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https://api.github.com/repos/materialsproject/pymatgen/issues/3670 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3670/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3670/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3670/events | https://github.com/materialsproject/pymatgen/pull/3670 | 2,167,476,811 | PR_kwDOACgets5on73O | 3,670 | Ensure `MSONAtoms` is indeed `MSONable` when `Atoms.info` is loaded with goodies | {
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"All ready to go!\r\n",
"Thanks!"
] | 2024-03-04T18:31:04 | 2024-03-05T12:14:34 | 2024-03-04T21:31:42Z | MEMBER | {
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Closes https://github.com/materialsproject/pymatgen/issues/3668.
The `Atoms.info` dictionary can be populated with all kinds of goodies that are challenging to deal with from a (de)serialization perspective. Oftentimes, this is from users hacking things into `Atoms.info`. For instance, in #3668, I put ... | {
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} | ## Summary
This PR fixes two bugs in the res writer:
- Fix 1: Add a blank line at the end of the file
- Fix 2: Do not write a blank line if REMS is empty
Closes #3636
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests ... | {
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This PR resets the label on any site changed by `Structure.replace_species()`. `Site.label` will fall back to use the default label instead (the species string).
Closes #3658
## Checklist
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"Meanwhile I noticed some input files are compressed for example: https://github.com/materialsproject/pymatgen/blob/8c5829ba0cc713ae1ead3d80e66a15b76ccf95da/tests/io/lobster/test_inputs.py#L1653-L1661\r\n\r\nI didn't see much point in compressing these small and \"human-oriented\" inputs files (`INCAR/POSCAR/KPOINT... | 2024-03-07T08:04:27 | 2024-03-08T12:49:38 | 2024-03-08T12:31:20Z | CONTRIBUTOR | {
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The second episode of cleaning up test files: VASP inputs, relocate VASP input files to a dedicated dir (`vasp/inputs`), following #3653.
## TODOs
- [x] Relocate `INCAR`: 2ebe5927e1e4ebd6752b34e8f17076f9c8986066
- [x] Relocate `KPOINTS`: c11758a333642f13beee17255e51a5a8594d... | {
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"good news: looks like linux CI dependency install time went from 2.5 to 1 min (2.5x speed up) and windows install time went from 9-14 min to 3-5 min (~3x speed up)!\r\n\r\nalso, `matgl` import error was indeed automatically fixed by `uv` and remaining failing tests due to `pydantic` import error are skipped until ... | 2024-03-07T08:21:29 | 2024-04-10T09:50:36 | 2024-03-07T09:16:12Z | MEMBER | {
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related PR: https://github.com/CederGroupHub/chgnet... | {
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"> i added a test\r\n\r\nThanks a lot. You did much more than you said 😄 \r\n"
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- Replace a hard coded hash `7` with proper hash method, see #3673.
The necessity of such method is unclear meanwhile.
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"I never use `AIRSS`, so just provide some info here, waiting a true master being called :).\r\n\r\nI assume update: https://github.com/materialsproject/pymatgen/blob/668fa574ab1e3e102065c5a9d7a785213dc5ac2f/pymatgen/io/res.py#L257-L269\r\n\r\nwith this might work:\r\n```diff\r\n @classmethod\r\n def _ions_fr... | 2024-03-07T16:02:09 | 2024-04-22T16:10:55 | 2024-04-22T16:10:55Z | NONE | {
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} | ### Python version
Python 3.10.8
### Pymatgen version
The latest
### Operating system version
_No response_
### Current behavior
The index of the SFAC block (second column) is not compatible with ARISS.
Currently, ResWriter gives a file as follows:
```
TITL mp-841-R2SCAN 0.00 63.1079 -46.08987 0.000000 0.00... | {
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"Thanks for the report, @JonathanSchmidt1. You are absolutely right that this is a bug that should be fixed. Are you interested in submitting a PR for this patch? \r\n\r\nCCing @tomdemeyere to let him know about the bug in case it is relevant to his work.",
"@JonathanSchmidt1 yes, please go ahead and submit a bug... | 2024-03-07T23:30:19 | 2024-03-08T09:34:14 | 2024-03-08T09:31:18Z | CONTRIBUTOR | {
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3.9.13
### Pymatgen version
2024.2.23
### Operating system version
_No response_
### Current behavior
Recently the get_pmg_structure and the get_phonopy_structure methods in pymatgen/io/phonopy.py were updated to include magnetic moments. ( https://github.com/materialsproject/pymatgen/pull/3... | {
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- fix: Change key in `get_pmg_structure` from `magnetic_moments` to `magmom`
- test: add `assert struct_pmg_round_trip.site_properties["magmom"] == struct_pmg.site_properties["magmom"]`
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"there's going to be a new `pmg` release soon to close #3744. do we want to get this in before that? let us know if others can help with this PR",
"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- This is an auto-generated comment: skip review by coderabbit.ai -->\n\n> [!IMPORTANT]\n> ... | 2024-03-09T00:06:36 | 2025-03-13T15:47:04 | 2025-03-10T17:09:12Z | CONTRIBUTOR | {
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} | ## Summary
The vaspout.h5 file appears to be a replacement for / supplement to the vasprun.xml file, and has been available in certain VASP versions >= 6. This PR aims to add support for parsing this file.
However the vaspout.h5 file appears to be still in development. For example, no electronic self-consistency ... | {
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"`borg` is a mystery for me partly because I never use it before, which looks like a parallelized VASP results collection tool. But in the unit tests, what files are being collected are not explicitly declared, nor commented. And the test data length is hard-coded:\r\nhttps://github.com/materialsproject/pymatgen/bl... | 2024-03-09T03:21:57 | 2024-03-12T01:53:44 | 2024-03-11T07:06:21Z | CONTRIBUTOR | {
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The third (hopefully the last) episode of cleaning up VASP test files: relocate dedicated VASP directories to `vasp/fixtures`, following #3653 and #3674.
