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https://api.github.com/repos/materialsproject/pymatgen/issues/4207 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4207/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4207/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4207/events | https://github.com/materialsproject/pymatgen/issues/4207 | 2,704,252,122 | I_kwDOACgets6hL5za | 4,207 | `test_symmetry_ops` for `TestMagneticSpaceGroup` of `symmetry.maggroups` is failing | {
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} | After fixing `assert_str_content_equal` implementations in #4205, noticed the following test for `TestMagneticSpaceGroup` of `symmetry.maggroups` is failing.
cc @mkhorton
`>>> pytest tests/symmetry/test_maggroups.py::TestMagneticSpaceGroup::test_symmetry_ops`
```
E AssertionError: Strings are not equal (w... | {
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"Thanks for reporting this and for providing the code snippet.\n\nI believe this is intended to \"not completely\" reduce some peroxides (Cs<sub>2</sub>O<sub>2</sub> in this case to CsO):\nhttps://github.com/materialsproject/pymatgen/blob/296a0ec856b22da847b2ccd0e55e146e071cb8fd/src/pymatgen/core/composition.py#L12... | 2024-11-29T09:38:27 | 2025-01-27T08:49:43 | NONE | {
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} | ### Python version
Python 3.11
### Pymatgen version
'2024.11.13'
### Operating system version
MacOSX
### Current behavior
From the docstring for reduced_composition:
```
@property
def reduced_composition(self) -> Self:
"""The reduced composition, i.e. amounts normalized by greatest common denominator.
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https://api.github.com/repos/materialsproject/pymatgen/issues/4209 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4209/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4209/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4209/events | https://github.com/materialsproject/pymatgen/pull/4209 | 2,706,613,692 | PR_kwDOACgets6DnaAx | 4,209 | Schedule `PymatgenTest` for migration from `unittest` to `pytest` | {
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"I would reopen this after #4212 is reviewed/merged as I opened too many PRs for me to track"
] | 2024-11-30T04:31:44 | 2025-03-28T18:57:27 | 2024-12-01T12:44:56Z | CONTRIBUTOR | {
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} | ### Summary
- Avoid catching all warnings, add a message filter, and clean up [assert no warning tests](https://docs.pytest.org/en/stable/how-to/capture-warnings.html#additional-use-cases-of-warnings-in-tests) with warnings filter
### Schedule `PymatgenTest` for migration after a grace period
- [x] We cannot mig... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4210 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4210/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4210/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4210/events | https://github.com/materialsproject/pymatgen/pull/4210 | 2,707,298,890 | PR_kwDOACgets6DoK6s | 4,210 | Fix `uv pip install` from binary distribution (wheels) usage | {
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- Fix `uv pip install` from binary distribution (wheels) usage, https://github.com/astral-sh/uv/issues/8155#issuecomment-2506014815
- Use `uv` to build wheel, https://docs.astral.sh/uv/guides/integration/github/
- [**REVERTED**] Test `mcsqs` install in 3f63f4b341674e31d597506de4e6a64de4ed5ea3, it's way... | {
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"There seems to be conflicts that need to be adjusted.",
"Fixed, thanks for reviewing. Looks like COD might be temporarily down thus the failure ",
"@shyuep Can you maybe review this? Merge conflicts solved. Thanks.",
"Thanks"
] | 2024-12-01T12:32:05 | 2025-04-17T14:45:56 | 2025-04-17T14:43:53Z | CONTRIBUTOR | {
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} | ### Summary
- Migrate `pymatgen` tests to `pytest`, to close #4202
- [x] `conftest.py` doesn't seem to be used at all
- [x] Add tests for legacy `PymatgenTest` to avoid accidental breakage
> [!WARNING]
> - [**NEED CONFIRM**] Deprecate `PymatgenTest` with `MatSciTest`, set **deadline at 2026-01-01**
---
###... | {
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.8.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.2...v0.8.1)
- [github.com/MarcoGorelli/cython-lint: v0.16.2 → v0.16.6](https://github.com/MarcoGorelli/cython-lint/compare/v0.16.2...v0.16.6)
- [github.com/igorshubovyc... | {
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"Dear @phyfang , could you further describe how you try to plot the bandstructure? \r\nDepending on what you do, it helps to put \\Gamma in backticks (``) like \\`\\Gamma\\` .",
"I guess it's related to #4025 (looks like `Gamma` is not escaped properly somewhere). I might open a PR later and let's fix this togeth... | 2024-12-03T07:52:19 | 2024-12-10T20:47:25 | 2024-12-04T14:42:18Z | NONE | {
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} | ### Python version
python--3.12
### Pymatgen version
2024.11.13
### Operating system version
Win-11
### Current behavior
When I was drawing the band structure, I found some problems that the gamma points were not displayed correctly.
![？？](https://github.com/user-attachments/assets/72a2a8fa-a297-49ac-87c4-bd0af... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4215 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4215/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4215/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4215/events | https://github.com/materialsproject/pymatgen/issues/4215 | 2,717,068,871 | I_kwDOACgets6h8y5H | 4,215 | Cannot init `Cohpcar` in `matgenb ` example notebook: `ValueError: setting an array element with a sequence.` | {
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"There is a second notebook. This one is not needed and outdated",
"Thanks for the quick response! This one `2019-01-11-How to plot and evaluate output files from Lobster.ipynb`? This [seems to be failing for the same reason](https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2019-01-11-How%20to... | 2024-12-04T09:17:54 | 2025-02-11T09:25:19 | CONTRIBUTOR | {
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} | Two LOBSTER examples in `matgenb` seems to be failing:
- https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2018-03-14-Plotting%20COHP%20from%20LOBSTER.ipynb
- https://github.com/materialsvirtuallab/matgenb/blob/master/notebooks/2019-01-11-How%20to%20plot%20and%20evaluate%20output%20files%20from%20L... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4216 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4216/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4216/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4216/events | https://github.com/materialsproject/pymatgen/issues/4216 | 2,717,711,734 | I_kwDOACgets6h_P12 | 4,216 | Consider 'LSORBIT = True', how to use pymatgen plot element-project-DOS？ | {
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"Hi @phyfang, I think this is fixed by my recent PR here: https://github.com/materialsproject/pymatgen/pull/4239"
] | 2024-12-04T13:16:59 | 2025-01-02T11:28:18 | NONE | {
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} | ### Python version
python--3.12
### Pymatgen version
2024.11.13
### Operating system version
Win-11
### Current behavior
for **LSORBIT = F** and **LNONCOLLINEAR = F**，I can get element-project-DOS easily, but if **LSORBIT = T** and **LNONCOLLINEAR = T**，how can I use pymatgen to get element-project-DOS？If I use... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4217 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4217/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4217/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4217/events | https://github.com/materialsproject/pymatgen/pull/4217 | 2,721,892,244 | PR_kwDOACgets6EQ4rW | 4,217 | Increase warnings `stacklevel` to 2, un-ignore RUFF `B028` | {
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} | ### Summary
- Increase warnings `stacklevel` to 2, to point to the caller instead of `warnings.warn`
- [x] Un-ignore [RUFF B028](https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/#no-explicit-stacklevel-b028): Checks for warnings.warn calls without an explicit stacklevel keyword argument
- [x] Replace explici... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4218 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4218/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4218/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4218/events | https://github.com/materialsproject/pymatgen/pull/4218 | 2,722,409,653 | PR_kwDOACgets6ESrIF | 4,218 | Explicit UTF-8 encoding for VASP input files with `zopen`, and `open` for other text files | {
