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"Thanks a lot for reporting. The [unit test for `chgnet` is failing for the same reason](https://github.com/CederGroupHub/chgnet/actions/runs/10312892054/job/28565439869?pr=184), following our recent migration of build system to NumPy 2 #3894, as in NumPy 2 [the default int type has been changed from `int32` to `in... | 2024-08-09T19:47:46 | 2024-08-24T08:54:11 | 2024-08-24T08:54:11Z | MEMBER | {
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} | ### Python version
3.11
### Pymatgen version
2024.8.9
### Operating system version
Windows
### Current behavior
As of pyamtgen 2024.8.8, there is an incompatibility with `Lattice.get_points_in_sphere` on Windows when using numpy < 2. Everything seems to run fine on numpy 2.0.1 and/or non-Windows ma... | {
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"@janosh I request a quick merge and release on this one so that it doesn't adversely affect anyone doing aqueous work (e.g. Pourbaix diagrams) that involve `I[-1]`. Sorry I didn't catch this in the original PR!"
] | 2024-08-09T21:02:25 | 2024-10-10T01:54:19 | 2024-08-11T19:52:16Z | CONTRIBUTOR | {
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My recent PR #3942 contained two bugs that were revealed by testing in downstream code (see [pyEQL PR](https://github.com/KingsburyLab/pyEQL/pull/169#issuecomment-2278396689)). This PR fixes those and expands the unit tests to catch them.
```
>>> Ion.from_formula('CO2-').reduced_formula
'C2O4[-0.5]'
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"@njzjz Perhaps you could give me some advice or comment here because I'm not a cython expert? Thanks a ton in advance.\r\n\r\nLooks like quite some code is broken when running on Windows system with NumPy < 2, because with 862c454bfd2e0428b27fdafe9e0a7d81654005b9 integer is explicitly declared as `int64` independe... | 2024-08-10T08:20:33 | 2024-10-10T06:44:09 | 2024-08-24T08:54:10Z | CONTRIBUTOR | {
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- Explicitly use `int64` in cython code to avoid OS inconsistency ([default int type changed in Windows](https://numpy.org/doc/stable/numpy_2_0_migration_guide.html)) as follow up PR of #3894, to fix #3990
- [x] Run unit test on Windows with `NumPy < 2`
- [x] Revert NumPy<2 pin after tests pass
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"Hi thanks for reporting and diagnosing and sorry for the trouble caused. I could confirm the issue and would fix ASAP."
] | 2024-08-11T15:52:56 | 2024-09-06T22:41:27 | 2024-08-20T10:13:20Z | NONE | {
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} | ### Python version
Python 3.10.14
### Pymatgen version
Version: 2024.7.18
### Operating system version
Red Hat Enterprise Linux Ver 8.6
### Current behavior
When using the `Kpoints` class from `pymatgen.io.vasp.inputs` to read a Gamma-centered KPOINTS file and then write it back, the fourth line of the KPOINTS f... | {
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- Set kpoints in `Kpoints.from_str` method as integer in auto Gamma-centered and Monkhorst-Pack modes, to fix #3993
It turns out typing `Kpoint` as a sequence of `float` is giving us quite some headache and confusion: https://github.com/materialsproject/pymatgen/blob/b28c9371d684b8a605830cd13060bef9a... | {
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Should a bug be found in either pymatgen's CIFWriter or spglib, a key package depended upon by pymatgen, this updated comment string will make it easier to find affected CIF files. | {
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Separated from #3994 to avoid PR pollution
- Docstring and format tweaks for `io.vasp.inputs`
- Get rid of some `mypy` errors by putting property `getter` and `setter` together, https://github.com/python/mypy/issues/1465
- Fix `use-named-expression` with `sourcery`, and some other tweaks
- Remove a... | {
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"Here are my comments:\r\n1. Axiom 1: No. of lines is not a good metric of whether a module should be broken up. In even the most basic IDEs, there are tools to show the class structure, not to mention keyboard shortcuts to jump to any class/method name/line. I can't recall when the last time I had to use mouse scr... | 2024-08-12T22:29:52 | 2024-08-21T19:07:26 | MEMBER | {
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} | ## Summary
Re-opening changes initially introduced by @janosh in #3865 and later reverted by @shyuep (see [thread](https://github.com/materialsproject/pymatgen/issues/3988)).
**I will be taking responsibility for this PR.** This PR will require approval from both @janosh and @shyuep before merging.
Specificall... | {
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"I believe that's correctly formatted and intended. On the website it's not an INCAR file which you could use directly as a VASP input file, but a dict representation instead. To convert to a VASP INCAR file, you might need the `Incar.from_dict` method and `write_file` if you wish to write out.\r\n\r\nExample INCAR... | 2024-08-13T03:02:09 | 2024-08-13T05:10:55 | 2024-08-13T03:59:12Z | CONTRIBUTOR | {
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} | [Here](https://next-gen.materialsproject.org/materials/mp-149/tasks/mp-1947498) gives the error `MAGMOM` format:
> [MAGMOM](https://www.vasp.at/wiki/index.php/MAGMOM) [0.6, 0.6]
It should be written as: `MAGMOM = 0.6 0.6`.
Regards,
Zhao | {
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"Pls fix the ruff errors. Thanks.",
"Done. (I am not sure why local pre-commit did not identify problems)",
"Thanks!"
] | 2024-08-14T12:48:15 | 2024-09-10T13:16:20 | 2024-08-15T16:52:02Z | CONTRIBUTOR | {
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} | ## Summary
This is a small patch improving error message when writing VASP input without VASP installation.
The original message thrown by Potcar constructor is very generic and sounds like VASP _must_ be installed:
pymatgen.io.vasp.inputs.PMG_VASP_PSP_DIR_Error: No POTCAR for H with functional='PBE' found. ... | {
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} | ### Feature Requested
Right now, when `PWInput` instance is written into a file, the underlying structure's coordinate information is restricted to 6 decimal digits. This causes issues when we need a higher precision, especially for the lattice matrix values (the `CELL_PARAMETERS` card), for PWscf to run without raisi... | {
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"Great. Thanks."
] | 2024-08-14T19:00:43 | 2024-09-10T13:15:50 | 2024-08-15T16:44:57Z | CONTRIBUTOR | {
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} | ## Summary
Add optional keyword argument `format_options` of type `dict`, which specifies
- `indent`: # of spaces for indentation (defaults to 2)
- `kpoints_crystal_b_indent` # of spaces for indentation in `K_POINTS` card with `crystal_b` option (defaults to 1)
- `coord_decimals`: # of decimal digits for struct... | {
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"@janosh Perhaps you could review this `ruff` fix on master branch? Thanks!",
"Thanks!"
