================================\n- Hits 51794 51415 -379 \n- Misses 14533 14958 +425 \n+ Partials 3076 3045 -31 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [...matgen/transformations/standard\\_transformations.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vdHJhbnNmb3JtYXRpb25zL3N0YW5kYXJkX3RyYW5zZm9ybWF0aW9ucy5weQ==) | `86.49% <91.66%> (+0.16%)` | :arrow_up: |\n| [pymatgen/core/lattice.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29yZS9sYXR0aWNlLnB5) | `93.77% <100.00%> (+0.03%)` | :arrow_up: |\n| [pymatgen/core/structure.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29yZS9zdHJ1Y3R1cmUucHk=) | `85.77% <100.00%> (ø)` | |\n| [pymatgen/io/lammps/data.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vbGFtbXBzL2RhdGEucHk=) | `96.96% <100.00%> (ø)` | |\n\n... and [7 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3238?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n",
"Unit test added!",
"Check if CubicSupercellTransformation already does what this does. If it doesn't, we need unit tests and documentation before accepting any PRs. ",
"@shyuep Thanks for the quick feedback. \r\n\r\n`CubicSupercellTransformation` can achieve supercells satisfying desired `min_length`, but it likely produce larger than needed supercells, as its \"iteratively increase the size of the supercell until the largest inscribed **cube’s** side length is at least `min_length`\". (quoted from pymatgen documentations) The `from_boundary_distance` method does not look for a supercell that can contain a cube inside it, instead, it directly focus on minimum boundary distance, so it is able to find relatively small supercells.\r\n\r\nTo verify my guess, I have used `CubicSupercellTransformation` (`cubic_trafo`) to generate supercells of all 154,718 MP relaxed structures. I have set `min_length=8`, inline with `min_boundary_dist=8` for from_boundary_distance. And I have used `force_diagonal=False` and `force_90_degrees=False`, so that `cubic_trafo` should produce smallest possible supercell from its implementation. **As in below plot, `CubicSupercellTransformation` generated supercells are in average over 1 time larger than supercells generated with `from_boundary_distance`.**\r\n<img width=\"593\" alt=\"Screenshot 2023-08-14 at 10 05 49 AM\" src=\"https://github.com/materialsproject/pymatgen/assets/54908836/ca8096e1-8e94-4b12-bf9f-0fcb16babae4\">\r\n\r\n**Unit tests are already added, and I think documentation are also written in the PR. Please let me know if they are okay or if documentation should be also added elsewhere.**\r\n\r\nLastly, I believe this function can be useful not only for what we are doing, but also for phonon calculations in MatCal. @janosh While it might be less useful, as MatCal is not doing DFT, and cell size is not a major concern I guess.",
"@JiQi535 I think CubicSupercell allows you to restrict max number of atoms. There is also value in having a \"cubic-like\" supercell. But I am fine with having this in SupercellTransform as well. But I would suggest you add some arg to enable limiting number of atoms. That is afterall what we really care about, not boundary distance."
] | 2023-08-13T23:08:18
| 2023-08-14T16:48:37
|
2023-08-14T16:38:53Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Added a method `from_boundary_distance` to `SupercellTransformation`, which can automatically find a `SupercellTransformation` that guarantee minimum distance periodic boundaries to be larger than a desired value (`min_boundary_dist`). This method allows high throughput generation of supercells for all 154,718 MP structures within 5 minutes.
## Major feature
Instead of simply expand lattice parameters with fixed lattice angles, this method also provides the option to rotate lattice angle (`allow_rotation`) to find potential supercell satisfying `min_boundary_dist` with a smaller number of atoms. Related evaluations have been done to all MP relaxed structures and listed below.
## Evaluation
All 154,718 MP ground-state structures are screened through with this implementation. As shown below, setting `allow_rotation=True` leads to noticeable decrease of supercell size for all three `min_boundary_dist` values of 6, 8, and 10 Å.
<img width="500" alt="Screenshot 2023-08-13 at 6 58 51 PM" src="https://github.com/materialsproject/pymatgen/assets/54908836/90c23485-de92-4fdf-8fa2-2eebc280d9b3">
<img width="500" alt="Screenshot 2023-08-13 at 6 59 33 PM" src="https://github.com/materialsproject/pymatgen/assets/54908836/9e5365c7-3ba7-4f47-9903-d7e86f722463">
<img width="500" alt="Screenshot 2023-08-13 at 7 06 51 PM" src="https://github.com/materialsproject/pymatgen/assets/54908836/9e699082-30b3-4018-8cad-d62afb7e5022">
## Todos
1. Unittests are not yet added.
2. Though this implementation tries to find smaller supercell with some lattice rotation, it does not guarantee to find the smallest possible supercell satisfying `min_boundary_dist`. Automatically identifying the smallest possible supercell seems a non-trivial task. Exhaustive enumeration needs more sophisticated scripts and more loops, while I expect the improvements to be small.