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"As you have started this already, let me know when I shall step in (if needed).",
"Thanks for saying that I could handle this as there aren't too many to fix across the entire code base (~300) and unsafe fixes from `ruff` is available, should be able to fix them pretty fast (though need to double check the `ruff... | 2024-12-06T08:36:47 | 2025-01-10T02:28:01 | 2025-01-09T20:37:59Z | CONTRIBUTOR | {
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} | ### Summary
- Explicit UTF-8 encoding when reading/writing VASP input files with `zopen`, to fix #4214
- Explicit UTF-8 encoding for standard `open`
- `pytest` ignore `UserWarning` only by default instead of all warnings
- [x] Add test for non-ASCII char in Kpoints comment
### Rationale
[PEP 597 – Add option... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4219 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4219/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4219/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4219/events | https://github.com/materialsproject/pymatgen/pull/4219 | 2,724,541,290 | PR_kwDOACgets6EZ9wX | 4,219 | `zopen`: explicit binary/text `mode` , and explicit `encoding` as UTF-8 | {
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} | ### Summary
- Explicit binary/text `mode` for `zopen`, I have opened a PR from `monty`'s side to prevent this https://github.com/materialsvirtuallab/monty/pull/730
- [x] Explicitly use UTF-8 `encoding` for `zopen`
Detailed reasoning and example are given in https://github.com/materialsvirtuallab/monty/pull/730#i... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4220 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4220/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4220/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4220/events | https://github.com/materialsproject/pymatgen/issues/4220 | 2,725,371,324 | I_kwDOACgets6icd28 | 4,220 | Specify equivalent sites included in different unit cells in `get_miller_index_from_site_indexes` of the `Structure` class | {
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} | ### Feature Requested
Now, we can specify only the `site_ids` of atoms to define an atomic plane for which a miller index is derived in the `get_miller_index_from_site_indexes` method of the `Structure` class. But this is quite inconvenient because we cannot get the Miller indices of the planes passing through atoms... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4221 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4221/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4221/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4221/events | https://github.com/materialsproject/pymatgen/pull/4221 | 2,731,650,249 | PR_kwDOACgets6Eyc1O | 4,221 | Revert "`zopen`: explicit binary/text `mode` , and explicit `encoding` as UTF-8" | {
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"Sure thing would look into this ",
"@shyuep I would look into (and be responsible for) those test failure in current master branch as they're seemingly related to my PRs, sorry for the trouble",
"AFAIK that is not related to #4219 but recent `monty` released `numpy<2` pin and `numpy` bumped to 2, while `netcdf... | 2024-12-11T02:21:15 | 2024-12-12T05:45:11 | 2024-12-11T02:21:23Z | MEMBER | {
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} | Reverts materialsproject/pymatgen#4219. Tests fail because of this. @DanielYang59 Pls fix and resubmit PR. | {
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} | - Reapply #4219, in response to #4221
- [x] Enable `PYTHONWARNDEFAULTENCODING` PEP 597, mark `monty.io.zopen` encoding warning as error, confirmed to work by https://github.com/materialsproject/pymatgen/actions/runs/12297641499
- [ ] After `monty` dropped custom encoding warning, modify warning filter
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"@shyuep This should fix failure.\r\n\r\nRegarding the `Namespace` issue from `monty` I would fix it ASAP but I don't think it's relevant anymore, i.e. after we fixed that implementation it still cannot be used (intentionally) as `pop` would not be allowed which \"redefines the keys\".\r\n ",
"Thanks!"
] | 2024-12-11T06:44:27 | 2024-12-11T14:38:46 | 2024-12-11T14:03:55Z | CONTRIBUTOR | {
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TODOs:
- [x] investigate netcdf4 compatibility with NP2
- [x] double check latest monty compatibility | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4224 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4224/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4224/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4224/events | https://github.com/materialsproject/pymatgen/pull/4224 | 2,735,259,621 | PR_kwDOACgets6E-93P | 4,224 | Skip another failing `Phonopy` test in Windows after NumPy bumped to 2 in CI | {
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} | Skip another failing `phonopy` test in Windows after NumPy bumped to 2 in CI
- https://github.com/phonopy/phonopy/issues/476
I could recreate this in my Windows PC, all four tests failing for the same reason:
```
Python 3.10.0
phonopy==2.33.0
numpy==2.0.2
```
```
$ pytest tests/io/test_phonopy.py
...... | {
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"Thanks for flagging this @lllangWV \r\n\r\nTagging @mhsiron @Andrew-S-Rosen for this one, I haven't used the Chargemol functionality myself. Not clear how this worked previously if it is an error?",
"Almost certainly this is the correct patch, although I must admit that I don't think I've used this function in a... | 2024-12-16T02:20:41 | 2025-04-20T19:39:28 | 2025-04-20T19:39:20Z | CONTRIBUTOR | {
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} | atomic_densities dir for chargemol is a dir not a file.
I am working with chargemol in a high throughput context with Atomate2. When trying to perform chargemol calculations I could not get past `if not os.path.isfile(atomic_densities_path):`. I believe this is because if you provide a directory, which is what `ato... | {
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} | - Bump `phonopy` to apply fix for NumPy 2 in Windows:
- https://github.com/phonopy/phonopy/issues/476
- Drop Python < 3.10 check | {
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"Thanks @DanielYang59!"
] | 2024-12-17T08:25:40 | 2025-01-01T02:23:19 | 2024-12-31T22:18:09Z | CONTRIBUTOR | {
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} | ### Summary
Replace some deprecated API:
- `spglib` dict interface
- [x] Revert deprecation warning as error
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"Hi @yantar92, \r\n\r\n> I need directions to add tests.\r\n\r\nYou can use this example here:\r\nhttps://github.com/materialsproject/pymatgen/blob/da607e86f9ce8aec942067c6c1a4fda6e04915dd/tests/io/test_ase.py#L186-L203\r\n\r\nAlso can you detail how this is different than the existing `set_constraint` method? It ... | 2024-12-17T09:13:37 | 2025-01-09T16:44:24 | 2025-01-09T16:44:20Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- Implement full selective_dynamics support when converting to/from ASE atoms.
## Todos
If this is work in progress, what else needs to be done?
- I need directions to add tests.
## Checklist
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations... | {
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} | ### Python version
Python 3.12
### Pymatgen version
2024.10.29
### Operating system version
_No response_
### Current behavior
When a structure does not contain any _symmetry_equiv_pos_as_xyz keys and pymatgen defaults to the P1 space group, the code currently generates three symmetry operations based on ("x", "... | {
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"Hi @IsaacGentle thanks for reporting and I could confirm this issue. For a quick guide on making contributions to a project, you could checkout [the guide here](https://github.com/materialsproject/pymatgen/blob/master/docs/contributing.md).\r\n\r\nI could confirm your fix indeed work, but things looks more complex... | 2024-12-20T22:07:59 | 2025-01-09T16:45:23 | 2025-01-09T16:45:23Z | NONE | {
"total": 0,
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} | ### Python version
Python 3.12.3
### Pymatgen version
2024.11.13
### Operating system version
Windows 10
### Current behavior
The following code leads to an error (ValueError: + is an invalid formula!)