## Tasks
- [x] Relocate dedicated VASP directories
- [x] Compress some hidden VASP outputs
- [x] Group s... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3682 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3682/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3682/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3682/events | https://github.com/materialsproject/pymatgen/issues/3682 | 2,177,206,575 | I_kwDOACgets6BxYkv | 3,682 | Create monolayer MoS2 from the bulk. | {
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```python
from pymatgen.core.structure import Structure
from pymatgen.core.surface import SlabGenerator
from pymatgen.io.vasp import Poscar
# Load the MoS2 structure (assuming you have the CIF file)
MoS2 = Structure.from_file("MoS2_mp-1434.cif")
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} | I am not sure if the current implementation of the [`CoherentInterfaceBuilder`](https://github.com/materialsproject/pymatgen/blob/daa0bb01477321828aa324c9ce9d07383db778e1/pymatgen/analysis/interfaces/coherent_interfaces.py#L23) class takes into account the deduplication problem of equivalent structures.
See [here](h... | {
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"i believe missing `icet` was deliberate as @esoteric-ephemera [added it only to `requirements-optional.txt`](https://github.com/materialsproject/pymatgen/pull/3593/files#diff-d52eaab4a615f02e5a1b6e6dd9e17be0c5f0519bcdb433cd28c45705b569da45R14) which is not used in CI.\r\n\r\nthough i could see how that is confusin... | 2024-03-10T04:32:28 | 2024-12-01T06:25:47 | 2024-08-06T14:57:49Z | CONTRIBUTOR | {
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- [ ] `graphviz`
- [ ] `critic2`: https://aoterodelaroza.github.io/critic2/installation/
- [ ] `zeo`
### Added
- [x] `Open Babel`: added in #3729
- [x] `enum_lib`: Added for Ubuntu only in #3729
- [x] `boltztrap2`: Fixed
- [x] `x_trans`: A... | {
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"`chgnet` cythonized graph converter doesn't compile on 3.12:\r\n\r\n```py\r\nchgnet/graph/cygraph.c:1208:10: fatal error: fast_converter_libraries/create_graph.c: No such file or directory\r\n 1208 | #include \"fast_converter_libraries/create_graph.c\"\r\n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\... | 2024-03-11T14:27:08 | 2024-05-01T00:27:53 | 2024-05-01T00:27:52Z | MEMBER | {
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} | ### Feature Requested
Not only fatband plots with lobster and VASP should be covered.
### Proposed Solution
Use POSCAR.lobster instead of vasprun.xml, POSCAR.lobster will be used. Efermi can be read from vasprun.xml
### Relevant Information
_No response_ | {
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} | ### Python version
Python 3.10.6
### Pymatgen version
Version: 2024.2.8
### Operating system version
Ubuntu (Windows WSL2)
### Current behavior
`Ion.oxi_state_guesses` fails for `Br`, and for `Br2` unless `all_oxi_state_guesses` is set. This is a problem because 1) `Composition.oxi_state_guesses` w... | {
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"@janosh I had to fight with mypy for the Structure. I did not see why it complained. Maybe, you see something... I added ignores for now.",
"Looks like the same download timeout error as #3675 from `uv` for large dependencies, see discussion [here](https://github.com/astral-sh/uv/issues/1921), maybe we should in... | 2024-03-13T16:15:21 | 2024-03-14T17:08:51 | 2024-03-14T17:08:51Z | MEMBER | {
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Todo:
- [x] More tests | {
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Current implementation of `Bandoverlaps` parser adds keys with '.' in `band_overlaps_dict` attribute leading to failure of pydantic checks in atomate2 lobster workflow https://github.com/materialsproject/atomate2/issues/769
# Changes
1. Rewrite output format of `band_overlaps_dict` attribute of `Bandove... | {
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"Notice multiple funcs with unused `include_index` and `include_image` args across `core.structure`, for example: https://github.com/materialsproject/pymatgen/blob/884946d0d3c022ae197e4188364db2b7ad9cde9a/pymatgen/core/structure.py#L1825-L1911\r\n\r\nThese args were marked \"Deprecated\" **five years ago** in #1610... | 2024-03-17T02:04:10 | 2024-08-14T05:06:55 | 2024-04-10T05:31:47Z | CONTRIBUTOR | {
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Major clean up of `core.surface`, I decide to split this task into two for readability: this PR to revise comments/docstrings with some relocation of code. Another follow up PR for functional changes/fixes.
### Non-breaking changes
- Major clean up of comments/docstrings (made more concise and add m... | {
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"help with getting consistent Google-style doc strings everywhere would be much appreciated!",
"Fixed in #3694"
] | 2024-03-18T08:06:46 | 2024-03-22T11:07:33 | 2024-03-22T11:07:33Z | CONTRIBUTOR | {
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Also it seems @janosh is working on reformat them to to Google style for example #3320.
Do we have any plan to use Google sty... | {
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"Thanks for pinging me here 😄 .\r\n\r\nBut for me personally I think initialize a `Species` or `Composition` with an atomic number feels a bit weird/unexpected...Because I think people are expecting chemical Species/Composition to look \"chemical\" like `Composition(\"LiFePO4\")`\r\n\r\nAlso init a Species/Composi... | 2024-03-18T09:39:00 | 2024-03-22T13:22:00 | 2024-03-22T13:21:59Z | MEMBER | {
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"Opened another Pandora's box of `mypy` errors. ",
"I guess it's not a good idea to reformat docstring and add type annotations (for modules I'm not quite familiar with especially) at the same time. I should focus on reformatting docstring for this PR and stop adding type annotations.\r\n\r\nI tried my best to fi... | 2024-03-18T09:44:06 | 2024-03-23T01:55:46 | 2024-03-22T10:40:37Z | CONTRIBUTOR | {
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There should be no functional changes. Any change made to the code is to resolve `mypy` type errors.