] | 2024-08-16T07:39:21 | 2024-08-16T10:52:18 | 2024-08-16T09:34:18Z | CONTRIBUTOR | {
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} | ### Summary
- Fix failing ruff `PT001` on master
- Bump `ruff` version in pre-commit
@shyuep please review this, thanks! | {
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"Because it doesn't matter whether it was set if ISMEAR=-5? And if we set SIGMA to 0, then 0.05 is the default value we use.",
"Thanks for the reply! \r\n\r\n> Because it doesn't matter whether it was set if ISMEAR=-5?\r\n\r\nSounds like it might be better to exclude SIGMA for tetrahedron method and include it la... | 2024-08-19T10:11:04 | 2024-08-22T02:28:32 | 2024-08-21T18:51:46Z | CONTRIBUTOR | {
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} | ### Summary
Why do we set SIGMA in INCAR for MPRelaxSet when ISMEAR is -5 ([SIGMA would be ignored in this case](https://www.vasp.at/wiki/index.php/ISMEAR))? Is it going to be corrected by #3322?
> Mind: [SIGMA](https://www.vasp.at/wiki/index.php/SIGMA) is ignored for the tetrahedron method.
https://github.com/m... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4005 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4005/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4005/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4005/events | https://github.com/materialsproject/pymatgen/issues/4005 | 2,474,746,028 | I_kwDOACgets6TgaCs | 4,005 | [CI] Unit test for `command_line.vampire` is failing | {
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Where `vc.output.critical_temp` is now `500` instead of expected `... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4006 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4006/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4006/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4006/events | https://github.com/materialsproject/pymatgen/issues/4006 | 2,474,762,639 | I_kwDOACgets6TgeGP | 4,006 | [CI] Unit test `test_all` for `io.qchem.outputs` is failing | {
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The following unit test for `io.qchem.outputs` is failing, **need help**: https://github.com/materialsproject/pymatgen/blob/3fee7d58fdc963b8fb8faf76ce92b68f7ccd0bf9/tests/io/qchem/test_outputs.py#L304-L316
It appears the dimension from `out_data` and `SINGLE_JOB_DICT` mismat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4007 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4007/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4007/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4007/events | https://github.com/materialsproject/pymatgen/issues/4007 | 2,474,765,970 | I_kwDOACgets6Tge6S | 4,007 | [CI] Multiple unit tests failing for `openbabel` related functions on Windows | {
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"See https://github.com/materialsproject/pymatgen/pull/3967#issuecomment-2264473437 for a similar problem.",
"Hi @hongyi-zhao thanks for the comment. However I don't think that's related to this issue, [currently matgl doesn't support torch>2.2.1](https://github.com/materialsproject/pymatgen/pull/3958#issuecommen... | 2024-08-20T05:44:32 | 2024-11-30T08:19:40 | CONTRIBUTOR | {
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~~[See the full CI log](https://github.com/materialsproject/pymatgen/actions/runs/10465243127)~~, multiple unit tests failing for `openbabel` related functions on Windows (skipped in f3dc772c25cc06b26b0702af37f1d278da8b6169 and f1393af2acfb098fe2e34c0bed193910e6f444e6).
Upd... | {
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} | ### Feature Requested
From this paper (https://www.sciencedirect.com/science/article/pii/S0927025617302069?via%3Dihub), it looks like enumlib should be able to enumerate unique displacements as well. Can this be implemented in pymatgen?
### Proposed Solution
Implement this feature in the class EnumlibAdaptor.
### ... | {
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"Thanks @janosh @shyuep ",
"Hey 👋🏻 \r\n\r\nI know it's just a minor thing, but I guess this [](https://python.org/downloads) should also be adjusted to [![Requires Python 3.10+](https://img.shields.io/badge/Pyt... | 2024-08-21T02:07:02 | 2024-08-28T01:05:04 | 2024-08-21T18:55:07Z | CONTRIBUTOR | {
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} | ### Summary
- Drop Python 3.9 support, following NumPy https://github.com/numpy/numpy/issues/24932
- Remove a few outdated TODOs
### TODOs
- [x] Implement https://github.com/materialsproject/pymatgen/pull/3958#issuecomment-2259644593
### Future PR
- Looks like Python 3.13 rc1 is not supported by microma... | {
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"\r\n> did you notice any cases where `strict=True` stood out as potentially problematic? \r\n\r\nSorry I didn't really go through each of these replacements (just a batch replace and fixed those CI failures in 89dc24775a9926f335ba271f477dd58890aae35d and b149ebb52918a35151a127cd99b555c809473e90). Perhaps I should ... | 2024-08-22T06:33:31 | 2024-08-22T09:21:15 | 2024-08-22T09:19:08Z | CONTRIBUTOR | {
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- Use `strict=True` when `zip` to ensure length equality @janosh, to finish https://github.com/materialsproject/pymatgen/pull/4009#discussion_r1724511180
### TODOs
- [x] Let's see how many tests are failing
- [x] Make sure `strict` keyword is for `zip` not other function
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} | Bumps [rexml](https://github.com/ruby/rexml) from 3.3.3 to 3.3.6.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/rexml/releases">rexml's releases</a>.</em></p>
<blockquote>
<h2>REXML 3.3.6 - 2024-08-22</h2>
<h3>Improvements</h3>
<ul>
<li>
<p>Removed duplicated entity exp... | {
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"All windows tests have passed.",
"Thanks for keeping an eye on this, perhaps we should bump `scipy` version also (to `>=1.14.1`)?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/pyproject.toml#L68",
"> perhaps we should bump `scipy` version also (to `>=1.14.1`)... | 2024-08-23T16:14:29 | 2024-08-30T06:12:43 | 2024-08-29T20:10:27Z | CONTRIBUTOR | {
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} | ## Summary
https://github.com/scipy/scipy/issues/21052 has been fixed and released in scipy 1.14.1. This PR removes the skip mark.
## 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`.
- [ ] ... | {
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"No problem, thanks for reviewing!"
] | 2024-08-25T08:17:52 | 2024-08-28T12:58:26 | 2024-08-28T10:27:56Z | CONTRIBUTOR | {
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} | ### Summary
Fix fixable `ruff` rules
### TODOs
- [x] Unit test of `io.aims` doesn't follow name convention, and has test files inside it.
- [x] Fix NPY201 https://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/pyproject.toml#L209
- [x] Fix PD011 (there might be a few false-... | {
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"> * Resolve following `mysql` dependency issue:\r\n\r\ni think `mysql` can be replaced with https://pypi.org/project/mysqlclient (based on [the advice here](https://pypi.org/project/mysql/))",
"Why bother? This is a small feature within pymatgen and we probably can count on a few fingers the number of people who... | 2024-08-26T02:36:09 | 2024-09-10T01:40:49 | 2024-09-09T21:09:43Z | CONTRIBUTOR | {
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- Also need to fix two `S608` violations (SQL injection): https://github.com/materialsproject/pymatgen/blob/41e4c69911f2b724734e0917c436ee5a1de63091/src/p... | {
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"> thanks a lot for all this work @DanielYang59! 🙏\r\n\r\nNo problem. Thanks for reviewing!\r\n\r\n> to make the messages more informative, i think it would be great to include the offending value/type in all `(Value|Type)Errors` (see [135f69e](https://github.com/materialsproject/pymatgen/commit/135f69ef7db4b1318c... | 2024-08-26T03:16:39 | 2024-08-31T06:02:29 | 2024-08-31T06:01:58Z | CONTRIBUTOR | {
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- Fix `S101`, replace all `assert` in code base
- [x] Use offending value in error message
**Please review all changes carefully to make sure the assert condition is correctly reversed** (there're just too many changes and I tried not to make mistakes).