```
from pymatgen.analysis.pourbaix_diagram import ion_or_solid_comp_object
fails = ion_or_solid_comp_objec... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4232 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4232/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4232/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4232/events | https://github.com/materialsproject/pymatgen/issues/4232 | 2,755,644,686 | I_kwDOACgets6kP80O | 4,232 | Wrong mapping of dielectric tasks in the mp-api | {
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"@Nokimann Hi thanks for reporting, this sounds like a MP API issue, if that's the case, could you please open this issue on the [API repo](https://github.com/materialsproject/api)?\r\n\r\n@tschaume Not sure if you could transfer the issue?",
"@DanielYang59\r\n\r\nI opened this problem on [MP API](https://github.... | 2024-12-23T09:47:19 | 2025-01-07T20:29:56 | 2025-01-07T20:29:56Z | NONE | {
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} | ### Python version
Python 3.12.2
### Pymatgen version
2024.11.13
### MP-API version
mp-api 0.44.0
### Operating system version
Ubuntu 20.04.6 LTS
### Current behavior
```
with MPRester(api_key) as mpr:
docs = mpr.materials.summary.search(material_ids='mp-16236')
docs[0].origins
```
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4233 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4233/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4233/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4233/events | https://github.com/materialsproject/pymatgen/pull/4233 | 2,756,264,573 | PR_kwDOACgets6GF7EP | 4,233 | Fix ion formula check in `ion_or_solid_comp_object` of `analysis.pourbaix_diagram` | {
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"Thanks.",
"@DanielYang59 Removing `ELEMENTS_HO` in https://github.com/DanielYang59/pymatgen/commit/9551b5a14227be7ed295c0f2d020709f4f16bb66 was a breaking change, and needed to be mentioned in https://github.com/materialsproject/pymatgen/blob/master/docs/compatibility.md\r\n\r\nThis kind of change is not recomme... | 2024-12-23T15:17:18 | 2025-01-27T09:03:31 | 2025-01-09T16:45:22Z | CONTRIBUTOR | {
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} | ### Summary
- Fix ion formula in `ion_or_solid_comp_object` of `analysis.pourbaix_diagram`, to fix #4231
- [x] Add tests
- [x] Add type annotations
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"Thanks. This is an old file because we used to actually test the gulp functionality. This is now more or less defunct.",
"No problem at all, yep we dropped the GULP binary but I forgot about these libs. \r\n\r\nAnd happy new year of course :)"
] | 2024-12-24T12:03:13 | 2025-01-01T02:25:34 | 2024-12-31T22:16:55Z | CONTRIBUTOR | {
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} | Drop GULP libs from code base and refactored `gulp_caller` to take potential file as arg, rationale:
- `pymatgen` just provides an interface to other packages, but we don't need to carry the dependencies/libs for them?
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"This should be fixed now. Though I generally do not use auto-merge much.",
"Great to know. Thanks for fixing that :)"
] | 2024-12-24T12:25:35 | 2025-01-18T02:48:43 | 2025-01-17T16:53:47Z | CONTRIBUTOR | {
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} | At some point [auto-merge is not working across `pymatgen`](https://github.com/materialsproject/pymatgen/pull/4102), according to @ab5424:
> I think that the branch protection rules require a check under the name test (ubuntu-latest, >3.10, lowest-direct, ci,optional) to pass (hence the "Required" tag at the end of th... | {
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"Thanks for the contribution."
] | 2024-12-26T14:52:47 | 2024-12-31T22:16:29 | 2024-12-31T22:16:23Z | CONTRIBUTOR | {
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The current implementation assume some oxidation and tries to evaluate and Ewald energy to get the ordered representation with the lowest energy.
https://github.com/materialsproject/pymatgen/blob/da607e86f9ce8aec942067c6c1a4fda6e04915dd/src/pym... | {
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"I'm able to parse the magnetization with `pymatgen==2024.11.13`, can you try parsing on a non-windows machine to see if that's the issue?",
"> I'm able to parse the magnetization with `pymatgen==2024.11.13`, can you try parsing on a non-windows machine to see if that's the issue?\r\n\r\nYes, the code can be pars... | 2024-12-28T02:05:09 | 2025-01-06T01:48:23 | 2025-01-05T07:26:22Z | NONE | {
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} | ### Python version
python 3.11.0 and python 3.10.0
### Pymatgen version
2024.11.13
### Operating system version
Windows 11 24H2 26100.2605
### Current behavior
Hi pymatgen developers, recently I am experiencing OUTCAR parsing issues again. After I performed a series of VASP calculations on Bohrium ... | {
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"Just to show it now in action, only `Spin.up` arrays present as desired:\r\n<img width=\"790\" alt=\"image\" src=\"https://github.com/user-attachments/assets/5c1d7d58-ea2a-469b-b669-97d064856967\" />\r\n",
"Many thanks for fixing this."
] | 2024-12-29T12:34:53 | 2024-12-31T22:15:18 | 2024-12-31T22:15:11Z | CONTRIBUTOR | {
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Currently, `pymatgen` does not correctly parse the density of states (DOS) from VASP SOC calculations. This issue was alluded to in https://github.com/materialsproject/pymatgen/issues/1540 & https://github.com/materialsproject/pymatgen/issues/1600.
The `tdos`, `idos`, `complete_dos`, and `pdos` attribute... | {
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"Thanks. Can you add a unittest for the functionality pls?",
"Done! Didn't add one at first as it _should_ be a relatively rare case where this actually matters (e.g. Dirac cone systems or toy test cases), but added now!\r\nSome tests seem to be failing for unrelated reasons",
"Are you sure they're unrelated? I... | 2024-12-29T13:59:35 | 2025-04-02T00:14:10 | 2025-01-17T17:36:40Z | CONTRIBUTOR | {
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| Time to close | 1 day, 6:49:59 | 1 day, 6:49:59 | 1 day, 6:49:59 |
| Time to answer | None | None | None |
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"this will close #4243 ",
"It would be great if this could be merged. Currently, all our imports from pymatgen where composition is used lead to failures. Additionally, a new release would be very helpful.\r\n\r\nThank you!"
] | 2025-01-02T11:08:48 | 2025-01-07T21:47:25 | 2025-01-07T21:47:25Z | CONTRIBUTOR | {
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Remove deprecated `is_rare_earth_metal` from `ElementBase` in periodic_table.py.
This function was deprecated [here](https://github.com/materialsproject/pymatgen/blob/1abc45936f839369854399369bc966732f85bf08/docs/CHANGES.md?plain=1#L342) since end of May 2024. Confirming it’s not used anymore elsewhere i... | {
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"CI failing on downstream packages \r\n\r\nhttps://github.com/JaGeo/LobsterPy/pull/357",
"Happy new year and sorry guys for the first bug of 2025, looks like [the repo checking mechanism in `monty.dev.deprecated` is not doing what I expected it to do](https://github.com/materialsvirtuallab/monty/blob/26acf0b2900b... | 2025-01-02T15:55:51 | 2025-01-31T09:13:11 | 2025-01-06T15:19:12Z | NONE | {
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All
### Pymatgen version
Master
### Current behavior
Throws deprecation warning in CI
### Expected Behavior
Removal
Deadline to remove 2025-01-01
https://github.com/materialsproject/pymatgen/blob/1abc45936f839369854399369bc966732f85bf08/src/pymatgen/core/periodic_table.py#L75... | {
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- Fix CI failure for `io.exciting.inputs` owing to `scipy` constant update https://github.com/scipy/scipy/pull/21605 https://github.com/materialsproject/pymatgen/blob/1abc45936f839369854399369bc966732f85bf08/src/pymatgen/io/exciting/inputs.py#L61-L62
- Add types | {
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.1 → v0.8.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.8.1...v0.8.6)
- [github.com/pre-commit/mirrors-mypy: v1.13.0 → v1.14.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.13.0...v1.14.1)
- [github.com/RobertCraigie/... | {
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"I'm sorry I keep merging to the wrong fork!"