Tasks:
- Corrected some already Google styled docstrings. Replaced keywords `Arg/Return/Raise` with its plural form `Args/Returns/Raises` even when ... | {
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"@aakhiltayal to be clear, this only occurs when there's a single absorbing atom in the unit cell, correct?",
"@matthewcarbone No it occurs even for two atom system as I shown for FeN. When I pull all the structure for FeN, for some of structures all the potentials are written. I think it is because they have com... | 2024-03-18T14:13:39 | 2024-03-18T17:34:00 | NONE | {
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@matthewcarbone
While using the Potentials card to write potential it was found that it did not write all the potentials in the feff.inp file which makes the feff.inp file not usable for the f... | {
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"The CI jobs seem to be failed due to network timeouts. \r\n- https://github.com/materialsproject/pymatgen/actions/runs/8336717393/job/22814307503?pr=3696\r\n- https://github.com/materialsproject/pymatgen/actions/runs/8336717393/job/22814308207?pr=3696"
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} | ## Summary
Removes stdout printing when trying to import phonopy for tidiness. These printing appeared in some downstream packages. For example
```shell
pip install mp_api
python -c "from mp_api.client import MPRester"
```
resulted in
```
No module named 'phonopy'
No module named 'phonopy'
```
## Check... | {
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"`pymatgen` isn't quite the right place for this feature request. [`crystaltoolkit`](https://github.com/materialsproject/crystaltoolkit) contains part of the relevant code. i added the behavior that MP ID will be included in the filename if it's found in `Structure.properties` in https://github.com/materialsproject... | 2024-03-20T15:19:31 | 2024-03-22T12:29:01 | CONTRIBUTOR | {
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} | ### Feature Requested
It would be great if files exported from the web site visualizer export button would indicate what MP ID the structure corresponds to. Right now they seem to only indicate the chemical formula.
### Proposed Solution
Add the MP ID as part of the filename (e.g. `Al2O3_mp_1143.poscar`) and/or add ... | {
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} | ### Python version
python 3.9.12
### Pymatgen version
2024.3.1
### Operating system version
Rocky Linux release 8.9
### Current behavior
I know this is related to the VASP error, but thought worth reporting the issue.
In some static calculations using VASP version 6.3.2, when the energy difference (dE) is ext... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent update introduces an `invert_axes` parameter to various plotter methods within pymatgen's phonon module, enhancing flexibility in data visualization by allowing axis inversion. Additio... | 2024-03-22T10:44:35 | 2024-03-26T11:30:36 | 2024-03-26T11:08:56Z | CONTRIBUTOR | {
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Major changes:
- feature 1: Add `invert_axes` to `PhononDOSPlotter` (similar to `DOSPlotter`)
- feature 2: Compare to more than one other `PhononBSPlotter`
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
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} | ### Python version
3.12.1
### Pymatgen version
2024.3.1
### Operating system version
_No response_
### Current behavior
Hello Developers, When defying a Structure where the periodicSites have an specific label , the cif file that is print by CifWriter doesnt use the labels when one is None,
from pymatgen.cor... | {
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"Great work 😄 ! I can take care of the rest if you don't mind.\r\n\r\nMeanwhile I noticed at least two modules are using naming conventions as `with_something` instead of `from_something`, do we have any plan to unify their namings as well?\r\n\r\n<img width=\"358\" alt=\"image\" src=\"https://github.com/materials... | 2024-03-22T18:26:23 | 2024-03-23T06:10:44 | 2024-03-22T18:47:05Z | MEMBER | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe update brings a mix of enhancements across different components: the pre-commit configuration, pymatgen library updates, and test suite improvements. It introduces a new argument for the `ruf... | 2024-03-23T09:19:15 | 2024-03-28T14:06:13 | 2024-03-26T06:44:56Z | MEMBER | {
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would be great to get other's opinions on this @rkingsbury @JaGeo @Andrew-S-Rosen
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} | ## Summary
XSF allows you to append a vector after the positions (usually forces). This makes it easier to visualize phonons with VESTA.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
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"[i added `Self` return type to `__new__` and `__enter__` methods](https://github.com/materialsproject/pymatgen/pull/3705/commits/2adde295d16126b84e4f346ff3294420003c9069). created 66 `mypy` errors unfortunately so feel free to revert if we don't want to deal with this now",
"> [i added `Self` return type to `__n... | 2024-03-24T02:50:41 | 2024-04-13T18:05:56 | 2024-03-29T09:38:53Z | CONTRIBUTOR | {
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} | ## Summary
Use `Self` for return type in Method Signatures, see reference [here](https://typing.readthedocs.io/en/latest/spec/generics.html#self).
### Major changes:
- Use `Self` type in Method Signatures
- Add related type annotations
- Some `sourcery` fixes
### Minor changes:
- Docstring tweaks
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https://api.github.com/repos/materialsproject/pymatgen/issues/3706 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3706/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3706/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3706/events | https://github.com/materialsproject/pymatgen/pull/3706 | 2,205,050,494 | PR_kwDOACgets5qns8r | 3,706 | Return `self` from `Structure` methods `replace`, `substitute`, `remove_species`, `remove_sites` | {
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"Sorry @janosh I still remember there is a comment from you about some classes that don't follow PascalCase naming (and you provided the `re` pattern). \r\n\r\nUPDATE: I found it [here](https://github.com/materialsproject/pymatgen/pull/3702#issuecomment-2016363666)",
"Fixed in #3725."
] | 2024-03-25T11:05:20 | 2024-03-29T11:25:10 | 2024-03-29T11:25:10Z | CONTRIBUTOR | {
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} | - Some methods should not be `staticmethods` (there should certainly be other wrong types I didn't notice).