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"**UPDATE: ignore the following**, it turns out I didn't understand \"package-data\" correctly before. In \"package-data\", we declare files to be included into the source distribution, and after that, with `include-package-data = true` we include them into the wheels.\r\n\r\n@janosh Would appreciate it if you coul... | 2024-08-26T06:28:54 | 2025-04-15T16:35:06 | 2025-04-15T16:21:01Z | CONTRIBUTOR | {
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- Remove explicit declare of package data, [sse Git plugin instead](https://setuptools.pypa.io/en/latest/userguide/datafiles.html): https://pypi.org/project/setuptools-scm/, also see https://github.com/pypa/setuptools-scm/issues/199
This would include "everything" tracked by Git, including "docs", ... | {
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"This is partially closed by #4065 "
] | 2024-08-26T10:39:27 | 2024-10-20T07:26:27 | CONTRIBUTOR | {
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} | ### Feature Requested
Support for LOBSTER 5.1.0 outputs file parsing.
Once added, downstream lobsterpy package and LOBSTER workflow in atomate2 can also be used.
### Proposed Solution
The LOBSTER output file parsers will be adapted to be able to tackle these new output files and tests will be added
### Relevant ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4020 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4020/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4020/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4020/events | https://github.com/materialsproject/pymatgen/pull/4020 | 2,489,056,044 | PR_kwDOACgets55jsfT | 4,020 | Add unit test for `io.vasp.help` | {
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"I’m on vacation right now but I’ll get to this once I’m back Monday!\r\n\r\nOn Wed, Aug 28, 2024 at 3:21 AM Janosh Riebesell ***@***.***>\r\nwrote:\r\n\r\n> ***@***.**** commented on this pull request.\r\n> ------------------------------\r\n>\r\n> In tests/io/vasp/test_help.py\r\n> <https://github.com/materialspro... | 2024-08-27T11:24:25 | 2024-09-04T14:08:17 | 2024-09-04T14:07:12Z | CONTRIBUTOR | {
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} | ### Summary
- Add unit test for `io.vasp.help`
- Bump python requirement to 3.10+ in README, thanks @QuantumChemist for pointing out (re pattern: `py(?:thon)?\s?3\.?9`)
- Reduce timeout for `requests` to 60 seconds, 600 seconds might be too impractical
### Not planned (for this PR?)
- [x] `test_get_incar_tags`... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4021 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4021/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4021/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4021/events | https://github.com/materialsproject/pymatgen/pull/4021 | 2,492,056,599 | PR_kwDOACgets55tYkd | 4,021 | Replace HTTP URLs with HTTPS, avoid `from pytest import raises/mark` | {
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"@janosh Please review this. Looks like we might need to regenerate docs, thanks!\r\n\r\nI reverted the rebuild doc commit because it makes it impossible to review. Would let you do this, appreciate that!",
"Currently on my phone. Could you apply the docs commit again?",
"> ideally, we should have a link check... | 2024-08-28T13:17:33 | 2024-08-30T06:54:25 | 2024-08-30T06:01:32Z | CONTRIBUTOR | {
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- Replace HTTP URLs with HTTPS
- Replace some expired URLs
- Avoid `from pytest import raises/mark` (a bit unsure about `MonkeyPatch` so just use `pytest.MonkeyPatch` if `pytest` is already imported)
- [ ] Regenerate documents | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4022 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4022/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4022/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4022/events | https://github.com/materialsproject/pymatgen/pull/4022 | 2,493,519,726 | PR_kwDOACgets55yJvY | 4,022 | Fix PT013: incorrect import of `pytest` | {
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"I might close this one because `approx` is heavily used and `pytest.approx` is way too verbose, [pytest doc also use `from pytest import approx`](https://docs.pytest.org/en/stable/reference/reference.html#pytest.approx) so perhaps we should not say it's \"incorrect import\".\r\n\r\nI might fix `from pytest import ... | 2024-08-29T05:58:18 | 2024-08-30T03:46:45 | 2024-08-29T06:18:53Z | CONTRIBUTOR | {
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- Fix [PT013: incorrect import of `pytest`](https://docs.astral.sh/ruff/rules/pytest-incorrect-pytest-import/)
> For consistency, pytest should be imported as import pytest and its members should be accessed in the form of pytest.xxx.yyy for consistency
Admittedly, `approx` is less verbose than `py... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4023 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4023/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4023/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4023/events | https://github.com/materialsproject/pymatgen/issues/4023 | 2,495,116,257 | I_kwDOACgets6UuHPh | 4,023 | Bug in inverse of MagSymmOp | {
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} | ### Python version
Python 3.11.7
### Pymatgen version
2023.7.18
### Operating system version
_No response_
### Current behavior
When the `inverse` of `MagSymmOp` is called, an error, `TypeError: MagSymmOp.__init__() missing 1 required positional argument: 'time_reversal'`, happens. This is probabl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4024 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4024/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4024/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4024/events | https://github.com/materialsproject/pymatgen/issues/4024 | 2,496,400,066 | I_kwDOACgets6UzArC | 4,024 | [Dev/CI] Check for accessibility of hyperlinks in CI | {
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} | Repost from https://github.com/materialsproject/pymatgen/pull/4021#pullrequestreview-2271225895, it might be good to check in CI workflow for the accessibility of hyperlinks to make sure they're still alive.