] | 2025-01-07T20:24:05 | 2025-01-07T20:24:44 | 2025-01-07T20:24:43Z | NONE | {
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"@abhardwaj73 from my group is using this in his research and has agreed to tackle this",
"Please post this issue on the atomate Issues?",
"Ok thanks.,"
] | 2025-01-07T21:45:19 | 2025-01-07T21:47:56 | CONTRIBUTOR | {
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} | ### Feature Requested
The `atomate` repository contains an input set for surface calculations - [`MPSurfaceSet`](https://github.com/hackingmaterials/atomate/blob/2e541f297165254ac054b50e8132adaa282a01e0/atomate/vasp/workflows/base/adsorption.py#L370) - whose parameters differ slightly from `MVLSlabSet` and appears to ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4248 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4248/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4248/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4248/events | https://github.com/materialsproject/pymatgen/issues/4248 | 2,776,159,636 | I_kwDOACgets6leNWU | 4,248 | Can we get a new release with scheduled deprecations removed | {
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"Hi @lbluque happy new year.\r\n\r\nLooks like you might be using Python 3.9, and unfortunately both `pymatgen` and ~~`monty`~~ have dropped Python 3.9 support.\r\n\r\n~~If you have to use Python 3.9, you might need to temporarily remove the `CI` environment variable to disable the deprecation check for now, https:... | 2025-01-08T19:28:51 | 2025-01-10T10:10:01 | 2025-01-10T05:13:00Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12
### Pymatgen version
v2024.11.13
### Operating system version
_No response_
### Current behavior
The latest release v2024.11.13 does not have deprecated functions past their deadlines removed:
```python-traceback
/opt/hostedtoolcache/Python/3.9.21/x64/lib/python3.9/site-package... | {
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"This is not a bug. The code tries to find the most orthogonal set of parameters to craete the slab. You can disable this by turning this off."
] | 2025-01-10T12:11:34 | 2025-01-10T16:29:26 | 2025-01-10T16:29:25Z | NONE | {
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} | ### Python version
Python 3.9
### Pymatgen version
Pymatgen 2024.8.9
### Operating system version
ubuntu 24
### Current behavior
The slab generator significantly modifies the x and y dimensions of the cell. While the oriented_unit_cell maintains the original parameters, the final slab has completely different x... | {
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"@JuJueTanWan Hi thanks for reporting this issue. While I'm happy to look into this issue, is it possible for you to provide the complete CIF file (looks like the provided is a snippet of it) for me to recreate this issue (GitHub doesn't support uploading cif files directly, but you could add a `.txt` extension as ... | 2025-01-12T11:34:52 | 2025-01-17T16:46:37 | 2025-01-17T16:46:36Z | NONE | {
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} | ### Python version
Python 3.9.21
### Pymatgen version
2024.8.9
### Operating system version
CentOS 7.9
### Current behavior
Hello, I encountered an issue when using pymatgen's CifParser to parse a .cif file. Specifically, I noticed that the fractional coordinates of some atoms (X and Y) parsed by CifParser do no... | {
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"Thanks for opening this. I will look into this ASAP, link to #4195\r\n\r\n---\r\n\r\nUpdate: I cannot reproduce this on MacOS 15.2, Python 3.12.8\r\n\r\n```python\r\nfrom pymatgen.io.vasp.outputs import Outcar\r\n\r\n\r\noutcar = Outcar('OUTCAR.txt')\r\n\r\nprint(outcar.data[\"nbands\"]) # 24 (seems to work fine)... | 2025-01-13T19:02:46 | 2025-01-17T16:42:19 | 2025-01-17T16:42:18Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.4
### Pymatgen version
2025.1.9
### Operating system version
Linux
### Current behavior
```
Traceback (most recent call last):
outcar = Outcar(os.path.join(wdir, "OUTCAR")).as_dict()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/LUMI_TYKKY_NMfA5bl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4252 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4252/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4252/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4252/events | https://github.com/materialsproject/pymatgen/issues/4252 | 2,785,503,501 | I_kwDOACgets6mB2kN | 4,252 | Add method `Trajectory.to_ase_trajectory()` | {
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"further context: there's a `pmg_to_ase_trajectory` helper function in https://s3.us-east-1.amazonaws.com/materialsproject-contribs/amorphous_diffusivity/trajectory_reader.ipynb by @esoteric-ephemera that looks like it would be generally useful",
"Hey @janosh I was actually working on this for the same reason, ho... | 2025-01-13T21:43:44 | 2025-01-15T17:23:15 | 2025-01-15T17:23:15Z | MEMBER | {
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} | ### Feature Requested
`class Trajectory` has a [`from_file` method](https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core/trajectory.py#L552) that supports ASE `.traj` files. arguably, if from ASE works, would be great if to ASE also works
### Proposed Solution
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4253 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4253/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4253/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4253/events | https://github.com/materialsproject/pymatgen/pull/4253 | 2,785,809,929 | PR_kwDOACgets6HohM3 | 4,253 | ASE <---> pymatgen trajectory conversion | {
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"@shyuep and @mkhorton should be ready for review whenever you get a chance",
"Looks good. Thanks. Merged."
] | 2025-01-14T00:30:25 | 2025-01-15T17:23:26 | 2025-01-15T17:23:14Z | CONTRIBUTOR | {
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} | Adds feature to convert between ASE and pymatgen trajectories via `from_ase` and `to_ase` methods on `Trajectory`. Allows for carrying energies, forces, stresses, etc. between ASE and pymatgen trajectories, rather than just structural info as previously implemented.
Merging would close #4252. From the discussion th... | {
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} | automatically add the override warning when using libxc
## Summary
Major changes:
- fix 1: libxc calls should automatically override warning
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixe... | {
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"Good catch, thanks @peikai!\r\n\r\nIf you could, can you change the check to ensure it is not case sensitive? This is probably the most robust solution, in case some people are still using entries serialised with the former `run_type`.",
"@mkhorton, Sure, I updated the calculation parameters for archive test ent... | 2025-01-16T23:51:59 | 2025-01-28T17:36:32 | 2025-01-23T17:40:36Z | CONTRIBUTOR | {
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} | The run_type for entries had been changed from 'R2SCAN' to 'r2SCAN', whereas the `MaterialsProjectDFTMixingScheme()` is still expecting to find 'R2SCAN' entries.
As a result, all r2SCAN entries would be ignored when carrying out GGA(+U)/R2SCAN mixing scheme corrections, thereby affecting the construction of GGA(+U)/... | {
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"Great thanks."
] | 2025-01-17T10:35:53 | 2025-01-17T16:43:36 | 2025-01-17T16:43:30Z | CONTRIBUTOR | {
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} | `Composition` objects initialised as e.g. `Composition({"Cd2+": 1, "Cd": 1, "Te2-": 2})` do not behave as expected, giving e.g. `Composition.formula = "Cd3 Te2"` instead of `Cd2 Te2`. This is due to `Composition.__getitem__()` matching all species and elements/non-species of a given input string; so that `Composition["... | {
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"Thanks."
] | 2025-01-17T11:42:57 | 2025-01-18T16:21:09 | 2025-01-18T16:21:05Z | CONTRIBUTOR | {
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} | See https://github.blog/changelog/2025-01-16-linux-arm64-hosted-runners-now-available-for-free-in-public-repositories-public-preview/
## Summary
Major changes:
- feature 1: ...
- fix 1: ...