- Some methods in `analysis.graphs` should be renamed from `with_*` to `from_*` for consistency.
For example (not exhaustive):
https://github.com/materialsproject/pymatgen/blob/05d3f9f5643c9585e15b297a5869... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates in the pymatgen library focus on transitioning static methods to class methods, incorporating type hinting with `Self` for return types. These changes aim to improve class inhe... | 2024-03-26T01:59:30 | 2024-03-26T07:37:56 | 2024-03-26T06:15:45Z | CONTRIBUTOR | {
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Major changes:
- Converted some `staticmethod` to `classmethod`, partially address #3708
Rationale:
These methods create an instance of the Class itself, and should be a `classmethod`, not `staticmethod`.
<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe changes across various files in the pymatgen library mainly focus on import statement adjustments, including the reordering and removal of `TYPE_CHECKING` blocks, as well as minor formatting ... | 2024-03-26T08:10:38 | 2024-03-26T13:43:54 | 2024-03-26T13:03:51Z | CONTRIBUTOR | {
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## Summary by CodeRabbit
- **Refactor**
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"Thanks for raising the issue.\r\n\r\nCould you be a bit more specific on the output that you get? For example, if you are using the cation-anion modus in the analysis, I would expect the anion neighbor lists to be empty.",
"Hello. I am using all the default settings of the ChemEnv module. This error also occurs ... | 2024-03-26T08:44:31 | 2024-03-27T18:41:03 | 2024-03-27T18:31:06Z | NONE | {
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} | ### Python version
Python 3.11.5
### Pymatgen version
2024.3.1
### Operating system version
(wsl) Ubuntu 22.04
### Current behavior
I have been using pymatgen.analysis.chemenv.coordination_environments to analyze atomic environments. In some cases, the code is unable to identify the neighboring atoms or environm... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates focus on enhancing code readability and efficiency in a scientific computing library. Changes include variable renaming for clarity, matrix manipulation optimization, and test ... | 2024-03-26T11:22:19 | 2024-03-26T11:48:25 | 2024-03-26T11:48:24Z | MEMBER | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **Refactor**
- Enhanced variable naming for better clarity in code and tests.
- Improved efficiency in matrix manipulation for chemical analysis tools.
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https://api.github.com/repos/materialsproject/pymatgen/issues/3714 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3714/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3714/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3714/events | https://github.com/materialsproject/pymatgen/pull/3714 | 2,208,770,883 | PR_kwDOACgets5q0dUG | 3,714 | Correct units of Element.atomic_orbitals | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates to the pymatgen library introduce a significant enhancement in representing atomic orbital energies. A new `atomic_orbitals_eV` property now provides these energies in electron... | 2024-03-26T16:43:25 | 2024-04-12T05:48:22 | 2024-03-26T18:43:21Z | CONTRIBUTOR | {
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} | The docstr for `pymatgen.core.Element.atomic_orbitals` indicates that the units of the LDA energies is eV. However the data in `periodic_table.json` was never converted to eV from Hartree, so `element.atomic_orbitals` prints energies in Hartree. (This is also true for pymatgen versions before the periodic table data wa... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3715 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3715/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3715/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3715/events | https://github.com/materialsproject/pymatgen/issues/3715 | 2,209,491,205 | I_kwDOACgets6DsikF | 3,715 | Default settings of `Structure.relax()` fails to synchronize tensor locations (CPU/GPU) on GPU-enabled environments | {
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"ADD: The `matgl` package installed is of version `1.0.0`."
] | 2024-03-26T23:00:06 | 2024-03-26T23:02:10 | CONTRIBUTOR | {
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} | ### Python version
Python 3.9.18
### Pymatgen version
2023.12.18
### Operating system version
Ubuntu 22.04.4 LTS
### Current behavior
Running the `relax()` method of `pymatgen.core.Structure` object with default settings on a GPU-enabled environment raises `RuntimeError`, saying the tensors involved in computati... | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
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- **Refactor**
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- Updated file paths and refactored variable names for better readability.
- Modified test setup procedures and ... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates focus on enhancing code maintainability and preparing for future modifications. A significant change is the deprecation of `QuasiharmonicDebyeApprox` in favor of a correctly ca... | 2024-03-27T18:19:49 | 2024-03-27T18:59:23 | 2024-03-27T18:59:22Z | MEMBER | {
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also rename `Quasi(h->H)armonicDebyeApprox` and deprecate old name
<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **Refactor**
- Deprecated `Quas... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3719 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3719/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3719/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3719/events | https://github.com/materialsproject/pymatgen/issues/3719 | 2,212,017,157 | I_kwDOACgets6D2LQF | 3,719 | Unexpected Tokenizing error when using `parse_lammps_dumps` | {
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} | ### Python version
Python 3.9.17
### Pymatgen version
Pymatgen 2024.3.1
### Operating system version
Linux HPC
### Current behavior
When using `pymatgen.io.lammps.outputs.parse_lammps_dumps` function to read a dump output, it incorrectly puts out an error on some dump files:
`ParserError: Error tokenizing da... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3720 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3720/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3720/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3720/events | https://github.com/materialsproject/pymatgen/issues/3720 | 2,213,270,699 | I_kwDOACgets6D69Sr | 3,720 | The inconsistent results when finding the transformatoin matrix between two space groups using StructureMatcher and Bilbao Crystallographic Server IDENTIFY GROUP. | {
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"I'm quite confused about what you're trying to achieve here. \r\n\r\nYour original structure certainly is not a conventional cell and its supercell as you mentioned in #3717:\r\n```\r\nwerner@X10DAi:~$ cat POSCAR_ms\r\nSi2-primitive cell from MS software\r\n1.0\r\n3.8670001030 0.0000000000 0.000000... | 2024-03-28T13:38:21 | 2024-04-03T13:37:45 | 2024-04-03T13:34:05Z | CONTRIBUTOR | {
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} | Based on the POSCARs [here](https://mp.weixin.qq.com/s?__biz=MzI2OTQ4OTExOA==&mid=2247485044&idx=2&sn=80178d0bda6de43e3a5e4a47a72aa158&chksm=eadec0c5dda949d31853dafa37ae593b96f872990bf7b7ada0cbb89bf5e64bbc66903d8794e4&scene=21#wechat_redirect), I try to find the transformation matrix between the following two POSCARs:
... | {
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} | ### Python version
3.10.8
### Pymatgen version
2024.2.8
### Operating system version
_No response_
### Current behavior
The Ge atoms index 0 and 3 are generated almost on top of each other, just at opposite ends of the unit cell. Input is:
`Structure.from_spacegroup(
154,
Lattice.from_parameters(4.985... | {
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"Hi Hongsheng,\r\n\r\nAs described in the [VASP wiki](https://www.vasp.at/wiki/index.php/KPOINTS_OPT) you mentioned:\r\n> KPOINTS_OPT is an optional input file to perform an additional one-shot calculation after self-consistency is reached. The format is the same as for the [KPOINTS](https://www.vasp.at/wiki/index.... | 2024-03-29T01:06:26 | 2024-03-29T11:47:33 | CONTRIBUTOR | {
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} | I'm not sure if Pymatgen currently supports [KPOINTS_OPT](https://www.vasp.at/wiki/index.php/KPOINTS_OPT) based one-shot calculation input file generation and the corresponding post-processing. Any tips and comments will be helpful.