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3238/reactions",
"total_count": 2,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 1,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3238/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3238",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3238",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3238.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3238.patch",
"merged_at": "2023-08-14T16:38:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3239
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3239/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3239/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3239/events
|
https://github.com/materialsproject/pymatgen/pull/3239
| 1,848,784,253
|
PR_kwDOACgets5X1FlZ
| 3,239
|
Add `Lattice` property `params_dict`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 1427867026,
"node_id": "MDU6TGFiZWwxNDI3ODY3MDI2",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/enhancement",
"name": "enhancement",
"color": "c5e06d",
"default": true,
"description": "A new feature or improvement to an existing one"
},
{
"id": 5563699492,
"node_id": "LA_kwDOACgets8AAAABS59RJA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/ux",
"name": "ux",
"color": "28DEA4",
"default": false,
"description": "User experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`100.00%`** and project coverage change: **`-0.01%`** :warning:\n> Comparison is base [(`182ccbf`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/182ccbf83c7e60e7e68cb12106ce6ea94b821eab?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.62% compared to head [(`41a424d`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.62%.\n\n> :exclamation: Current head 41a424d differs from pull request most recent head 6cdd0da. Consider uploading reports for the commit 6cdd0da to get more accurate results\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3239 +/- ##\n==========================================\n- Coverage 74.62% 74.62% -0.01% \n==========================================\n Files 230 230 \n Lines 69403 69406 +3 \n Branches 16161 16161 \n==========================================\n+ Hits 51795 51796 +1 \n- Misses 14533 14534 +1 \n- Partials 3075 3076 +1 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/core/lattice.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vY29yZS9sYXR0aWNlLnB5) | `93.77% <100.00%> (+0.03%)` | :arrow_up: |\n| [pymatgen/io/lammps/data.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vbGFtbXBzL2RhdGEucHk=) | `96.96% <100.00%> (ø)` | |\n\n... and [1 file with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3239?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-08-13T23:32:59
| 2023-08-14T00:14:08
|
2023-08-14T00:14:07Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
16be0518e add `Lattice` property `params_dict`
47699ef57 use new prop in `Lattice.as_dict`
069852f6d test keys in `TestLattice.test_to_from_dict`
41a424db4 add `TestLattice.test_parameters`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3239/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3239/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3239",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3239",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3239.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3239.patch",
"merged_at": "2023-08-14T00:14:07Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3240
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3240/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3240/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3240/events
|
https://github.com/materialsproject/pymatgen/pull/3240
| 1,850,323,440
|
PR_kwDOACgets5X6UFp
| 3,240
|
Fix a bug in feff.inputs
|
{
"login": "kaifengZheng",
"id": 48105165,
"node_id": "MDQ6VXNlcjQ4MTA1MTY1",
"avatar_url": "https://avatars.githubusercontent.com/u/48105165?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/kaifengZheng",
"html_url": "https://github.com/kaifengZheng",
"followers_url": "https://api.github.com/users/kaifengZheng/followers",
"following_url": "https://api.github.com/users/kaifengZheng/following{/other_user}",
"gists_url": "https://api.github.com/users/kaifengZheng/gists{/gist_id}",
"starred_url": "https://api.github.com/users/kaifengZheng/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/kaifengZheng/subscriptions",
"organizations_url": "https://api.github.com/users/kaifengZheng/orgs",
"repos_url": "https://api.github.com/users/kaifengZheng/repos",
"events_url": "https://api.github.com/users/kaifengZheng/events{/privacy}",
"received_events_url": "https://api.github.com/users/kaifengZheng/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 2414169365,
"node_id": "MDU6TGFiZWwyNDE0MTY5MzY1",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/needs%20testing",
"name": "needs testing",
"color": "66ddab",
"default": false,
"description": "PRs that are not ready to merge due to lacking tests"
},
{
"id": 4704350623,
"node_id": "LA_kwDOACgets8AAAABGGaxnw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/awaiting%20user",
"name": "awaiting user",
"color": "b60205",
"default": false,
"description": "Needs more information from OP."