## Todos
If this is work in progress, what else needs to be done?
- feature 2: ...
- fix 2:
## Checklist
... | {
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"I could recreate this with Python 3.13 as [`pipes` has been removed in Python 3.13](https://docs.python.org/3/library/pipes.html):\n> This module is no longer part of the Python standard library. It was [removed in Python 3.13](https://docs.python.org/3/whatsnew/3.13.html#whatsnew313-pep594) after being deprecated... | 2025-01-20T21:19:38 | 2025-01-23T17:51:42 | 2025-01-23T17:34:10Z | NONE | {
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} | ### Python version
3.13.1
### Pymatgen version
2024.10.3
### Operating system version
EndeavorOS
### Current behavior
I have installed pymatgen using the official instructions but I fail to install the crystal-toolkit module. It stops with the error that it cannot find a different module called `pipes`.
### Exp... | {
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"I agree with this in general. But I would suggest something like `<comp>-<date/time>-<md5 hash of vasprun.xml>` as the entry id. ",
"This has been fixed.",
"Nice, thanks @shyuep!"
] | 2025-01-22T23:09:32 | 2025-01-23T18:56:28 | 2025-01-23T17:34:37Z | CONTRIBUTOR | {
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} | When using the ``get_computed_entry()`` method for ``Vasprun``, the ``entry_id`` is automatically set to `f"vasprun-{datetime.now(tz=timezone.utc)}"`:
https://github.com/materialsproject/pymatgen/blob/876b9998d0622161f48ecf29348cf479e3b54ad0/src/pymatgen/io/vasp/outputs.py#L871
This means that `entry_id` changes when ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4260 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4260/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4260/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4260/events | https://github.com/materialsproject/pymatgen/pull/4260 | 2,807,326,820 | PR_kwDOACgets6IyPRe | 4,260 | Draft: Use external Package for FHI-aims IO interface | {
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"If the idea is to move FHI aims to a new external package, I think it should be done completely. Then there is no need for the unit tests to be done here. It can be done in the new package. We can also remove all the FHI related test files.",
"Okay that is reasonable, I will move the tests there."
] | 2025-01-23T16:12:29 | 2025-03-11T16:01:31 | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- moved FHI-aims specific content into a separate package (pyfhiaims) for ease of maintenance (stop multiple libraries from implementing the same basic interface)
## Todos
If this is work in progress, what else needs to be done?
- Workout how to best test the aims io interface... | {
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} | ### Python version
Python 3.11.11
### Pymatgen version
2025.1.23
### Operating system version
_No response_
### Current behavior
Hello, I recently tried using the MaterialsProjectDFTMixingScheme() to construct a GGA/GGA+U/R2SCAN phase diagram for Fe-O by following the code on the materials project documentation.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4262 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4262/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4262/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4262/events | https://github.com/materialsproject/pymatgen/pull/4262 | 2,809,358,263 | PR_kwDOACgets6I5OZA | 4,262 | WIP: add script to generate lobster basis information | {
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"[lobster_bases_PAWv64.zip](https://github.com/user-attachments/files/18561485/lobster_bases_PAWv64.zip)\r\n\r\nI made some minor changes to script that are system specific, and ran it with the v6.4-PAWs. I used different values for the minimal occupation and excluded any GW potential. I have also made some simple ... | 2025-01-24T12:36:38 | 2025-01-27T16:44:22 | MEMBER | {
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} | ## Summary
This is a script to read in POTCARs and generate the required basis set information files for all LOBSTER modules.
As we might want to generate these files for newer versions of POTCARs, I wanted to make them available.
(@Luccerboi for information) | {
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} | ### Python version
Python 3.11.11
### Pymatgen version
2025.1.24
### Operating system version
Ubuntu 20.04.6 LTS
### Current behavior
For a given structure, when I try to create an instance of the `SpacegroupAnalyzer` class, I get an immediate segmentation fault. I suspect it's an issue with spglib (I have v2.5.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4264 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4264/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4264/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4264/events | https://github.com/materialsproject/pymatgen/issues/4264 | 2,810,745,299 | I_kwDOACgets6niJHT | 4,264 | 36 tests failed | {
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} | ### Python version
3.11
### Pymatgen version
2025.1.23
### Operating system version
FreeBSD 14.2
### Current behavior
[log](https://freebsd.org/~yuri/py-pymatgen-2025.1.23-tests.log)
### Expected Behavior
n/a
### Minimal example
```Python
```
### Relevant files to reproduce this bug
_No response_ | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4265 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4265/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4265/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4265/events | https://github.com/materialsproject/pymatgen/pull/4265 | 2,810,918,796 | PR_kwDOACgets6I-iI- | 4,265 | Clarify return float/int type for `core.Composition.reduced_composition` and siblings, minor type clean up for `core.Composition` | {
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} | ## Summary
- Clarify return float/int type for `core.Composition.reduced_composition` and siblings, `factor` returned by `reduce_formula` would be int instead of float (as a union type of float | int): https://github.com/materialsproject/pymatgen/blob/296a0ec856b22da847b2ccd0e55e146e071cb8fd/src/pymatgen/core/compos... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4268 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4268/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4268/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4268/events | https://github.com/materialsproject/pymatgen/pull/4268 | 2,811,907,126 | PR_kwDOACgets6JBpa4 | 4,268 | Add `Structure.get_symmetry_dataset` convenience method | {
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"it occurs to me i forgot to add a `@due.dcite` decorator to this method. @lan496 do you have something you'd like users of this method to cite? maybe just a Zenodo release or a `citation.cff` file for now? here's a similar example:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/296a0ec856b22da847b2ccd0e5... | 2025-01-27T01:16:55 | 2025-01-30T11:43:07 | 2025-01-28T20:29:31Z | MEMBER | {
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} | `moyopy` is a successor to `spglib` that's faster and written in Rust. in my usage so far for analyzing MLFF-relaxed WBM structures for https://matbench-discovery.materialsproject.org/tasks/geo-opt, it seems about 4x faster than `spglib` and gives identical results in nearly all 257k cases. a few exceptions were report... | {
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"Hi thanks for reporting this and looks like a bug to me, and I could recreate this issue :)\n\n```python\nfrom pymatgen.core import Element\n\n\nele_hg = Element.from_Z(80)\n\nprint(ele_hg.full_electronic_structure)\n# [(1, 's', 2), (2, 's', 2), (2, 'p', 6), (3, 's', 2), (3, 'p', 6), (4, 's', 2), (3, 'd', 10), (4,... | 2025-01-27T03:35:06 | 2025-02-18T17:15:40 | 2025-02-18T17:15:40Z | NONE | {
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} | ### Python version
3.10.16
### Pymatgen version
2025.1.24
### Operating system version
_No response_
### Current behavior
It seems pymatgen returns incorrect valence configuration while parsing VASP POTCAR. Consider following code, where the POTCAR file corresponds to Hg (VASP-5.4, GGA, PBE, PAW, default):
```py... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4270 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4270/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4270/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4270/events | https://github.com/materialsproject/pymatgen/pull/4270 | 2,813,617,100 | PR_kwDOACgets6JHewv | 4,270 | Add `seed: int = 0` parameter to `Structure.perturb()` method | {
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"I am confused why this is really needed. The definition of a random perturbation means it is non-deterministic. The only determinism is an inequality based on the amplitude of the perturbation.",
"needed for downstream packages that use the `perturb` method in testing"
] | 2025-01-27T17:26:06 | 2025-01-28T22:50:02 | 2025-01-28T20:10:07Z | MEMBER | {
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} | - Update tests to verify reproducible random perturbations with same seed
- Add test cases for different seed values and min_distance parameter
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https://api.github.com/repos/materialsproject/pymatgen/issues/4271 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4271/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4271/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4271/events | https://github.com/materialsproject/pymatgen/pull/4271 | 2,815,895,830 | PR_kwDOACgets6JPRVh | 4,271 | Add missing parenthesis to `electronic_structure.boltztrap.BoltztrapAnalyzer.get_extreme.is_isotropic` | {
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} | ## Summary
- Add missing parenthesis to `electronic_structure.boltztrap.BoltztrapAnalyzer.get_extreme.is_isotropic`, to fix #4165
- Minor type/comment/var name cleanup
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} | ### Python version
3.11
### Pymatgen version
2025.1.24
### Operating system version
Windows
### Current behavior
Plotly 6.0.0 was released mere minutes ago, and I got unlucky. It turns out this seems to cause issues with the `PDPlotter` utility:
```python
from pymatgen.analysis.phase_diagram import PhaseDiagram... | {
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"I see this was closed but just curious, was there an issue here?",
"Nope."