Regards,
Zhao | {
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- Remove legacy `analysis.interface` (deprecated 3 years ago, see [discussion](https://github.com/materialsproject/pymatgen/pull/3702#issuecomment-2016370354))
- Rename several classes to PascalCase (see [discussion](https://github.com/materialsproject/pymatgen/pull/3702#issuecomment-2016363666))
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```py
@unique
class ElementType(Enum):
"""Enum for element types."""
noble_gas = "noble_gas" # He, Ne, Ar, Kr, Xe, Rn
transition_metal = "transition_metal" # Sc-Zn, Y-Cd, La-Hg, Ac-Cn
post_transition_metal = "post_transition_metal" # Al, Ga, In, Tl, Sn, Pb, Bi, Po
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## Checklist
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- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fi... | {
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Major changes:
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"I fixed it.Thank you very much!",
"> I fixed it.Thank you very much!\r\n\r\nHi! Is it possible for you to tell me how to fix it? I am having the same issue as you!"
] | 2024-04-02T01:54:11 | 2024-04-17T20:52:36 | NONE | {
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} | ### Python version
python3.9
### Pymatgen version
2023.12.18
### Operating system version
ubuntu 22.04 LTS
### Current behavior
when I install atomate2 and configure pymatgen, and then type pmg config --add PMG_VASP_PSP_DIR /abs/path/to/psp PMG_MAPI_KEY my_api_key , there are some errors.
pmg co... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent updates across various modules in pymatgen focus on enhancing clarity and consistency. Key changes include renaming variables for better understanding, correcting typos in documentatio... | 2024-04-02T07:50:37 | 2024-04-02T08:03:20 | 2024-04-02T08:00:31Z | MEMBER | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **Refactor**
- Improved variable naming and clarity across multiple modules for better readability and consistency.
- **Documentation**
- Corr... | {
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"You need to use the 3-integer specification of the rotation axis. Not 4. In hexagonal structures, one of the indices (the third) is redundant. ",
"> You need to use the 3-integer specification of the rotation axis. Not 4. In hexagonal structures, one of the indices (the third) is redundant.\r\n**when I change co... | 2024-04-02T12:43:00 | 2024-04-02T14:21:42 | 2024-04-02T14:15:28Z | NONE | {
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} | ### Python version
Python3.10
### Pymatgen version
2024.3.1
### Operating system version
ubuntu22.04-py310-torch2.1.2-tf2.14.0-1.13.1
### Current behavior
from pymatgen.core import Structure, Element
from pymatgen.analysis.gb.grain import GrainBoundary, GrainBoundaryGenerator
angle = GrainBoundaryGenerator... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n\n## Walkthrough\n\nThe update introduces the `formal_chempots` attribute to the `ChemicalPotentialDiagram` class, enhancing its ability to manage formal chemical potentials. This addition enriches the class's fun... | 2024-04-03T08:33:37 | 2024-04-05T07:41:35 | 2024-04-05T07:41:35Z | CONTRIBUTOR | {
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When a ChemicalPotentialDiagram is generated with more than 2 elements and then shown as a 2D plot via an elements argument with two entries, the formal_chempots=False setting of the initial ChemicalPotentialDiagram is not passed on, resulting in formal chemical potentials in all cases.
Major changes:
... | {
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"The complete bug reproduction code snippet is shown below:\r\n\r\n```python\r\nIn [12]: from pymatgen.symmetry.groups import SpaceGroup, PointGroup\r\n ...: \r\n ...: # Create an instance of the SpaceGroup for 'P212121'\r\n ...: sg = SpaceGroup('P212121')\r\n ...: \r\n ...: # Fetch the point group s... | 2024-04-03T14:46:53 | 2024-08-08T04:49:30 | NONE | {
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Python 3.9.18
### Pymatgen version
2024.2.8
### Operating system version
Fedora 38
### Current behavior
Loading the SpaceGroup `P212121` works fine, but the `point_group` symbol it reports (`D2^4`) is not recognised. I believe it should be `222`. The issue appears to be here: https://github.co... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent update across `pymatgen` LAMMPS-related modules brings improvements in file handling, data manipulation, and code robustness. Changes include adopting Unicode encoding, refining dictio... | 2024-04-05T02:34:50 | 2024-05-15T00:59:47 | 2024-04-05T06:10:26Z | CONTRIBUTOR | {
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- Avoid using `exec`, especially from potentially untrusted source (external filename in this case) to avoid potential security issue (alerted by the `xz` backdoor)
- Minor `sourcery` fixes
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- Add type annotations for `io.vasp.inputs/optics`
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### Originally
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThis update brings a nuanced but pivotal modification to the pymatgen library, specifically within the VASP input configuration. The essence of the change revolves around enhancing the precision ... | 2024-04-09T01:07:17 | 2024-04-12T05:49:49 | 2024-04-09T03:41:05Z | CONTRIBUTOR | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **Refactor**
- Updated the data type for the `ENCUT` parameter to enhance precision in calculations.