},
{
"id": 4705117170,
"node_id": "LA_kwDOACgets8AAAABGHJj8g",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/question",
"name": "question",
"color": "DB336A",
"default": true,
"description": "Questions about functionality and design choices"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"What's the bug you encountered?",
"Hi Janosh,\r\nI found a small bug inside the feff.inputs module.\r\n\r\natom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]\r\n\r\nThe argument 'absorbing_atom' is misused, which generated bugs. Based on my understanding, this \"absorbing_atom\" is the index of the absorbing atom in the original structure, but this sentence misused this index for the absorbing atom in the generated cluster, which should be 0.\r\n\r\nFirstly, I think I need to change this argument to 0. However, after I scrutinize the codes, I found that this sentence is not useful, so I delete it.\r\n\r\nPlease let me know what you think.\r\n\r\nBest,\r\nKaifeng\r\n\r\n\r\n",
"Could you post a minimal example that demonstrates the bug? We also need a test that failed before and passes with this change.",
"Dear Janosh,\r\nI prepared two notebooks(in the zip folder) to describe this problem. One notebook named test_beforechange.ipynb is the test before I modified the code, and there is an out-of-range problem. Another notebook shows how the program ran well after I modified the code, and I mentioned two ways to change the code. Either approach should work.\r\n\r\nBy the way, I need to learn how to pass the workflow test. If the first modification approach doesn't work, I will try the second one.\r\n\r\nBest regards,\r\nKaifeng Zheng\r\n\r\n\r\n[pymatgen_test.zip](https://github.com/materialsproject/pymatgen/files/12340230/pymatgen_test.zip)\r\n",
"Sorry, I forgot to send the requirements.txt for packages\r\n\r\n[requirements.txt](https://github.com/materialsproject/pymatgen/files/12340296/requirements.txt)\r\n",
"Hi @janosh, do I need to provide more information?",
"Yes, as I mentioned above, we're missing a new test for this fix.",
"Hi @janosh, I sent a zip file containing the test. The html files also show the running results before and after the changes. If something else is needed, please let me know. What is the format for the test file? Do I need to create a folder and upload it via github?",
"Please have a look at the existing tests in https://github.com/materialsproject/pymatgen/blob/0f352bfd6050a4ad362c6ff82ed5123dde36fed6/tests/io/feff/test_sets.py#L17",
"Hi @janosh, I just updated my test files. I appended a function in test_sets.py named test_cluster_index(), which will check the functionalities of cluster creation.\r\nThe old code will create the error(IndexError):\r\n\r\n\r\nThe index problem can also lead to a mis-indexing of the absorbing atom for simple crystals when is running well without exception, However, I think it is fine since the absorber atom is deleted from the potential list in the 'get_atom_map' function, \r\n\r\nThis is my first time to contribute on GitHub. Please let me know if I need to provide more information. Thanks\r\n "
] | 2023-08-14T18:28:48
| 2023-08-19T01:59:27
|
2023-08-19T01:59:27Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
## Summary
Major changes:
- features: fix the bug in the feff.inputs
- fix 1: .delete atom_sym = get_absorbing_atom_symbol_index(absorbing_atom, self._cluster)[0]
- fix 2: change the argument: self.pot_dict = get_atom_map(self._cluster, self.absorbing_atom)
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
- [ ] Google format doc strings added. Check with `ruff`.
- [ ] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172))
Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
|
{
"login": "kaifengZheng",
"id": 48105165,
"node_id": "MDQ6VXNlcjQ4MTA1MTY1",
"avatar_url": "https://avatars.githubusercontent.com/u/48105165?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/kaifengZheng",
"html_url": "https://github.com/kaifengZheng",
"followers_url": "https://api.github.com/users/kaifengZheng/followers",
"following_url": "https://api.github.com/users/kaifengZheng/following{/other_user}",
"gists_url": "https://api.github.com/users/kaifengZheng/gists{/gist_id}",
"starred_url": "https://api.github.com/users/kaifengZheng/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/kaifengZheng/subscriptions",
"organizations_url": "https://api.github.com/users/kaifengZheng/orgs",
"repos_url": "https://api.github.com/users/kaifengZheng/repos",
"events_url": "https://api.github.com/users/kaifengZheng/events{/privacy}",
"received_events_url": "https://api.github.com/users/kaifengZheng/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3240/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3240/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3240",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3240",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3240.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3240.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3241
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3241/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3241/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3241/events
|
https://github.com/materialsproject/pymatgen/issues/3241
| 1,851,114,335
|
I_kwDOACgets5uVcNf
| 3,241
|
Dependency issue of boto3 missed with pymatgen>=v2023.7.20
|
{
"login": "ZLI-afk",
"id": 75076820,
"node_id": "MDQ6VXNlcjc1MDc2ODIw",
"avatar_url": "https://avatars.githubusercontent.com/u/75076820?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/ZLI-afk",
"html_url": "https://github.com/ZLI-afk",
"followers_url": "https://api.github.com/users/ZLI-afk/followers",
"following_url": "https://api.github.com/users/ZLI-afk/following{/other_user}",
"gists_url": "https://api.github.com/users/ZLI-afk/gists{/gist_id}",
"starred_url": "https://api.github.com/users/ZLI-afk/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/ZLI-afk/subscriptions",
"organizations_url": "https://api.github.com/users/ZLI-afk/orgs",
"repos_url": "https://api.github.com/users/ZLI-afk/repos",
"events_url": "https://api.github.com/users/ZLI-afk/events{/privacy}",
"received_events_url": "https://api.github.com/users/ZLI-afk/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"Also running into this issue, with this traceback:\r\n```\r\nImportError while loading conftest '/home/runner/work/PyTASER/PyTASER/tests/conftest.py'.\r\ntests/conftest.py:6: in <module>\r\n from pytaser.generator import TASGenerator\r\npytaser/generator.py:8: in <module>\r\n from pymatgen.ext.matproj import MPRester\r\n/opt/hostedtoolcache/Python/3.8.[17](https://github.com/WMD-group/PyTASER/actions/runs/5866399133/job/15905131705#step:6:18)/x64/lib/python3.8/site-packages/pymatgen/ext/matproj.py:28: in <module>\r\n from mp_api.client import MPRester as _MPResterNew\r\n/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/mp_api/client/__init__.py:5: in <module>\r\n from .core import MPRestError\r\n/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/mp_api/client/core/__init__.py:1: in <module>\r\n from .client import BaseRester, MPRestError\r\n/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/mp_api/client/core/client.py:[20](https://github.com/WMD-group/PyTASER/actions/runs/5866399133/job/15905131705#step:6:21): in <module>\r\n import boto3\r\n ModuleNotFoundError: No module named 'boto3'\r\n```",
"Please report all mp-api related issues on the MP API Github repo. https://github.com/materialsproject/api",
"I am fixing this issue now."