Something like [markdown-link-check](https://github.com/tcort/markdown-link-check) might be useful, but this ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4026 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4026/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4026/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4026/events | https://github.com/materialsproject/pymatgen/issues/4026 | 2,496,733,175 | I_kwDOACgets6U0R_3 | 4,026 | GAMMA in xticks, how to fix it to Greek alphabet style | {
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"problem solved by changing \"GAMMA\" to \"\\Gamma\" in KPOINTS"
] | 2024-08-30T09:38:20 | 2024-08-30T10:28:05 | 2024-08-30T10:26:54Z | NONE | {
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<div type='discussions-op-text'>
<sup>Originally posted by **1lifetime1** August 30, 2024</sup>
</div> | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4027 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4027/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4027/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4027/events | https://github.com/materialsproject/pymatgen/pull/4027 | 2,500,115,535 | PR_kwDOACgets56HiSk | 4,027 | Recover commented out code in tests and mark with `pytest.mark.skip` instead | {
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"Looks like there isn't more commented out code in tests (searched with `#\\s+def ` and `#\\s+class `, using `\\s+` in case multiple spaces are inserted).\r\n\r\nAlso we only have 104 lines of code commented in tests (might include a few false positive), should be possible to enable `ERA` for tests at some point.",... | 2024-09-02T06:30:56 | 2024-09-02T09:11:02 | 2024-09-02T08:47:47Z | CONTRIBUTOR | {
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- Recover commented out code in tests and mark with `pytest.mark.skip` instead (with `TODO: need someone to fix this` message for easy search), though currently [`ERA`](https://docs.astral.sh/ruff/rules/commented-out-code/) is ignored: https://github.com/materialsproject/pymatgen/blob/c06abf1a3c8d1507d9b... | {
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"Hey @anyangml this works fine with `primitive = False` and then calling `get_primitive_structure` on the structure:\r\n```\r\nfrom pymatgen.io.cif import CifParser\r\n\r\ndef read_file(fpth: str):\r\n cif = CifParser(fpth)\r\n structures = [\r\n s.get_primitive_structure() for s in cif.parse_structure... | 2024-09-02T12:43:47 | 2024-10-25T12:34:59 | 2024-10-17T02:50:36Z | NONE | {
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} | ### Python version
python 3.11.5
### Pymatgen version
2024.7.18
### Operating system version
_No response_
### Current behavior
I have some cif files generated by diffusion models, and they are likely to be invalid. I am trying to use CifParser (default setting) to read those files, and save the structure if the... | {
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.0 → v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.0...v0.6.3)
- [github.com/pre-commit/mirrors-mypy: v1.11.1 → v1.11.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.1...v1.11.2)
- [github.com/RobertCraigie/... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4030 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4030/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4030/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4030/events | https://github.com/materialsproject/pymatgen/issues/4030 | 2,501,937,687 | I_kwDOACgets6VIIoX | 4,030 | [DOCS] Links to source in each function returns a 404 error | {
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"Thanks for reporting @tawe141. I could confirm this and would fix soon."
] | 2024-09-03T05:16:48 | 2024-09-03T08:41:30 | 2024-09-03T08:41:30Z | CONTRIBUTOR | {
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} | The main pymatgen code now falls under a src parent directory, but in the documentation (as of 2024.8.9 at least), this change caused all of the hyperlinks for each function pointing to the code in Github to fail. Pretty easy fix, just need to add "src" in the link to point to the right files. | {
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"could you share the `OUTCAR` file so we can repro?",
"> ```python\r\n> ```python\r\n> print(outcar.noncollinear) # 'True' for LNONCOLLINEAR=.TRUE.\r\n> ```\r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> \r\n> ```\r\n\r\nYes. Please check the attached file (Please ... | 2024-09-03T05:49:39 | 2024-09-04T16:39:14 | 2024-09-04T16:39:14Z | NONE | {
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} | ### Python version
Python 3.11.0
### Pymatgen version
2024.7.18
### Operating system version
Ubuntu 22.04 LTS
### Current behavior
I expect that `outcar.noncollinear` is `True` for noncollinear calculations. But I got `False`.
### Expected Behavior
I expect that `outcar.noncollinear` is `True` for noncollinear... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4032 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4032/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4032/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4032/events | https://github.com/materialsproject/pymatgen/pull/4032 | 2,502,249,895 | PR_kwDOACgets56OwU0 | 4,032 | Fix missing `/src` in doc links to source code | {
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"No problem. Thanks for the better title :)",
"Looks like there might be a off-by-one error with the URL generator, need a closer look:\r\n<img width=\"833\" alt=\"image\" src=\"https://github.com/user-attachments/assets/c112fe52-ce68-4a72-8cd8-ffef37b79385\">\r\n\r\nThis only happens for some classes, in https:/... | 2024-09-03T08:30:17 | 2024-09-04T07:37:59 | 2024-09-03T08:41:30Z | CONTRIBUTOR | {
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- Fix missing `src` in hyperlinks to source code in docs | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4033 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4033/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4033/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4033/events | https://github.com/materialsproject/pymatgen/issues/4033 | 2,502,374,791 | I_kwDOACgets6VJzWH | 4,033 | Outcar class returns empty magnetization attribute when parsing OUTCAR file on Windows operating system | {
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"Thanks for providing the OUTCAR and code snippet, it's super helpful. I could confirm this.\r\n\r\nIt's owing to difference in `reverse_readfile` from `monty` (different line endings for Windows `\\r\\n` and Linux`\\n`): https://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/src... | 2024-09-03T09:28:29 | 2025-03-26T20:32:22 | 2025-03-26T20:32:22Z | NONE | {
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} | ### Python version
Python 3.11.5
### Pymatgen version
2024.7.18
### Operating system version
Windows 11, 24H2
### Current behavior
When using the Outcar class to parse an OUTCAR file from VASP on Windows 11, the magnetization attribute returns an empty tuple (). However, this issue does not occur on Ubuntu 22.04... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4034 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4034/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4034/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4034/events | https://github.com/materialsproject/pymatgen/pull/4034 | 2,502,718,221 | PR_kwDOACgets56QXFj | 4,034 | Fix `LNONCOLLINEAR` match in `Outcar` parser | {
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"Thanks @KylinGuo for reporting this and providing the test OUTCAR. Can I have your permission to include your OUTCAR as a test file for `pymatgen`?",
"> Thanks @KylinGuo for reporting this and providing the test OUTCAR. Can I have your permission to include your OUTCAR as a test file for `pymatgen`?\r\n\r\nIt's ... | 2024-09-03T12:13:13 | 2024-09-05T01:17:15 | 2024-09-04T16:39:13Z | CONTRIBUTOR | {
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} | ### Summary
- Fix `LNONCOLLINEAR` match in `Outcar` parser, to fix #4031
- [x] Add unit test
- Avoid hard coding number of spaces in `re` pattern
### For a future PR
- [**Reverted**] Turn on `terminate_on_match` to early exit upon match, I wish I didn't misunderstand the usage, but early exit should speed up... | {
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- [PLC0206](https://docs.astral.sh/ruff/rules/dict-index-missing-items/) | {
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"Beautiful! That's an impressive performance gain! \r\n\r\nI guess we should also be aware of the potential [memory leakage issue for `lru_cache` when applied on methods](https://docs.astral.sh/ruff/rules/cached-instance-method/) (I believe a reference to the `cls` would also be held in the case of class methods, *... | 2024-09-03T21:48:13 | 2024-09-10T13:19:27 | 2024-09-06T15:56:52Z | CONTRIBUTOR | {
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This adds an LRU cache to the structure matcher, specifically to the StructureMatcher._get_reduced_structure function.