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe recent updates across the pymatgen library aim to enhance code efficiency and readability by simplifying conditional checks and leveraging truthiness. These changes streamline logic and improve... | 2024-04-09T03:17:17 | 2024-04-09T10:00:22 | 2024-04-09T10:00:22Z | CONTRIBUTOR | {
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Replace unnecessary usage of `len` for iterable existence check:
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
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"there was this PR https://github.com/materialsproject/pymatgen/pull/3624 which you know the downstream implications of better than I.\r\n\r\nthere also [appears to have been an accidental change](https://github.com/materialsproject/pymatgen/pull/3705/files#r1558895539) in https://github.com/materialsproject/pymatg... | 2024-04-10T05:48:03 | 2024-04-16T04:58:16 | 2024-04-16T04:55:46Z | MEMBER | {
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} | ### Feature Requested
I would like to ask for a new pymatgen version after many new implementations in the last month. We currently face a bug in the atomate2 LOBSTER workflow that can only be fixed with a new version. (Cc @naik-aakash )
### Proposed Solution
Release of a new version.
I am wondering if the many ... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe recent changes in the `pymatgen` library bring enhancements to file handling and data consistency across various modules. These updates aim to streamline processes and improve clarity in code s... | 2024-04-11T05:57:12 | 2024-05-15T01:07:27 | 2024-04-11T08:28:26Z | CONTRIBUTOR | {
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Fixed a flawed change in `io.cp2k.input.DataFile.from_file` made by me in #3705, discussed in https://github.com/materialsproject/pymatgen/pull/3705#discussion_r1558895539. Also added comment to prevent this from happening again.
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- Collect test files `csv/cif` into their own folders
- Separate `json` files by modules
- Relocate test files by modules
## Tasks
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- [x] Separate `json` files by modules
- [x] Many of the files under `molecules` are specific to `io.qchem`, but there is terribly ... | {
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} | ### Python version
Python 3.9.12
### Pymatgen version
2023.5.10
### Operating system version
Ubuntu
### Current behavior
I have a very limited understanding of the materials side of our project. We have some code to generate slabs using pymatgen, however I noticed that on two different machines with identical so... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- This is an auto-generated comment: skip review by coderabbit.ai -->\n\n> [!IMPORTANT]\n> ## Auto Review Skipped\n> \n> Draft detected.\n> \n> Please check the settings in the CodeRabbit UI or the `.coderabbit.yaml` file in this repository... | 2024-04-12T02:35:20 | 2024-06-04T17:34:30 | 2024-06-03T20:42:18Z | CONTRIBUTOR | {
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A follow-up PR for #3691.
- Clarify misleading arg name `shift` for **private** method `SlabGenerator.get_slab`
- Fix typing of `slab` in function `center_slab` (should be `Structure` instead of `Slab`)
### Rationale
- This method should be a private method (as per the docstring).
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe recent updates in pymatgen involve refining function signatures, variable names, return types, and plot settings for improved usability and clarity. These changes enhance the overall user exper... | 2024-04-12T04:40:21 | 2024-04-12T05:41:30 | 2024-04-12T05:41:29Z | MEMBER | {
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also fixes the return types in many doc strings and adds `Returns:` section to several doc strings that were missing them
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the rename of `Cohpl.has_antib(''->a)nd_states_below_efermi` confuses it's purpose and broke | {
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"Thanks for fixing! Just tracked them down and found these were added in 2adde29 (guess we were both too distracted because there were just too many `mypy` errors), and wondering why unit tests didn't capture such errors (we don't explicitly install `typing_extensions` in our CI too)?",
"Mistakes happen. It's not... | 2024-04-12T17:19:11 | 2024-06-03T12:23:53 | 2024-04-12T19:36:05Z | MEMBER | {
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} | Hi! Thanks for your work on `pymatgen`! 😃
Just to flag, this update seems to be causing some failures on our GitHub Actions tests (for [`ShakeNBreak`](https://shakenbreak.readthedocs.io/en/latest/) and [`doped`](https://doped.readthedocs.io/en/latest/)) with the latest `pymatgen` version. I'm not sure if it just nee... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe recent updates to the `pymatgen` codebase involve enhancing type handling and code readability. Changes include updating the `ruff-pre-commit` repository version, consolidating imports in core ... | 2024-04-12T17:36:57 | 2024-06-01T13:36:42 | 2024-04-12T19:36:04Z | MEMBER | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **Refactor**
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- Enhanced type hinting and conditional type checking across various modules.