] | 2023-08-15T08:58:19
| 2023-08-15T18:15:52
|
2023-08-15T14:51:20Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
#### Description
Error of **ModuleNotFoundError: No module named 'boto3'** with latest version (pymatgen>=v2023.7.20). BTW the __version__ isn't updated for those versions.
#### Fixed by
`pip install boto3`
#### Environment
Relevant versions and platform info:
- OS: Mac, Linux
- Version>=v2023.07.20)
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3241/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3241/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3242
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3242/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3242/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3242/events
|
https://github.com/materialsproject/pymatgen/pull/3242
| 1,851,601,151
|
PR_kwDOACgets5X-ncb
| 3,242
|
More concise `test_from_boundary_distance`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-15T15:04:11
| 2023-08-15T16:37:28
|
2023-08-15T16:37:27Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
f56656470 make `test_from_boundary_distance` more concise
eb5835b90 snake_case vars
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3242/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3242/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3242",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3242",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3242.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3242.patch",
"merged_at": "2023-08-15T16:37:27Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3243
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3243/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3243/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3243/events
|
https://github.com/materialsproject/pymatgen/pull/3243
| 1,851,932,409
|
PR_kwDOACgets5X_tPv
| 3,243
|
Breaking: remove deprecated keyword `properties` from `Species`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5457867742,
"node_id": "LA_kwDOACgets8AAAABRVBz3g",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/breaking",
"name": "breaking",
"color": "41396E",
"default": false,
"description": "Breaking change"
},
{
"id": 5529392097,
"node_id": "LA_kwDOACgets8AAAABSZPT4Q",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/api",
"name": "api",
"color": "D21149",
"default": false,
"description": "Application programming interface"
},
{
"id": 5648629103,
"node_id": "LA_kwDOACgets8AAAABUK89bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/core",
"name": "core",
"color": "299448",
"default": false,
"description": "Pymatgen core"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-15T18:36:03
| 2023-08-15T19:16:10
|
2023-08-15T19:16:09Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
4b9033a0e remove deprecated kwarg `properties` from `Species`+`DummySpecies`
38b30a340 snake_case vars
48b8f1678 fix `Structure.add_spin_by_element` and `add_spin_by_site`
4ffc37130 fix tests that used `Species(properties={...})`
33283b0fb update `Substitutor.pred_from_structures` doc str
7ba3245f5 fix `MagOrderingTransformation._add_dummy_species`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3243/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3243/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3243",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3243",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3243.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3243.patch",
"merged_at": "2023-08-15T19:16:09Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3244
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3244/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3244/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3244/events
|
https://github.com/materialsproject/pymatgen/pull/3244
| 1,853,999,061
|
PR_kwDOACgets5YGuYK
| 3,244
|
[FIX] Fix major bug where some Kpoints are generated using wrong mesh types
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-16T22:50:18
| 2023-08-16T22:53:00
|
2023-08-16T22:53:00Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Addresses #3220. Also adds a lot of tests to (hopefully) make sure nothing like this happens again.
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3244/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3244/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3244",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3244",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3244.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3244.patch",
"merged_at": null
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3245
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3245/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3245/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3245/events
|
https://github.com/materialsproject/pymatgen/pull/3245
| 1,854,029,217
|
PR_kwDOACgets5YG0yM
| 3,245
|
Fix some Kpoints generated using wrong mesh types
|
{
"login": "matthewkuner",
"id": 82329282,
"node_id": "MDQ6VXNlcjgyMzI5Mjgy",
"avatar_url": "https://avatars.githubusercontent.com/u/82329282?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/matthewkuner",
"html_url": "https://github.com/matthewkuner",
"followers_url": "https://api.github.com/users/matthewkuner/followers",
"following_url": "https://api.github.com/users/matthewkuner/following{/other_user}",
"gists_url": "https://api.github.com/users/matthewkuner/gists{/gist_id}",
"starred_url": "https://api.github.com/users/matthewkuner/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/matthewkuner/subscriptions",
"organizations_url": "https://api.github.com/users/matthewkuner/orgs",
"repos_url": "https://api.github.com/users/matthewkuner/repos",
"events_url": "https://api.github.com/users/matthewkuner/events{/privacy}",
"received_events_url": "https://api.github.com/users/matthewkuner/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"@janosh seems like the tests that are failing are unrelated? Not 100% sure. If they are indeed unrelated, this should be ready for merging",