This suggested improvement is motivated by the performance of the AflowPrototypeMatcher._match_prototype function (and in turn the robocrys builder that uses it). We believe this will ... | {
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"[this broke the release workflow](https://github.com/materialsproject/pymatgen/actions/runs/10794178560/job/29939315099)\r\n\r\n> Error: Unable to download artifact(s): Artifact not found for name: artifact\r\n Please ensure that your artifact is not expired and the artifact was uploaded using a compatible ... | 2024-09-03T22:40:22 | 2024-09-10T14:35:53 | 2024-09-06T15:56:38Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/actions/download-artifact/releases">actions/download-artifact's releases</a>.</em></p>
<blockquote>
<h2>v4.1.7</h2>
<h2>What's Chang... | {
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"I'm currently looking into this. I believe this `linkcode_resolve` is working correctly, and the issue should be related to the source code locating mechanism. \r\n\r\nThe final URL is reported on a specific version (the correct behaviour): https://github.com/materialsproject/pymatgen/blob/54046154d3f97d1227b2bfc0... | 2024-09-04T07:41:42 | 2025-02-25T09:24:09 | CONTRIBUTOR | {
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Seems to have off-by-one errors for some classes, but not all.
For example in https://pymatgen.org/pymatgen.alchemy.html, pointer to `AbstractStructureFi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4039 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4039/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4039/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4039/events | https://github.com/materialsproject/pymatgen/pull/4039 | 2,504,591,768 | PR_kwDOACgets56WuxS | 4,039 | Fix incorrect attribute name in `Lobster.outputs.Cohpcar` docstring | {
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"I will merge this as it only changes the doc string. Thanks @DanielYang59 !",
"Thanks for reviewing!"
] | 2024-09-04T08:00:08 | 2024-09-10T13:18:57 | 2024-09-06T14:51:29Z | CONTRIBUTOR | {
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- Fix incorrect attribute name in `Lobster.outputs.Cohpcar` docstring, `orb_cohp` -> `orb_res_cohp`
https://github.com/materialsproject/pymatgen/blob/edcd4654cc5048d7f0f00417d82755d98b03b739/src/pymatgen/io/lobster/outputs.py#L261
```python
from pymatgen.io.lobster.outputs import Cohpcar
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https://api.github.com/repos/materialsproject/pymatgen/issues/4040 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4040/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4040/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4040/events | https://github.com/materialsproject/pymatgen/issues/4040 | 2,506,630,458 | I_kwDOACgets6VaCU6 | 4,040 | [CI] Unit test of `boltztrap2` generate files inplace | {
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} | Should use temporary scratch directory such that unit test wouldn't generate files inplace.
Test of `boltztrap2` generate files locally:
- [x] `TestBztTransportProperties` generate `bztTranspoPros.json.gz`
- [x] `TestBztInterpolator` generates `bztinterp.json.gz` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4041 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4041/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4041/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4041/events | https://github.com/materialsproject/pymatgen/issues/4041 | 2,506,635,663 | I_kwDOACgets6VaDmP | 4,041 | [Enhancement] Enable `terminate_on_match` for `Outcar` parser | {
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"Another related proposal, perhaps we should consider:\r\n- Write a lazy version of `read_pattern`, to get a collection of all patterns and walk through the file once\r\nAND/OR\r\n- State machine\r\n- Refactor `read_pattern` to process in memory"
] | 2024-09-05T02:27:48 | 2024-11-25T07:26:07 | CONTRIBUTOR | {
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} | Post from https://github.com/materialsproject/pymatgen/pull/4020#discussion_r1734263672, there are quite some INCAR tags missing from `incar_parameters.json` (the type recording file), perhaps we should update it.
We also want to [make this json file more permissive](https://github.com/materialsproject/pymatgen/pull... | {
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} | ### Feature Requested
With the advent of universal machine learning potentials (MLPs), we now have the capability of generating free energy corrections such as vibrational entropy at specific temperatures. This allows the generation of finite temperature phase diagrams.
### Proposed Solution
I propose to implement ... | {
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"Thanks! I would have a look at this later. \r\n\r\nI'm not hoping `enable-cache: true` would work for our test workflow because I believe [GitHub-hosted runner is disposed of after each run](https://docs.github.com/en/actions/writing-workflows/choosing-where-your-workflow-runs/choosing-the-runner-for-a-job).\r\n> ... | 2024-09-05T19:45:34 | 2024-09-13T10:58:14 | 2024-09-13T10:58:14Z | MEMBER | {
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} | `uv` now has 1st-party GitHub Action support with built-in caching which could speedup our `test.yml` workflow. not sure if it clashes with our `mamba` setup
https://github.com/materialsproject/pymatgen/blob/1404220105d4dc1e421ac603b1cb83daf6b085c5/.github/workflows/test.yml#L64-L72
but if not, would be good to a... | {
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} | After [installing `BoltzTraP` in CI](https://github.com/materialsproject/pymatgen/pull/3985), turns out the `BoltztrapPlotter` is completely broken after #3237, see [the CI log](https://github.com/materialsproject/pymatgen/actions/runs/10731988727/job/29762940665?pr=3985).
The entire `TestBoltztrapPlotter` has been... | {
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"Hi @nightroxide thanks for reporting this. This is a duplicate of #3990 and has been fixed by #3992. "
] | 2024-09-06T18:59:45 | 2024-09-08T20:03:08 | 2024-09-07T10:31:53Z | NONE | {
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} | ### Python version
Python 3.12.5
### Pymatgen version
2024.8.9
### Operating system version
Windows 11
### Current behavior
Value error when trying to make interfaces
### Expected Behavior
A list of possible homojunction structures
### Minimal example
```Python
from pymatgen.analysis.interfaces import Cohere... | {
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} | `PMG_VASP_PSP_DIR_Error` is a class and hence should use PascalCase.
no downstream effects expected from this (strictly speaking) breaking change.
`PMG_VASP_PSP_DIR_Error` was only added 3 weeks ago in https://github.com/materialsproject/pymatgen/pull/3999 and [the last release](https://github.com/materialsproje... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4051 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4051/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4051/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4051/events | https://github.com/materialsproject/pymatgen/issues/4051 | 2,511,679,827 | I_kwDOACgets6VtTFT | 4,051 | BUG: INCAR Updates not working | {
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"Tagging @esoteric-ephemera and @janosh as this is likely due to the move from atomate2 to pymatgen inputs. ",
"[`incar` is a `VaspInput` property](https://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/src/pymatgen/io/vasp/inputs.py#L2910) which returns a new `Incar` every tim... | 2024-09-07T07:38:29 | 2024-09-09T16:57:19 | 2024-09-07T14:38:10Z | MEMBER | {
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} | Currently, this line https://github.com/materialsproject/atomate2/blob/f14586c7b29a7d5cbf7eabfe399728ab6362e0e7/src/atomate2/vasp/files.py#L195 does not have the intended effect of updating the INCAR.