] | 2025-01-28T20:31:52 | 2025-01-31T19:54:23 | 2025-01-28T20:31:56Z | MEMBER | {
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} | This reverts commit 4375e342f31a10fc023c9b07df5db6f316c738d4.
## Summary
Major changes:
- feature 1: ...
- fix 1: ...
## 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 a... | {
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"Thanks @Tinaatucsd, it looks like `occ_tol` should have been placed as an attribute of the class since only the first two parameters are called by the `alchemy` part of the code. \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/296a0ec856b22da847b2ccd0e55e146e071cb8fd/src/pymatgen/alchemy/materials.py#L12... | 2025-01-28T22:50:29 | 2025-02-18T17:14:03 | 2025-02-18T17:13:57Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- fix 1: Fixed incompatibility between `OrderDisorderedStructureTransformation` and `StandardTransmuter`:
- Previously, `occ_tol` was a method parameter in `apply_transformation`, making it unconfigurable when used with `StandardTransmuter` (which only passes transformation and optionall... | {
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"I realized I wrote some review messages here too that you can't see ;-)\r\n\r\n> I think here it should be\r\n> SELF.transformation_kwargs = {\"check_ordered_symmetry\": False, \"timeout\".....",
"I also tested this one and it works fine.\r\n",
"Thanks for testing!",
"Just to be sure, I found that line 670 s... | 2025-01-29T19:00:09 | 2025-02-18T17:53:23 | 2025-02-18T17:14:29Z | CONTRIBUTOR | {
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} | ## Summary
- Fix default `transformation_kwargs` in `analysis.magnetism.analyze.MagneticStructureEnumerator`, to close #4184
- Minor comment and type cleanup
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"Hi @fraricci sorry for the late response, can you help me test if this patch works? I don't have a \"slow enough\" enumlib job to test with (the unit test job last only 0.04 s and I'm not sure if it's really validating the behaviour), thanks a lot!",
"Hey @DanielYang59, I just saw your fix here. Sure I can test ... | 2025-01-29T20:10:21 | 2025-02-18T17:54:57 | 2025-02-18T17:11:29Z | CONTRIBUTOR | {
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} | ## Summary
- Fix timeout in `command_line.enumlib_caller.EnumlibAdaptor`, to fix #4185
- [x] Fix unit test, current unit test doesn't seem to work correctly (`Fortran runtime error: Cannot open file 'struct_enum.in': No such file or directory`)
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| Metric | Average | Median | 90th percentile |
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| Time to first response | 14:26:33 | 7:57:22 | 1 day, 4:06:28 |
| Time to close | 3 days, 16:04:18 | 2 days, 7:57:02 | 6 days, 8:27:55 |
| Time to answer | None | None | None |
| Metric | Count |
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| Number of ite... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4278 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4278/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4278/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4278/events | https://github.com/materialsproject/pymatgen/pull/4278 | 2,825,173,535 | PR_kwDOACgets6JuvNf | 4,278 | [Breaking] Fix valence electron configuration parsing for `PotcarSingle.electron_configuration` | {
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"I have a feeling that we might need to rewrite the `electron_configuration` property to parse the \"Atomic configuration\" section of POTCAR instead of generating from Madelung energy ordering rule, as electron configuration from POTCAR may or may not agree with periodic table (now that it's a property of `PotcarS... | 2025-02-01T12:05:41 | 2025-02-18T17:53:01 | 2025-02-18T17:15:39Z | CONTRIBUTOR | {
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} | ## Summary
- Fix valence electron configuration parsing in `PotcarSingle.electron_configuration`, to fix #4269
- Likely a follow up PR of #3944
- [x] Update unit tests
- [x] Test other versions of PSP?
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https://api.github.com/repos/materialsproject/pymatgen/issues/4279 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4279/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4279/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4279/events | https://github.com/materialsproject/pymatgen/pull/4279 | 2,825,712,163 | PR_kwDOACgets6Jwa7q | 4,279 | Fix P1 SymmOp string for `CifParser.get_symops` | {
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"Thanks @DanielYang59!",
"No problem at all!"
] | 2025-02-02T09:56:18 | 2025-02-10T08:22:25 | 2025-02-10T03:50:28Z | CONTRIBUTOR | {
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- Fix P1 SymmOp string for `CifParser.get_symops`, to close #4230
- [x] Unit test | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4280 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4280/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4280/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4280/events | https://github.com/materialsproject/pymatgen/pull/4280 | 2,828,551,793 | PR_kwDOACgets6J57dl | 4,280 | pre-commit autoupdate | {
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.2 → v0.9.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.2...v0.9.4)
- [github.com/codespell-project/codespell: v2.3.0 → v2.4.1](https://github.com/codespell-project/codespell/compare/v2.3.0...v2.4.1)
- [github.com/igorshubov... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4281 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4281/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4281/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4281/events | https://github.com/materialsproject/pymatgen/pull/4281 | 2,831,119,906 | PR_kwDOACgets6KCybZ | 4,281 | Add method to get the Pearson symbol to SpaceGroupAnalyzer | {
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"Thanks Rhys!"
] | 2025-02-04T19:30:42 | 2025-03-07T02:49:49 | 2025-03-07T02:49:49Z | CONTRIBUTOR | {
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} | ## Summary
Add a simple convenience method to SGA to return the Pearson Symbol.