"Tests were fine on `master`. Looks like something you changed turned `magmons` from `tuple` to `list`. I pushed a fix.\r\n\r\n```py\r\nself._cell\r\n>>> (((...), (...), (...)), ((...),), (1,), ([...],))\r\n```\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/c335e43b5f1454786dcbfcdf20b47fd677132665/pymatgen/symmetry/analyzer.py#L103-L118",
"@janosh This could possibly be discovering some other issue with the magmoms, because I don't think a single line from my new code has anything to do with magmoms? ¯\\_(ツ)_/¯ unsure\r\n",
"Not sure either why this is surfacing now. I think this is good to go except for one thing. Do we need to add 3 new POSCAR files? How about you pick some of 31 that we already have:\r\n\r\n```py\r\nfrom collections import defaultdict\r\nfrom glob import glob\r\n\r\nfrom pymatgen.io.vasp.inputs import Poscar\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\nfrom pymatgen.util.testing import TEST_FILES_DIR\r\n\r\n# glob all POSCARs in test files dir and count their crystal types\r\ncrys_sys_counts = defaultdict(int)\r\ntest_potcars = [*glob(f\"{TEST_FILES_DIR}/*POSCAR*\"), *glob(f\"{TEST_FILES_DIR}/**/*POSCAR*\")]\r\nprint(f\"{len(test_potcars)=}\")\r\n\r\nfor filepath in test_potcars:\r\n try:\r\n poscar = Poscar.from_file(filepath)\r\n crys_sys = SpacegroupAnalyzer(poscar.structure).get_crystal_system()\r\n crys_sys_counts[crys_sys] += 1\r\n except Exception:\r\n pass\r\n```\r\n\r\n`crys_sys_counts = {'cubic': 15, 'trigonal': 3, 'hexagonal': 3, 'monoclinic': 3, 'orthorhombic': 2, 'triclinic': 2}`",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`66.66%`** and project coverage change: **`-0.57%`** :warning:\n> Comparison is base [(`ccc1831`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/ccc1831ba6b8f5ab47723f41a3035265da78f3d5?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.65% compared to head [(`2bf1d96`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.08%.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #3245 +/- ##\n==========================================\n- Coverage 74.65% 74.08% -0.57% \n==========================================\n Files 230 230 \n Lines 69384 69386 +2 \n Branches 16154 16155 +1 \n==========================================\n- Hits 51799 51408 -391 \n- Misses 14513 14941 +428 \n+ Partials 3072 3037 -35 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/analysis/chemenv/utils/scripts\\_utils.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vYW5hbHlzaXMvY2hlbWVudi91dGlscy9zY3JpcHRzX3V0aWxzLnB5) | `10.61% <0.00%> (ø)` | |\n| [pymatgen/symmetry/analyzer.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vc3ltbWV0cnkvYW5hbHl6ZXIucHk=) | `87.89% <ø> (ø)` | |\n| [pymatgen/io/vasp/inputs.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vdmFzcC9pbnB1dHMucHk=) | `87.14% <100.00%> (+0.33%)` | :arrow_up: |\n\n... and [6 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/3245?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n"
] | 2023-08-16T23:34:37
| 2023-10-12T18:19:49
|
2023-08-18T14:23:16Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Addresses https://github.com/materialsproject/pymatgen/issues/3220. Also adds a lot of tests to (hopefully) make sure nothing like this happens again.
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3245/reactions",
"total_count": 1,
"+1": 1,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3245/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3245",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3245",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3245.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3245.patch",
"merged_at": "2023-08-18T14:23:16Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3247
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3247/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3247/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3247/events
|
https://github.com/materialsproject/pymatgen/issues/3247
| 1,854,394,870
|
I_kwDOACgets5uh9H2
| 3,247
|
Construct supercells based on partial occupancy or Wyckoff position
|
{
"login": "Asif-Iqbal-Bhatti",
"id": 7361722,
"node_id": "MDQ6VXNlcjczNjE3MjI=",
"avatar_url": "https://avatars.githubusercontent.com/u/7361722?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/Asif-Iqbal-Bhatti",
"html_url": "https://github.com/Asif-Iqbal-Bhatti",
"followers_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/followers",
"following_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/following{/other_user}",
"gists_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/gists{/gist_id}",
"starred_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/subscriptions",
"organizations_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/orgs",
"repos_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/repos",
"events_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/events{/privacy}",
"received_events_url": "https://api.github.com/users/Asif-Iqbal-Bhatti/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[
"I have no idea what you mean by partial occupancy. Does it mean that some Wyckoff sites are occupied or do you mean all sites are occupied by a partial occupied composition. Either case, this is already implemented in pymatgen. You can refer to the matgenb examples.",
"So what I meant is:\r\nAs an example, Li6PS5Cl in the literature has different experimental structure, and they have shown the coordinates, partial occupancy, and Wyckoff position. (From Vesta)\r\n\r\nx y z Occ. U Site Sym.\r\n1 Li Li1 0.31610 0.31610 -0.02290 0.440 0.088 48h …m\r\n2 P P 0.50000 0.50000 0.50000 1.000 0.046 4b -43m\r\n3 Cl Cl1 0.00000 0.00000 0.00000 0.370 0.016 4a -43m\r\n4 Cl Cl2 0.75000 0.75000 0.75000 0.630 0.041 4d -43m\r\n5 S S1 0.00000 0.00000 0.00000 0.630 0.016 4a -43m\r\n6 S S2 0.75000 0.75000 0.75000 0.370 0.041 4d -43m\r\n7 S S3 0.12110 -0.01211 0.62110 1.000 0.058 48h …m\r\n\r\nSOmetimes S2 has 4d or 4c site. Well what I mean by is the 4th column \"\"Occ\"\"\r\n\r\nHowever I will check matgenb. Thanks."