This reproduces the error:
```py
from atomate2.vasp.sets.base import VaspInputGenerator
from mp_api.client i... | {
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"this is not enough information to understand your problem. please paste a code snippet and error message and what you're trying to accomplish",
"I guess he refers to the fact that [we don't have a `__init__.py` file for the first level `pymatgen` package](https://github.com/materialsproject/pymatgen/tree/master/... | 2024-09-07T08:35:03 | 2024-09-07T15:30:34 | 2024-09-07T14:22:31Z | NONE | {
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Python3.9.19
### Pymatgen version
2024.8.9
### Operating system version
Linux: miniconda
### Current behavior
In the conda env, pip install pymatgen, no "_init_.py" file
### Expected Behavior
_init_.py" file
### Minimal example
_No response_
### Relevant files to reproduce this bug
_No r... | {
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"closing as duplicate of #4049."
] | 2024-09-07T08:36:58 | 2024-09-07T10:57:55 | 2024-09-07T10:57:42Z | NONE | {
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Python3.9.19
### Pymatgen version
2024.8.9
### Operating system version
Linux: miniconda
### Current behavior
![Snipaste_2024-09-07_16-31-47](https://github.com/user-attachments/as... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4052 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4052/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4052/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4052/events | https://github.com/materialsproject/pymatgen/pull/4052 | 2,511,683,161 | PR_kwDOACgets56u3mx | 4,052 | Fix in-place `VaspInput.incar` updates having no effect if `incar` is dict (not `Incar` instance) | {
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"Thanks @janosh ! "
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"> [Question] Should we recommend the following alias (I thought pmg would be a shorthand of pymatgen instead of pymatgen.core):\r\n\r\nno strong opinion but leaning towards not proliferating that usage",
"> > [Question] Should we recommend the following alias (I thought pmg would be a shorthand of pymatgen inste... | 2024-09-08T02:06:50 | 2024-09-09T02:12:38 | 2024-09-08T15:49:35Z | CONTRIBUTOR | {
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} | ### Summary
- Avoid importing namespace package `pymatgen` directly
- [**Question**] Should we recommend the following alias (I thought `pmg` would be a shorthand of `pymatgen` instead of `pymatgen.core`): https://github.com/materialsproject/pymatgen/blob/15dc137c9325b58e7ce6b14bc14bd434e5f907f3/docs/index.md?plai... | {
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## Summary
Major changes:
- Make AimsSpeciesFile a dataclass
## Todos
## 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 clas... | {
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- [ ] Add docs builder as an automatic workflow, I think we already have one `jekyll-gh-pages.yml` but it doesn't seem to be used
- [ ] Exclude generated HTMLs from main branch, we would need a dedicated branch just to host docs
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"This fixed implementation is tested and shown to be working in the attached notebook as well",
"Done!\r\nAlso checked that this test fails with the old code (for `fractional=True`), but works all fine with the new code."
] | 2024-09-09T17:39:59 | 2024-09-09T22:01:15 | 2024-09-09T22:01:15Z | CONTRIBUTOR | {
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} | ## Summary
`Structure.apply_operation()` fails when using the `fractional=True` operation.
The issue is that the ``SymmOp`` is applied to the site frac coords (in the original lattice), but then these new frac coords (in the old basis) are used directly with the new (transformed) lattice, giving a 'doubled' transform... | {
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"@janosh The [release just failed](https://github.com/materialsproject/pymatgen/actions/runs/10794178560) and I think this should solve it.",
"thanks @ab5424! 👍 could you also bump the `sdist` `upload-artifacts`?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/48e7c984e7c981b395af43734b43d2b544ece43d/.g... | 2024-09-10T14:18:36 | 2024-09-13T14:10:09 | 2024-09-10T17:50:28Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- `upload-artifacts` was recently bumped to `v4` (see #4037). I think that this breaks the release workflow because from `v4` upwards they are not allowed to have the same name anymore (see https://github.com/actions/upload-artifact/issues/478). This PR should fix it, according to [this... | {
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"Hi @Nokimann thanks for reporting this. I could confirm this issue introduced by #3690, would fix ASAP.\r\n\r\nMeanwhile is it possible to share your files such that we could enhance unit test (this function is not covered by unit test)? Thanks a lot!\r\n\r\n\r\n"
] | 2024-09-11T02:35:44 | 2024-09-11T05:15:29 | NONE | {
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} | ### Python version
PYthon 3.12.5
### Pymatgen version
2024.8.9
### Operating system version
CentOS 7.6
### Current behavior
in pymatgen/io/vasp/output.py
`get_band_structure_from_vasp_multiple_branches`
`if os.path.isfile(f"{dir_name}/branch_0"):`
### Expected Behavior
`get_band_structure_from_vasp_mu... | {
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"@shyuep Perhaps you could review this as well? \r\n\r\nI tried to add a unit test but I don't have any real test file for \"VASP multi-branch bandstructure calculation\" and had to create a dummy one instead, so I guess this is as far as I could get :)\r\n",
"@shyuep Can you review this please? I guess this has ... | 2024-09-11T05:26:08 | 2025-05-01T21:34:20 | CONTRIBUTOR | {
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- Fix branch directory check in `io.vasp.outputs.get_band_structure_from_vasp_multiple_branches`, to fix #4060
- [ ] Improve unit test (waiting for data, I don't have experience with "VASP multi-branch bandstructure calculation") | {
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"@janosh Turns out there isn't much speed advantage for `setup-uv` over `pip install uv`, the first time running `setup-uv` is even slower. Perhaps we just keep things simple (also easy to maintain) and still use `pip install uv` for now.",
"> Turns out there isn't much speed advantage for `setup-uv` over `pip i... | 2024-09-12T04:14:27 | 2024-09-13T11:01:30 | 2024-09-13T10:58:13Z | CONTRIBUTOR | {
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- [Use `setup-uv` in CI tests workflow](https://docs.astral.sh/uv/guides/integration/github/), to close #4044
## Performance benchmark
The following word "native" refers to package installed by native github action setups: `setup-Python/micromamba/uv`
**NOTE**: `setup-uv` installer might provide... | {
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https://github.com/materialsproject/pymatgen/blob/6bb293896945106476d6676cb2b65550d791edb5/pyproject.toml#L218 | {
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"@naik-aakash thanks! I was about to start doing it myself 🙈",
"I think we also don't have a parser for the polarization file 😅. But maybe, this can be done in a subsequent pull request ",
"@naik-aakash should we maybe get a part of this merged as a bug fix and do the other things later?",
"> @naik-aakash s... | 2024-09-13T07:47:16 | 2024-10-17T16:32:45 | 2024-10-17T16:32:39Z | CONTRIBUTOR | {
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This PR aims to update the `lobster.io.inputs` and `lobster.io.outputs` modules to support LOBSTER v5. There are some changes in v5.1, mainly with the format of output files. Also, new output files are generated from fragment orbital analysis. A few new keywords have also been added.
# Todos
- [x... | {
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"@shyuep I guess this PR has been forgotten, can you please review this? Thanks!",
"Thanks!"