## 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 [`duec... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4282 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4282/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4282/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4282/events | https://github.com/materialsproject/pymatgen/issues/4282 | 2,835,047,385 | I_kwDOACgets6o-2PZ | 4,282 | Redefinition of the ASE Atoms class in pymatgen.io.ase is problematic with type checkers | {
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def __init__(self, *args, **kwargs):
raise NO_ASE_ERR
In my code I would then have ""pymatgen.io.ase.Atoms" is not assignable to "ase.atoms.Atoms"" everywhere, because the type checker is confused about the redefinition. Is it really necessary to have thi... | {
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"Thanks @janosh! Enabled auto-merge on this, looks like there's an unrelated linting error",
"@mkhorton i fixed the lint error. now there's another unrelated issue:\r\n\r\n```py\r\nfrom coverage.sqldata import CoverageData as CoverageData # pylint: disable=useless-import-alias\r\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^... | 2025-02-06T23:44:29 | 2025-02-13T19:20:01 | 2025-02-13T19:20:01Z | MEMBER | {
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} | This PR extends the existing bracket normalization for square brackets `[...]` to curly brackets `{...}`. Important e.g. for a few of the 8k+ metallic glass compositions reported in Ward et al. (2018) https://doi.org/10.1016/j.actamat.2018.08.002. previously, some of those formulas raised
```py
ValueError: Invalid ... | {
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"#4100 should unblock Python 3.13. But I'm a bit unsure about [the CI failure](https://github.com/materialsproject/pymatgen/actions/runs/13219577081/job/36902930489?pr=4100) (it wasn't there before), and I'm looking into it.\n\nFor some reason I cannot recreate that error (which looks like some float point number p... | 2025-02-08T15:56:50 | 2025-04-20T19:35:33 | 2025-04-20T19:35:33Z | MEMBER | {
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https://github.com/materialsproject/pymatgen/blob/5b997f78c9ae785e7a18a157c697d996f7dba746/pyproject.toml#L24 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4285 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4285/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4285/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4285/events | https://github.com/materialsproject/pymatgen/issues/4285 | 2,840,668,251 | I_kwDOACgets6pUShb | 4,285 | [Python 3.13 support roadmap] Replace `pybtex` with `bibtexparser` | {
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"I would give it a try and make it optional for now (0b2574515928e9b8add0b0c5cd05a3038b3984ab)",
"@shyuep Can I have some comment on this? Current `pybtex` is a mandatory dependency and does not support Python 3.13 therefore blocking pymatgen upgrade to Python 3.13 support. Can we make it optional or do we want t... | 2025-02-09T13:15:24 | 2025-04-18T08:25:00 | 2025-04-18T08:24:59Z | CONTRIBUTOR | {
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} | Looks like development on `pybtex` might have stalled ([no release since Jan 2021](https://pypi.org/project/pybtex/#history)), and the following would error out on MacOS Python 3.13:
```python
from pybtex.database import BibliographyData, Entry
```
Gives:
```
Traceback (most recent call last):
File "/Users/yang/dev... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4286 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4286/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4286/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4286/events | https://github.com/materialsproject/pymatgen/issues/4286 | 2,844,157,595 | I_kwDOACgets6phmab | 4,286 | typo in 'core/structure.py' | {
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"Thanks for catching this, I would fix it!"
] | 2025-02-11T02:58:00 | 2025-02-18T17:09:35 | 2025-02-18T17:09:34Z | NONE | {
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} | Hi, I noticed a small typo in the comment in <kbd>core/structure.py</kbd>. The comment mentions "translation," but the function actually implements a "rotation" operation. (See line 4677 & 5298)
https://github.com/materialsproject/pymatgen/blob/153ccb46155f665b9933babfd48b563ac24dfaca/src/pymatgen/core/structure.py#L52... | {
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"I would rather not have two surface sets with only slgihtly different parameters and confusing names. The changes to the inputs are small enough that you can go ahead and modify MVLSlabSet directly and atomate should use MVLSlabSet.",
"@abhardwaj73 it looks like the adsorption workflows in `atomate2` use a modif... | 2025-02-11T17:14:52 | 2025-05-01T21:19:13 | 2025-05-01T21:18:30Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- feature 1: Addition of MPSurfaceSet mentioned [here](https://github.com/hackingmaterials/atomate/blob/2e541f297165254ac054b50e8132adaa282a01e0/atomate/vasp/workflows/base/adsorption.py#L370)
## Todos
- feature 2: Addition of tests for this new vasp input set
Mentioned in thi... | {
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"Just to note, the linting test failure is unrelated to this PR, seems to be something due to `Xdatcar` parsing? (Possibly due to a `mypy` version update)?",
"Tests are all passing btw"
] | 2025-02-11T19:27:10 | 2025-02-18T17:16:20 | 2025-02-18T17:16:20Z | CONTRIBUTOR | {
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} | Following discussion with @esoteric-ephemera after the updates to this function in https://github.com/materialsproject/pymatgen/pull/4240; the best approach for determining the VBM/CBM eigenvalues from a DOS object is to interpolate between the DOS points above/below the chosen threshold `tol`, and take the eigenvalues... | {
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"The minimal example also throws an error for me. It looks like this bug is occurring [on](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/io/ase.py#L205-L215) lines 205 - 215 of pymatgen.io.ase\n\n\n```python\n # Atoms.info <---> Structure.properties\n if properties := structure.... | 2025-02-11T21:46:47 | 2025-02-28T18:03:16 | 2025-02-28T18:03:16Z | CONTRIBUTOR | {
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} | ### Python version
3.12.4
### Pymatgen version
2025.1.24
### Operating system version
MacOS
### Current behavior
Problems arise when converting `Structure`'s **with spacegroup information embedded in structure.properties** into `ase.Atoms` objects.
**MINIMAL EXAMPLE**
```
import json
from pymatgen.core import ... | {
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} | ## Summary
- Migrate some type annotation tweaks from #4100, make it easier to review
- Fix #4286 | {
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- Remove deprecated memory units from `core` | {
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"Great. Thanks!"
] | 2025-02-17T19:11:42 | 2025-02-18T17:09:07 | 2025-02-18T17:09:02Z | CONTRIBUTOR | {
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`titlefont` has been deprecated in `plotly` v6, refactored to `title.font`.
This updates to use the new syntax, and requires a bump in `plotly` requirement from `>=4.5,<6` to `>=5`. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4293 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4293/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4293/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4293/events | https://github.com/materialsproject/pymatgen/issues/4293 | 2,860,823,124 | I_kwDOACgets6qhLJU | 4,293 | Wrong reassignment of translations for edges in __mul__ method of StructureGraph object | {
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"Another example with errors in redefining translations is as follows:\n\n```\nerror_structure = {\n '@module': 'pymatgen.analysis.graphs',\n '@class': 'StructureGraph',\n 'structure': {'@module': 'pymatgen.core.structure',\n '@class': 'Structure',\n 'charge': 0.0,\n 'lattice': {'matrix': [[1.57, -2.719319767... | 2025-02-18T15:33:42 | 2025-03-04T14:26:01 | NONE | {
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} | ### Python version
Python 3.9.13
### Pymatgen version
2023.2.22
### Operating system version
Windows 11
### Current behavior
When I multiply StructureGraph object and create supercell, the edges of the graph
are not relabeled properly. In the example we have a layer inside unit cell. The layer lies in (001) pla... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4294 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4294/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4294/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4294/events | https://github.com/materialsproject/pymatgen/pull/4294 | 2,863,240,894 | PR_kwDOACgets6Lvp1u | 4,294 | Bump nokogiri from 1.16.5 to 1.18.3 in /docs | {
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} | Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.16.5 to 1.18.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/sparklemotion/nokogiri/releases">nokogiri's releases</a>.</em></p>
<blockquote>
<h2>v1.18.3 / 2025-02-18</h2>
<h3>Security</h3>
<ul>
<li>[CRuby] V... | {
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} | ### Summary
- Pass `kwargs` to `IStructure.to` method in JSON format, #3018
**Rationale:**
Allow more fine grained control of `json.dumps` behaviour when needed (without changing current behaviour AFAIK), also consistent with other formats | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4296 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4296/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4296/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4296/events | https://github.com/materialsproject/pymatgen/pull/4296 | 2,863,775,214 | PR_kwDOACgets6LxetK | 4,296 | Make dict representation of `SymmetrizedStructure` MSONable | {
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"Thanks @DanielYang59, and thanks for flagging it as breaking. Could you clarify what is actually breaking here? As far as I can see it's just the extra keys in the dict representation?\r\n\r\nIf breaking, could you also make sure the PR includes an update to the [compatibility page](https://github.com/materialspro... | 2025-02-19T16:01:24 | 2025-03-17T13:44:31 | 2025-03-17T13:39:56Z | CONTRIBUTOR | {
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} | ### Summary
- Make dict representation of `SymmetrizedStructure` MSONable, to fix #3018
- [x] Unit test
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4297 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4297/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4297/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4297/events | https://github.com/materialsproject/pymatgen/pull/4297 | 2,864,307,423 | PR_kwDOACgets6LzRCn | 4,297 | Bugfix: Structure/ase.Atoms interconversion side effects | {
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"Thanks, @wolearyc! Happy to merge this as-is. I fixed your failing tests by updating your branch."