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"Thanks for the report. I had used it recently and noticed a few endpoints broken, but wasn’t sure if it was them being out of spec or an issue with the parsing logic — seems likely the latter.\r\n\r\nWhen this client was first added there was no good alternative, but now there is a very nice client from @ml-evs ov... | 2024-04-12T18:14:06 | 2024-04-13T12:48:37 | 2024-04-13T12:48:37Z | MEMBER | {
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3.11
### Pymatgen version
2024.3.1
### Operating system version
Linux
### Current behavior
OptimadeRester seems to be broken. Will not get any results via:
```py
from pymatgen.ext.optimade import OptimadeRester
with OptimadeRester(aliases_or_resource_urls=["mcloud.mc3d"]) a... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe `OptimadeRester` class has been enhanced with additional database aliases, expanding its connectivity to new endpoints like \"alexandria\", \"odbx\", and \"odbx.gnome\". This update also introd... | 2024-04-12T20:18:28 | 2024-04-13T13:31:47 | 2024-04-13T05:37:38Z | CONTRIBUTOR | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **New Features**
- Updated the `OptimadeRester` with new database aliases for enhanced connectivity options, including "alexandria", "odbx", "odbx.gnome"... | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
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- **Chores**
- Updated the linting tool from "TID" to "flake8-tidy-imports" for improved code quality checks.
- **Refactor**
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URLs with paths need to have trailing slashes otherwise `urljoin` mangles them. OPTIMADE base URLs do not need to have trailing slashes, hence an issue arises for any provider that serves multiple databases from different URL paths.
This PR dynamically fixes these URLs when they occur (so that the a... | {
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Started by @ml-evs in #3646:
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- Format tweaks (`sourcery`), I should not have done this (make it hard to view difference)
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As discussed in https://github.com/materialsproject/pymatgen/commit/6a06f3cb0a8b551ed782d86ed5963cd8aaed6674#r140944147.
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This PR adds a separate test suite run for the case that only mandatory dependencies have been installed (directly via `pip install -e .[dev]`), attempting to mimic what a user will actually have when they just `pip install pymatgen`. This will then hopefully catch errors where either optional ... | {
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"Hopefully the fix produces satisfactory results for you @HERTZCAI (feel free to ping me if you have more suggestions). \r\n\r\nAlso to improve the overlapping markers, you could now pass a `marker_size` arg for example:\r\n\r\n```python\r\nplotter = BSPlotterProjected(bs=bs_data)\r\nplotter.get_projected_plots_dot... | 2024-04-16T11:47:51 | 2024-05-04T04:29:01 | 2024-05-02T14:28:53Z | NONE | {
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} | ### Python version
3.11.7
### Pymatgen version
2024.4.13
### Operating system version
Ubuntu 22.04.3 LTS
### Current behavior
I try to get band structures with specific elements and orbitals with `get_projected_plots_dots()`. While a figure with 3 subfigures is expected, the program returns a figure with only o... | {
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"One of the reasons labels should be unique: they are used to indicate bonding (and angles, torsions, etc). If they are not unique, this information is useless. (And I am working on a PR to add that capability to pymatgen.)",
"I can confirm that this is likely a bug (in terms of having agreement with the CIF spec... | 2024-04-16T17:58:13 | 2024-04-25T18:36:00 | 2024-04-25T18:36:00Z | NONE | {
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Python 3.11.6
### Pymatgen version
2023.10.4
### Operating system version
macOS 14.4.1
### Current behavior
Read a structure with symmetry, and write it to a CIF file. My example is:
```
$ cat MOF-71.cif
data_MOF-71
_audit_creation_method 'generated by CrystalMaker 8.6.5'
_pub... | {
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"Hi @fxcoudert ,\r\n\r\nhave you tested some of other algorithms in the same module as well? I fear CrystalNN might be optimized mostly for typical inorganic crystals. \r\n\r\nJust a reminder: the alogrithm uses Voronoi partitioning, solid angles/distances, electronegativities and so on. I would assume the H atoms ... | 2024-04-16T20:06:39 | 2024-04-18T06:37:52 | 2024-04-18T06:36:41Z | NONE | {
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} | ### Python version
Python 3.11.6
### Pymatgen version
2023.10.4
### Operating system version
macOS 14.4.1
### Current behavior
1. Take this CIF file: https://gist.github.com/fxcoudert/f13193d91eacc7e3d67cf355f805ee36
2. Run this:
```
structure = Structure.from_file("/Users/fx/Documents/structures/MOFs/MOF... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nA new method named `get_string` has been introduced in the `pymatgen/io/vasp/inputs.py` as an alias to the existing `get_str` method. This update enhances usability without impacting the existing f... | 2024-04-16T20:29:59 | 2024-05-01T18:44:11 | 2024-04-17T17:09:21Z | CONTRIBUTOR | {
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} | ## Summary
Minor changes:
- add `get_string` alias for `get_str` function in Poscar class for convenience/compatibility purposes with earlier implementation(s)
Major changes:
- none
## Checklist
```bash
(.venv) ➜ pymatgen git:(chore/add-poscar-get-string-alias) pre-commit run --all-files ... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe update to `pymatgen/analysis/local_env.py` includes a note on default weights optimized for inorganic crystal structures and introduces an initialization example for Metal-Organic Frameworks (M... | 2024-04-17T10:58:19 | 2024-05-01T18:43:06 | 2024-04-18T06:36:40Z | MEMBER | {
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} | Closes #3762 with additional information provided in the documentation.
If you want to add something (e.g., a citation), @Andrew-S-Rosen , please feel free.
<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **Documentation**
- Enhanced documentation for `... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- This is an auto-generated comment: skip review by coderabbit.ai -->\n\n> [!IMPORTANT]\n> ## Auto Review Skipped\n> \n> Review was skipped due to path filters\n> \n> <details>\n> <summary>Files ignored due to path filters (1)</summary>\n> ... | 2024-04-18T00:05:31 | 2024-04-23T22:06:33 | 2024-04-23T22:06:33Z | CONTRIBUTOR | {
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<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit
- **New Features**
- Enhanced the convergence detection logic in relaxation runs to include scenarios where `EDIFFG=0`.