] | 2023-08-17T07:07:11
| 2023-08-17T15:42:56
|
2023-08-17T14:05:34Z
|
NONE
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Hello All,
Is there a module in Pymatgen that can construct supercells based on partial occupancy or Wyckoff position?
A supercell with partial occupancy would be a great feature. If that is already implemented, that would be great.
Asif
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3247/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3247/timeline
| null |
completed
| false
| false
|
{
"url": "",
"html_url": "",
"diff_url": "",
"patch_url": "",
"merged_at": ""
}
|
||
https://api.github.com/repos/materialsproject/pymatgen/issues/3249
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3249/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3249/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3249/events
|
https://github.com/materialsproject/pymatgen/pull/3249
| 1,855,489,219
|
PR_kwDOACgets5YLyic
| 3,249
|
Typo in Docs for PeriodicsSite
|
{
"login": "jmmshn",
"id": 14003693,
"node_id": "MDQ6VXNlcjE0MDAzNjkz",
"avatar_url": "https://avatars.githubusercontent.com/u/14003693?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/jmmshn",
"html_url": "https://github.com/jmmshn",
"followers_url": "https://api.github.com/users/jmmshn/followers",
"following_url": "https://api.github.com/users/jmmshn/following{/other_user}",
"gists_url": "https://api.github.com/users/jmmshn/gists{/gist_id}",
"starred_url": "https://api.github.com/users/jmmshn/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/jmmshn/subscriptions",
"organizations_url": "https://api.github.com/users/jmmshn/orgs",
"repos_url": "https://api.github.com/users/jmmshn/repos",
"events_url": "https://api.github.com/users/jmmshn/events{/privacy}",
"received_events_url": "https://api.github.com/users/jmmshn/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-17T18:17:35
| 2023-08-17T18:36:56
|
2023-08-17T18:36:56Z
|
CONTRIBUTOR
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Typo in Docs for PeriodicsSite
|
{
"login": "shyuep",
"id": 577107,
"node_id": "MDQ6VXNlcjU3NzEwNw==",
"avatar_url": "https://avatars.githubusercontent.com/u/577107?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/shyuep",
"html_url": "https://github.com/shyuep",
"followers_url": "https://api.github.com/users/shyuep/followers",
"following_url": "https://api.github.com/users/shyuep/following{/other_user}",
"gists_url": "https://api.github.com/users/shyuep/gists{/gist_id}",
"starred_url": "https://api.github.com/users/shyuep/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/shyuep/subscriptions",
"organizations_url": "https://api.github.com/users/shyuep/orgs",
"repos_url": "https://api.github.com/users/shyuep/repos",
"events_url": "https://api.github.com/users/shyuep/events{/privacy}",
"received_events_url": "https://api.github.com/users/shyuep/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3249/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3249/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3249",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3249",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3249.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3249.patch",
"merged_at": "2023-08-17T18:36:55Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3250
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3250/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3250/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3250/events
|
https://github.com/materialsproject/pymatgen/pull/3250
| 1,855,581,438
|
PR_kwDOACgets5YMGiW
| 3,250
|
Fix `Vasprun.converged_electronic` check if `ALGO=CHI` in `INCAR`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5304335471,
"node_id": "LA_kwDOACgets8AAAABPCm8bw",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/io",
"name": "io",
"color": "c2e0c6",
"default": false,
"description": "Input/output functionality"
},
{
"id": 5318590534,
"node_id": "LA_kwDOACgets8AAAABPQNARg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/fix",
"name": "fix",
"color": "40DE1F",
"default": false,
"description": "Bug fix PRs"
},
{
"id": 5457739150,
"node_id": "LA_kwDOACgets8AAAABRU59jg",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/vasp",
"name": "vasp",
"color": "BF4B01",
"default": false,
"description": "Vienna Ab initio Simulation Package"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-17T19:29:54
| 2023-08-17T19:53:25
|
2023-08-17T19:53:24Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
`if self.incar not in ["CHI"]` looks like a mistake here. Thanks @matthewkuner for catching.