] | 2025-02-19T20:11:45 | 2025-02-28T18:03:15 | 2025-02-28T18:03:15Z | CONTRIBUTOR | {
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} | ## Summary
This PR resolves #4289. There were bugs in `pymatgen.io.ase.AseAtomsAdaptor` in which `Structure` and `ase.Atoms` objects were modified when converted into one another. Specifically, `Atoms.info` and `Structure.properties` shared memory, leading to side effects.
Minor changes:
- `AseAtomsAdaptor` n... | {
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} | Hi there,
I'm interested in understanding if `pymatgen` depends on any graph algorithms from its usage of NetworkX? If so,
- What algorithms are used for what purpose?
- What graph sizes are they being used with?
- Have users experienced any slowdowns or issues with algorithms provided by NetworkX? (Speed, algorithm ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4299 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4299/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4299/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4299/events | https://github.com/materialsproject/pymatgen/pull/4299 | 2,869,420,486 | PR_kwDOACgets6MEg4h | 4,299 | Update inequality in `get_linear_interpolated_value` | {
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"Also there was a pre-commit `codespell` failure due to a variable name in `local_env` which was fixed in https://github.com/materialsproject/pymatgen/pull/4299/commits/8fdea1637b7c6ae933102d769ded02d1ca23163e ",
"This also adds some very small updates to make the behaviour of `DOS.get_interpolated_gap` and `Dos.... | 2025-02-21T16:00:10 | 2025-02-25T07:28:23 | 2025-02-25T07:28:23Z | CONTRIBUTOR | {
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} | This is a small but important fix for the `get_linear_interpolated_value` function in `pymatgen.util.coord`, used in various places within the codebase.
This function works by finding the first index in `x_values` that is greater than / equal to `x`, and then uses this index and the previous (`idx-1`) with `x_value... | {
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} | ### Pymatgen version
2025.2.18
### Current behavior
@esoteric-ephemera, @rkingsbury:
In [MP24RelaxSet.yaml](https://github.com/materialsproject/pymatgen/blob/1b8c5f8d80ce598b7d56f8bcbef6f0de47c33a66/src/pymatgen/io/vasp/MP24RelaxSet.yaml#L9) and [MPSCANRelaxSet.yaml](https://github.com/materialsproject/pymatgen/bl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4302 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4302/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4302/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4302/events | https://github.com/materialsproject/pymatgen/issues/4302 | 2,874,894,264 | I_kwDOACgets6rW2e4 | 4,302 | Ok, I it is not a bug | {
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} | ### Python version
Python 3.12.7
### Pymatgen version
Version: 2024.11.13
### Operating system version
_No response_
### Current behavior
I download the structure from JARVIS dft_3d, let's take the structure JVASP-23862 (NaCl)
Jarvis atoms:
{'lattice_mat': [[3.4360963088789007, -2.8895741e-09, 1.98383170055150... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4303 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4303/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4303/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4303/events | https://github.com/materialsproject/pymatgen/pull/4303 | 2,876,797,411 | PR_kwDOACgets6MYung | 4,303 | Fix mcl kpoints | {
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"Thanks for catching this @dgaines2! A fairly subtle bug, I hope there are not more present. Perhaps a good excuse to go back over these to be sure. Out of interest, what was the third-party software you noticed the bug in?\r\n\r\nIncluding a screenshot from [the paper](https://arxiv.org/pdf/1004.2974) for documen... | 2025-02-25T03:32:21 | 2025-04-24T17:05:49 | 2025-04-20T19:37:52Z | CONTRIBUTOR | {
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} | Fixed errors in two of the k-points for the MCL reciprocal lattice (according to Table 16 in Setyawan-Curtarolo 2010)
M2 and D1 aren't included in the recommended k-point path, but third-party software that plots k-point paths using pymatgen labelled M2 in the path instead of M1 due to it being the "same" k-point.
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https://api.github.com/repos/materialsproject/pymatgen/issues/4305 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4305/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4305/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4305/events | https://github.com/materialsproject/pymatgen/issues/4305 | 2,885,349,129 | I_kwDOACgets6r-u8J | 4,305 | Default `fmt` of `IStructure.to` doesn't agree with docstring | {
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} | As per the `IStructure.to` docstring: https://github.com/materialsproject/pymatgen/blob/b5d03d7e313c4933ccad27ac0037cba4a1538351/src/pymatgen/core/structure.py#L2920-L2932
The default `fmt` should be `json` when `filename` is not provided.
However:
```python
from pymatgen.core import Structure, Lattice
structure =... | {
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- `IStructure.to` default to JSON when `filename` not specified, to close #4305 | {
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"I have confirmed that @mkhorton is correct in that the total and diff are spin up and spin down, respectively, unlike the CHGCAR."
] | 2025-02-28T17:53:48 | 2025-03-02T02:55:34 | MEMBER | {
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} | ### Pymatgen version
2025.2.18
### Current behavior
As @mkhorton has aptly noted:
https://github.com/materialsproject/pymatgen/blob/b5d03d7e313c4933ccad27ac0037cba4a1538351/src/pymatgen/io/vasp/outputs.py#L3944-L3947
https://github.com/materialsproject/pymatgen/blob/b5d03d7e313c4933ccad27ac0037cba4a1538351/src/pyma... | {
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"depending on use case, viable workaround may be to use `from moyopy import SpaceGroupType` instead"
] | 2025-03-01T15:38:07 | 2025-04-10T20:15:31 | 2025-04-10T20:15:31Z | MEMBER | {
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} | ### Python version
3.13
### Pymatgen version
2025.2.18
### Operating system version
macOS
### Current behavior
```py
from pymatgen.symmetry.groups import SpaceGroup
File "/opt/hostedtoolcache/Python/3.11.11/x64/lib/python3.11/site-packages/pymatgen/symmetry/groups.py", line 21, in <module>
from pymatgen.co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4310 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4310/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4310/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4310/events | https://github.com/materialsproject/pymatgen/issues/4310 | 2,889,601,493 | I_kwDOACgets6sO9HV | 4,310 | Fix `SpaceGroup.symbol` to return short HM symbol always (incl. monoclinic spacegroups) | {
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> question for @kaueltzen and @JaGeo: the `SpaceGroup.symbol` [is documented](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.groups.SpaceGroup.symbol) to return the full HM symbol but as reported in https://github.com/spglib/moy... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4311 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4311/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4311/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4311/events | https://github.com/materialsproject/pymatgen/pull/4311 | 2,892,043,666 | PR_kwDOACgets6NMfWO | 4,311 | pre-commit autoupdate | {
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.9.4 → v0.9.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.4...v0.9.9)
- [github.com/pre-commit/mirrors-mypy: v1.14.1 → v1.15.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.14.1...v1.15.0)
- [github.com/RobertCraigie/... | {
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