- **Tests**
- Added a new test to ensure accurate ha... | {
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"Thanks for reporting it. I will look into it. ",
"Hey @davidwaroquiers , could you also have a look? ",
"I think i solved it:\r\nChemEnv is typically refining the structure with the help of the symmetry analysis module. For some reason (I did not check the details), this fails for your structure or produces a ... | 2024-04-18T06:46:14 | 2024-04-19T06:15:11 | 2024-04-19T06:15:11Z | NONE | {
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Python 3.11.5
### Pymatgen version
2024.3.1
### Operating system version
(wsl) Ubuntu 22.04
### Current behavior
Hello. I would like to ask a question and raise an issue about pymatgen.analysis.chemenv.
Question:
Why does chemenv expand the sites of a some cif files but kee... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- This is an auto-generated comment: rate limited by coderabbit.ai -->\n\n> [!WARNING]\n> ## Rate Limit Exceeded\n> \n> @janosh has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait **35 minute... | 2024-04-18T08:38:47 | 2024-04-26T06:28:16 | 2024-04-25T18:35:59Z | CONTRIBUTOR | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe recent changes across the `pymatgen/io/vasp/outputs.py` and `tests/io/vasp/test_outputs.py` files focus on improving code readability and maintainability. These modifications include importing ... | 2024-04-18T10:50:11 | 2025-04-14T04:30:53 | NONE | {
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This is my first contribution to `pymatgen`. I am relatively new to opensource and would appreciate your feedback and guidance in improving the added features and this PR. In further commits, I will add `read_from_hdf5` functionality to `Chgcar` and write all the tests.
## Summary
Major changes... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe modification updates the source of `potcar_symbols` in the `incar_updates` method, transitioning from using `self.poscar.site_symbols` to `self.potcar_symbols`. This change centralizes the de... | 2024-04-19T10:30:11 | 2024-04-23T02:18:33 | 2024-04-23T02:17:29Z | CONTRIBUTOR | {
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The POTCARs used to generate the input set are incorrect and do not match `PBE_54` POTCARs. Currently, the `potcar_symbols` variable stores element symbols, which leads to the input set trying to find potcars matching element symbols only.
# Fix
Correctly refer to potcars that should be used based on s... | {
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"This is because `if \"magmom\" in site.properties` is true for this structure at https://github.com/materialsproject/pymatgen/blame/2d008e0dd5c430692e8dcac2505340a6bdff1642/pymatgen/io/cif.py#L1516C21-L1516C51\r\n\r\nBut I am not writing magnetic moments, and I do not know why that should override labels.",
"@fx... | 2024-04-19T12:26:39 | 2024-04-22T12:54:44 | NONE | {
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} | ### Python version
Python 3.11.6
### Pymatgen version
2024.4.13
### Operating system version
macOS 14.4.1
### Current behavior
This is related to https://github.com/materialsproject/pymatgen/issues/3761 but different. I have upgraded my pymatgen from 2023.10.4 and 2024.4.13 and I have workflows tha... | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThe recent update enhances the documentation in the `pymatgen` library, particularly focusing on the `average_gruneisen` function in the phonon module. This improvement involves adding a specific... | 2024-04-19T12:26:42 | 2024-05-01T18:42:54 | 2024-04-19T12:41:08Z | MEMBER | {
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Major changes:
- `BeautifulSoup` is listed in `requirements.txt` but not in `setup.py`, possibly leading to an `ImportError` when installing `pymatgen` from pypi. Since it is only used in two places anyway, I moved it to `requirements-optional.txt` and changed the imports.
## Checklist
- [x] Goog... | {
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} | ## Collect some Python 3.12 related issues
Might be good to collect some Python 3.12 related issues.
### 1. For `UserDict`, `d.get(key)` and `d[key]` return different values, as `.get` method don't call `__getitem__`
As previously noticed in https://github.com/materialsproject/pymatgen/pull/3757#issuecomment-2... | {
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"@janosh While you are working on improving dcostrings, can you please skip this `io.vasp.outputs` part to avoid overlapping? I would help fixing some docstring issues while adding types. Thanks!",
"I'm now facing significant resistance from the \"default value as `None` behavior\" (most `mypy` errors are more or... | 2024-04-21T12:08:57 | 2024-06-01T01:12:52 | 2024-05-31T19:06:12Z | CONTRIBUTOR | {
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} | ## Summary
- Add type annotations for `io.vasp.outputs`, a follow-up PR of #3740.
- Use `PathLike` as type over `str` for all paths.
- Add missing docstrings and clean up docstrings.
- Lazily import `Vasprun/Xdatcar` in `Trajectory` to be consistent with other part of the class. | {
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\n\nThis update focuses on enhancing error handling, initializing variables before use, and refining logic in a Python project. Changes include adding or adjusting timeouts for HTTP requests, initial... | 2024-04-21T12:41:21 | 2024-04-23T13:43:21 | 2024-04-23T02:18:57Z | CONTRIBUTOR | {
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- `pyright` fixes, a follow up PR of #3757.
- Enable `pyright` in linting workflow and `pre-commit`. | {
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- Improve path logic
- Allow Chargemol to run in different directory (previously the code has implemented but is not working)
- Fix `os.path.isfile` bug. Change it into `os.path.exists`
## Todos
- add test
- Download chargemol and run real chargemol analysis. This should close #3474
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"<!-- This is an auto-generated comment: summarize by coderabbit.ai -->\n<!-- walkthrough_start -->\n\n## Walkthrough\nThe recent update in pymatgen's `io.res` module involves a significant change from using a set to a list for handling species in the `ResSFAC` class. This adjustment enhances the consistency and fu... | 2024-04-22T13:40:15 | 2024-04-22T18:12:38 | 2024-04-22T16:10:54Z | CONTRIBUTOR | {
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Closes #3677
## Summary
Major changes:
- fix 1: Fixes an issue where the species indices in the sites listing did not match the SFAC listing
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `myp... | {
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