https://github.com/materialsproject/pymatgen/blob/13e46fdf65ecdb60ddd491dd640f236ed3c5ce7a/pymatgen/io/vasp/outputs.py#L608
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3250/reactions",
"total_count": 1,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 1
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3250/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3250",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3250",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3250.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3250.patch",
"merged_at": "2023-08-17T19:53:24Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3251
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3251/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3251/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3251/events
|
https://github.com/materialsproject/pymatgen/pull/3251
| 1,856,010,261
|
PR_kwDOACgets5YNih8
| 3,251
|
Fix `ruff` D212
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 5436106752,
"node_id": "LA_kwDOACgets8AAAABRARoAA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/housekeeping",
"name": "housekeeping",
"color": "64CC86",
"default": false,
"description": "Moving around or cleaning up old code/files"
},
{
"id": 5456916296,
"node_id": "LA_kwDOACgets8AAAABRUHvSA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/docs",
"name": "docs",
"color": "35B067",
"default": false,
"description": "Documentation, examples, user guides"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-18T04:00:15
| 2023-08-18T04:06:54
|
2023-08-18T04:06:53Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
d60bad590 ruff auto-fix D212 (multi-line-summary-first-line) excl. `"""Args:`
eb9cc3ec3 fix doc str return type indentation
572f67c1e reformat long unpackings
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3251/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3251/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3251",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3251",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3251.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3251.patch",
"merged_at": "2023-08-18T04:06:53Z"
}
|
|||
https://api.github.com/repos/materialsproject/pymatgen/issues/3253
|
https://api.github.com/repos/materialsproject/pymatgen
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3253/labels{/name}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3253/comments
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3253/events
|
https://github.com/materialsproject/pymatgen/pull/3253
| 1,856,993,348
|
PR_kwDOACgets5YQ4ux
| 3,253
|
Use `numpy.testing.assert_allclose` over `assert np.allclose`
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
[
{
"id": 4974004892,
"node_id": "LA_kwDOACgets8AAAABKHlKnA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/tests",
"name": "tests",
"color": "654021",
"default": false,
"description": "Issues with or changes to the pymatgen test suite"
},
{
"id": 5698361208,
"node_id": "LA_kwDOACgets8AAAABU6YXeA",
"url": "https://api.github.com/repos/materialsproject/pymatgen/labels/dx",
"name": "dx",
"color": "73339B",
"default": false,
"description": "Developer experience"
}
] |
closed
| false
|
{
"login": "",
"id": 0,
"node_id": "",
"avatar_url": "",
"gravatar_id": "",
"url": "",
"html_url": "",
"followers_url": "",
"following_url": "",
"gists_url": "",
"starred_url": "",
"subscriptions_url": "",
"organizations_url": "",
"repos_url": "",
"events_url": "",
"received_events_url": "",
"type": "",
"user_view_type": "",
"site_admin": false
}
|
[] | null |
[] | 2023-08-18T16:34:19
| 2023-08-18T19:03:41
|
2023-08-18T19:03:40Z
|
MEMBER
|
{
"total": 0,
"completed": 0,
"percent_completed": 0
}
|
Reason: significantly more helpful error messages on failed tests.
Example before with `assert np.allclose`:
```py
tests/analysis/gb/test_grain.py:100: AssertionError
def test_as_dict_and_from_dict(self):
d1 = self.Cu_GB1.as_dict()
d2 = self.Cu_GB2.as_dict()
Cu_GB1_new = GrainBoundary.from_dict(d1)
Cu_GB2_new = GrainBoundary.from_dict(d2)
assert Cu_GB1_new.sigma == approx(self.Cu_GB1.sigma)
assert Cu_GB1_new.rotation_angle == approx(self.Cu_GB1.rotation_angle)
assert Cu_GB1_new.rotation_axis == self.Cu_GB1.rotation_axis
assert Cu_GB1_new.gb_plane == self.Cu_GB1.gb_plane
assert np.allclose(Cu_GB1_new.init_cell.lattice.matrix, self.Cu_GB1.init_cell.lattice.matrix)
> assert np.allclose(
Cu_GB1_new.oriented_unit_cell.lattice.matrix + 1e-3,
self.Cu_GB1.oriented_unit_cell.lattice.matrix,
)
E assert False
E + where False = <function allclose at 0x1102feab0>((array([[-10.84922172, 0. , 10.84922172],\n [-14.46562896, 10.84922172, -18.0820362 ],\n [ -7.23281448, 3.61640724, -7.23281448]]) + 0.001), array([[-10.84922172, 0. , 10.84922172],\n [-14.46562896, 10.84922172, -18.0820362 ],\n [ -7.23281448, 3.61640724, -7.23281448]]))
E + where <function allclose at 0x1102feab0> = np.allclose
E + and array([[-10.84922172, 0. , 10.84922172],\n [-14.46562896, 10.84922172, -18.0820362 ],\n [ -7.23281448, 3.61640724, -7.23281448]]) = Lattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n B : -14.46562896 10.84922172 -18.0820362\n C : -7.23281448 3.61640724 -7.23281448\n pbc : True True True.matrix