] | 2024-09-15T04:09:58 | 2025-03-26T20:58:33 | 2025-03-26T20:32:21Z | CONTRIBUTOR | {
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} | ### Summary
- Test `monty` fix for reverse readline, close #4033 and close #4237
- Replace `reverse_readline` with faster `reverse_readfile`
- Fix incorrect `monty` imports
- [x] Enhance unit test for reported Outcar parser (need to test **unzipped format**)
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} | Added DebyeCalculator as an external tool
## 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 annotations included.... | {
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"Sigh... why does this have to happen again?!\r\n",
"I have released an emergency version. Thanks for tracking this down.",
"@yang-ruoxi thanks for finding and fixing! 👍 \r\n\r\n\r\n> Sigh... why does this have to happen again?!\r\n\r\n@shyuep you should have asked for a unit test to prevent future regressions... | 2024-09-16T23:31:55 | 2024-09-19T03:35:55 | 2024-09-17T03:09:13Z | MEMBER | off-topic | {
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} | ## Summary
This PR fixed the break of phase diagram plot caused by commit 41e6d99 which made changes not only to syntax but also plotting logic without careful review. This is a small fix but did require human hour to track down the issue, and caused downstream breakage on MP website and for pymatgen users who plot ph... | {
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"Tagging @utf for awareness.",
"Thanks,"
] | 2024-09-17T11:59:55 | 2024-09-18T01:12:33 | 2024-09-18T01:12:28Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
This PR fixes the bug when parsing non-self-consistent calculation done with `ALGO=Exact` and `NELM=1`. In such senario, the electronic step of the calculation will never truly converge. However, this is what we expect in non-self-consistent calculations, as we only have one electronic s... | {
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"Can you try reverting the entire commit doing the in place assignment change and see if it solves the problem on your machine?",
"reverting this particular line solved the issue. Would you prefer reverting the entire commit for this PR? ",
"OK, if it already fixes it. I will merge now. Thanks for the fix.",
... | 2024-09-17T21:59:59 | 2024-09-18T17:16:17 | 2024-09-18T01:08:36Z | MEMBER | {
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} | ## Summary
A strange behavior was caught for chemical potential diagram where the planes were crossed.
Using the in-place [assignment expression](https://github.com/materialsproject/pymatgen/blob/150f816c55be80dd146cb20ebbf5f930633c8aeb/src/pymatgen/analysis/chempot_diagram.py#L649), the plot shows below:
<img w... | {
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- Use binary distribution (wheels) to install `pymatgen` in test suite, currently neither source distribution nor binary distribution is tested against test suite, might lead to breakage if we miss anything from them (heard this happened before). The reason to use binary distribution over source distribu... | {
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"Beautiful! I believe I have seen issues related to this at some point. \r\n\r\nI just did a global search (re pattern `return np\\..* [><=]`) and there are a few more cases that perhaps you could fix as well? Thanks!\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ea7c3390e2db99a35f3eee242073ffc2830bbd4c/... | 2024-09-20T17:04:47 | 2024-10-12T23:47:24 | 2024-09-24T22:14:12Z | CONTRIBUTOR | {
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The return signature of this function is currently `np.bool_` which can cause serialization problems with older atomate1 workflows.
Changed to `bool` instead. | {
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Currently the `Vasprun` parser crashes (with `ParseError`) if the file is not complete. If one sets `exception_on_bad_xml=False` this can be avoided, but then most of the information is not parsed (even though it is still present in the file). This can occur fairly often when large VASP calcula... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4076 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4076/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4076/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4076/events | https://github.com/materialsproject/pymatgen/pull/4076 | 2,542,086,595 | PR_kwDOACgets58VxnM | 4,076 | Install `BoltzTraP2` directly through `uv` | {
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"I tried but still cannot figure out why build for `BoltzTrap2` fails for Windows runners. But in any case, this wouldn't worsen our tests as it was installed for Ubuntu-only before."
] | 2024-09-23T09:38:06 | 2024-10-03T01:52:50 | 2024-10-02T20:12:42Z | CONTRIBUTOR | {
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- Install `BoltzTraP2` directly through `uv` as `BoltzTraP2` now support PEP-517 with build isolation
- [ ] ~~Look into why install failed for Windows~~
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"Pls state whether you are using MPRester basic or the mp-api version. If it is the mp-api version, then you will have to post this in that repo. If it is basic, then let us know.",
"It happens with both, but it's really a problem with pymatgen rather than mp-api. If numpy>2.0 is installed, the following two comm... | 2024-09-23T22:45:41 | 2024-09-26T07:17:54 | NONE | {
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} | ### Python version
Python 3.12.5
### Pymatgen version
2024.9.17
### Operating system version
Linux Mint V22, windows10 64 bit,
### Current behavior
>>> from pymatgen.ext.matproj import MPRester
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.1.1 as it may crash. To support ... | {
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"Thanks @benrich37, I will review this",
"> Thanks @benrich37, I will review this\r\n\r\n@mkhorton Sorry didn't see your comment, will pause on new commits until you're finished. Thank you!\r\n\r\nEdit: Also, it looks like there are some typos baked into how JDFTx creates out files, which is causing pre-commit to... | 2024-09-24T20:05:48 | 2025-01-24T18:29:51 | 2025-01-24T18:29:51Z | CONTRIBUTOR | {
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} | ## Summary
This PR has been divided into the following 3 PR's
- 1: (#4187) (Code change) Addition of `valences` property to ElementBase and Species
- 2: (#4189) (Code addition) Addition of `inputs.py` module to `pymatgen.io.jdftx` and helper modules for representing and parsing JDFTx inputs
- 3: (#4190) (Cod... | {
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"Hi @msiron-entalpic thanks for reporting this, I could confirm this issue.\r\n\r\nThe reason being we added `strict=True` to ensure the two iterators (`mols` and `lattices`) to unpack are of the same length: https://github.com/materialsproject/pymatgen/blob/e9ea813107ea223d5ce693bdf5e4f74fe29f76db/src/pymatgen/io... | 2024-09-25T12:20:38 | 2024-10-02T19:41:01 | 2024-10-02T19:41:01Z | NONE | {
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} | ### Python version
3.12.5
### Pymatgen version
v2024.9.17.1
### Operating system version
MacOSX
### Current behavior
When parsing cp2k output using
```
from pymatgen.io.cp2k.outputs import Cp2kOutput
o = Cp2kOutput('cp2k.out', auto_load=True)
```
With any version of Pymatgen after v2024.8.9 stacktrace:
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https://api.github.com/repos/materialsproject/pymatgen/issues/4081 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4081/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4081/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4081/events | https://github.com/materialsproject/pymatgen/pull/4081 | 2,551,457,094 | PR_kwDOACgets581_uy | 4,081 | Allow more than 20 terminal groups in CompoundPhaseDiagram | {
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"There are merge conflicts. Pls fix them first. Thanks.",
"Resolved, thanks."
] | 2024-09-26T20:15:44 | 2024-10-21T21:00:09 | 2024-10-21T21:00:09Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- fix 1: CompoundPhaseDiagram can now have more than 20 terminal groups | {
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"Thanks @kavanase! Will merge. \r\n\r\n@knc6, notifying yourself too as a courtesy since I think you originally contributed this functionality, just in case the bug has affected you.",
"Realised we should have asked for a test modification here too, but the fix seems clear enough to me."
] | 2024-09-26T22:41:53 | 2024-09-27T02:18:34 | 2024-09-27T02:17:34Z | CONTRIBUTOR | {
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} | This fixes some bugs in the `slme` code:
- Avoids overwriting the input data, which was leading to SLME results changing every time the function was (repeatedly) called.
- Removes some hard-coded settings for the plot and adds some labels | {
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## Summary
Major changes:
- fix 1: Species Defaults need to be read from SETTINGS object
## 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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"Given that no one has commented, I will merge. People can complain if they run into problems.",
"Thanks, anyone with experience in CP2K please feel free to comment.",
"@shyuep @janosh @mkhorton Could a new version of pymatgen be released? We see Cp2k output related failures showing up in atomate2 ",
"Done",
... | 2024-09-29T03:53:44 | 2024-10-03T17:30:10 | 2024-10-02T19:41:00Z | CONTRIBUTOR | {
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} | ### Summary
- Fix usage of `strict=True` during `zip` in `cp2k.outputs`, to fix #4079
- [ ] Add unit tests? (**need input**)
- Rename and clean up some tests
I have to revert to `strict=False` for now, but **it's better if we could know the reason for such mismatch**. Anyone experienced with CP2K please fee... | {
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"Thanks for the detailed diagnosis, I could recreate this "
] | 2024-09-29T18:19:40 | 2024-10-02T19:41:23 | 2024-10-02T19:41:23Z | NONE | {
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} | ### Python version
Python 3.10.14
### Pymatgen version
Version: 2024.9.17
### Operating system version
Red Hat Enterprise Linux Ver 8.6
### Current behavior
A `Poscar` object created from a POSCAR string with Selective Dynamics stores `selective_dynamics` as a NumPy array of booleans. However, thes... | {
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"Thanks.",
"I realized I didn't really test other data types other than string, list and np.array (all are sequences of some sort). **Would `np.array_equal` fail for any dtype?** From the source code, looks like it would return `False` directly for any dtype that cannot be converted to an array: https://github.co... | 2024-09-30T08:20:27 | 2024-10-03T03:19:15 | 2024-10-02T19:41:22Z | CONTRIBUTOR | {
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} | ### Summary
- Fix dict equality check with numpy array, to fix #4085
- Added a helper function to compare two dicts because I have a feeling some other parts of the code might need it as well
- [x] Add unit tests
- [x] Add unit tests for new util function
### Efficiency
Turns out `np.testing.assert_equal`... | {
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"Thank you @Jaebeom-P ! Tagging @Andrew-S-Rosen and @samblau as well.\r\n\r\nThis looks clean and straightforward to me. We will need to make sure all the existing tests pass too (i.e., this doesn't break any of the previous versions), but I don't think it should. Because this is your first contribution to pymatgen... | 2024-09-30T17:39:05 | 2024-10-02T19:39:14 | 2024-10-02T19:39:01Z | CONTRIBUTOR | {
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Additional parser update for #3578, similar to #3580, for Q-chem 6.1.1+. This PR addresses errors in the `QCOutput._read_optimization_data()` and `QCOutput._read_frequency_data()` functions, which are essential for FFOpt (Frequency Flattening Optimization) functionality from `custodian` and `atomate2` pac... | {
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} | ### Python version
3.11.9
### Pymatgen version
2024.9.17.1
### Operating system version
Linux
### Current behavior
When calling `bader_analysis_from_path`, I get an indexing error due to poor glob logic.
### Expected Behavior
No indexing error
### Minimal example
The following files are... | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/ruby/webrick/releases">webrick's releases</a>.</em></p>
<blockquote>
<h2>v1.8.2</h2>
<h2>What's Changed</h2>
<ul>
<li>Drop commented-out line by <a href="https... | {
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"Wrong fork"
] | 2024-10-02T23:09:33 | 2024-10-02T23:10:52 | 2024-10-02T23:10:02Z | CONTRIBUTOR | {
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## Summary
Major changes:
- valence electron dictionary replaced with references to Element class
- get_atom_valence_electrons method created within data.py to circumvent current error raised on the "valence" property of an Element
- missing __init__.py... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4092 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4092/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4092/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4092/events | https://github.com/materialsproject/pymatgen/pull/4092 | 2,563,031,745 | PR_kwDOACgets59cncJ | 4,092 | Enhance test for util function `is_np_dict_equal` | {
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"The experimental implementation (with try-except) is slightly slower than using `np.array_equal`:\r\n```\r\nArray size: 10\r\nis_np_dict_equal: 3.38 µs\r\nis_np_dict_equal_try_except: 2.03 µs\r\n--------------------------------------------------\r\nArray size: 100\r\nis_np_dict_equal: 1.64 µs\r\nis_np_dict_equal_t... | 2024-10-03T03:19:04 | 2024-10-22T02:05:46 | 2024-10-21T20:59:52Z | CONTRIBUTOR | {
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- Enhance test for `is_np_dict_equal` with different data types, follow up #4086 | {
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"Thanks."
] | 2024-10-03T20:01:47 | 2024-10-22T02:43:26 | 2024-10-22T02:43:20Z | CONTRIBUTOR | {
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Example is H2. Also see See, for example, Table 10.1 and Appendix B of C. Cramer “Essentials of Computational Chemistry”, 2nd Ed. | {
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"Thanks. Looks like a useful package!"
] | 2024-10-04T01:26:12 | 2024-10-04T01:49:33 | 2024-10-04T01:49:10Z | CONTRIBUTOR | {
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} | ## Summary
I'm the maintainer of [ramannoodle](https://github.com/wolearyc/ramannoodle), an new API for calculating off-resonance Raman spectra from first principles calculations. The API includes an interface with pymatgen, and I wish to add it to pymatgen's list of external packages.
Cheers,
Willis | {
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} | ### Summary
- Prevent unit test of `boltztrap2` from modifying files in place, to close #4040
- [x] relocate tests from `setUp` method
> [!CAUTION]
> [NEED CONFIRM] replace very general `BoltztrapError` with more semantic exception type, cec569fef7d63dd70dd220c12d6389d4f4bb346d
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updates:
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I noticed I was getting some deprecation warnings like these, when parsing `vasprun.xml` files with `python=3.12`:
```
[DeprecationWarning("Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead."), DeprecationWarning("Testing an ... | {
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"diff_url": "https://github.com/materialsproject/pymatgen/pull/4097.diff",
"patch_url": "https://github.com/materialsproject/pymatgen/pull/4097.patch",
"merged_at... |
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