E + where Lattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n B : -14.46562896 10.84922172 -18.0820362\n C : -7.23281448 3.61640724 -7.23281448\n pbc : True True True = Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0].lattice
E + where Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0] = Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 87.14641575163476\n angles : 9.61799283329482...e: Cu (-45.26, 18.33, -34.41) [0.5261, 0.1568, 0.6344]\nPeriodicSite: Cu (-45.26, 20.14, -36.21) [0.508, 0.5483, 0.5413].oriented_unit_cell
E + and array([[-10.84922172, 0. , 10.84922172],\n [-14.46562896, 10.84922172, -18.0820362 ],\n [ -7.23281448, 3.61640724, -7.23281448]]) = Lattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n B : -14.46562896 10.84922172 -18.0820362\n C : -7.23281448 3.61640724 -7.23281448\n pbc : True True True.matrix
E + where Lattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.130102354156051 90.0 95.7391704...72\n B : -14.46562896 10.84922172 -18.0820362\n C : -7.23281448 3.61640724 -7.23281448\n pbc : True True True = Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0].lattice
E + where Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 10.849221720000001\n angles : 8.1301023541560...cSite: Cu (-16.27, 9.041, -10.85) [0.3889, 0.8333, 0.0]\nPeriodicSite: Cu (-12.66, 9.041, -14.47) [0.05556, 0.8333, 0.0] = Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 87.14641575163476\n angles : 9.61799283329482...e: Cu (-45.26, 18.33, -34.41) [0.5261, 0.1568, 0.6344]\nPeriodicSite: Cu (-45.26, 20.14, -36.21) [0.508, 0.5483, 0.5413].oriented_unit_cell
E + where Structure Summary\nLattice\n abc : 15.343116497616757 25.571860829361263 87.14641575163476\n angles : 9.61799283329482...e: Cu (-45.26, 18.33, -34.41) [0.5261, 0.1568, 0.6344]\nPeriodicSite: Cu (-45.26, 20.14, -36.21) [0.508, 0.5483, 0.5413] = <tests.analysis.gb.test_grain.TestGrainBoundary testMethod=test_as_dict_and_from_dict>.Cu_GB1
```
After changing to `numpy.testing.assert_allclose`:
```py
def test_as_dict_and_from_dict(self):
d1 = self.Cu_GB1.as_dict()
d2 = self.Cu_GB2.as_dict()
Cu_GB1_new = GrainBoundary.from_dict(d1)
Cu_GB2_new = GrainBoundary.from_dict(d2)
assert Cu_GB1_new.sigma == approx(self.Cu_GB1.sigma)
assert Cu_GB1_new.rotation_angle == approx(self.Cu_GB1.rotation_angle)
assert Cu_GB1_new.rotation_axis == self.Cu_GB1.rotation_axis
assert Cu_GB1_new.gb_plane == self.Cu_GB1.gb_plane
assert np.allclose(Cu_GB1_new.init_cell.lattice.matrix, self.Cu_GB1.init_cell.lattice.matrix)
> assert_allclose(
Cu_GB1_new.oriented_unit_cell.lattice.matrix + 1e-3,
self.Cu_GB1.oriented_unit_cell.lattice.matrix,
)
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=1e-07, atol=0', 'verbose': True}
E AssertionError:
E Not equal to tolerance rtol=1e-07, atol=0
E
E Mismatched elements: 9 / 9 (100%)
E Max absolute difference: 0.001
E Max relative difference: 0.00027652
E x: array([[-1.084822e+01, 1.000000e-03, 1.085022e+01],
E [-1.446463e+01, 1.085022e+01, -1.808104e+01],
E [-7.231814e+00, 3.617407e+00, -7.231814e+00]])
E y: array([[-10.849222, 0. , 10.849222],
E [-14.465629, 10.849222, -18.082036],
E [ -7.232814, 3.616407, -7.232814]])
```
aa84b6577 fix return type doc str indentation
6f4bb2852 don't use pytest.approx() with assert len(...)
b12e7ebff use numpy.testing.assert_allclose over assert np.allclose
e025ffb73 np.allclose(np.array(...), ...) to np.allclose(..., ...)
|
{
"login": "janosh",
"id": 30958850,
"node_id": "MDQ6VXNlcjMwOTU4ODUw",
"avatar_url": "https://avatars.githubusercontent.com/u/30958850?v=4",
"gravatar_id": "",
"url": "https://api.github.com/users/janosh",
"html_url": "https://github.com/janosh",
"followers_url": "https://api.github.com/users/janosh/followers",
"following_url": "https://api.github.com/users/janosh/following{/other_user}",
"gists_url": "https://api.github.com/users/janosh/gists{/gist_id}",
"starred_url": "https://api.github.com/users/janosh/starred{/owner}{/repo}",
"subscriptions_url": "https://api.github.com/users/janosh/subscriptions",
"organizations_url": "https://api.github.com/users/janosh/orgs",
"repos_url": "https://api.github.com/users/janosh/repos",
"events_url": "https://api.github.com/users/janosh/events{/privacy}",
"received_events_url": "https://api.github.com/users/janosh/received_events",
"type": "User",
"user_view_type": "public",
"site_admin": false
}
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/issues/3253/reactions",
"total_count": 0,
"+1": 0,
"-1": 0,
"laugh": 0,
"hooray": 0,
"confused": 0,
"heart": 0,
"rocket": 0,
"eyes": 0
}
|
https://api.github.com/repos/materialsproject/pymatgen/issues/3253/timeline
| null | true
| false
|
{
"url": "https://api.github.com/repos/materialsproject/pymatgen/pulls/3253",
"html_url": "https://github.com/materialsproject/pymatgen/pull/3253",
"diff_url": "https://github.com/materialsproject/pymatgen/pull/3253.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/3253.patch",
"merged_at": "2023-08-18T19:03:40Z"
}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.