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https://api.github.com/repos/materialsproject/pymatgen/issues/4099 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4099/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4099/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4099/events | https://github.com/materialsproject/pymatgen/pull/4099 | 2,577,317,772 | PR_kwDOACgets5-JfDv | 4,099 | Ion: bugfix for CO2(aq) reduced formula | {
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} | My recent changes to `Ion` in #3991 introduced a problem in which the `reduced_formula` of `CO2(aq)` would incorrectly be shown as `C2O4(aq)`. Other properties such as `composition` etc were not affected.
```
>>> from pymatgen.core.ion import Ion
>>> Ion.from_formula('CO2').composition
Composition('C1 O2')
>>> I... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4100 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4100/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4100/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4100/events | https://github.com/materialsproject/pymatgen/pull/4100 | 2,577,566,945 | PR_kwDOACgets5-KPi3 | 4,100 | Support python3.13 | {
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"might close this one now as too many packages don't support python 3.13, feel free to take over this",
"Also cannot recreate the `Windows fatal exception: access violation` failure on my Windows machine (https://github.com/pytest-dev/pytest/issues/7634)",
"I'm pretty much stuck with the Windows runner failure,... | 2024-10-10T04:44:06 | 2025-04-17T20:00:42 | 2025-04-17T20:00:24Z | CONTRIBUTOR | {
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} | ### Summary
- Support python 3.13, to close #4284
- [ ] Remove all `pybtex` check after #4361
- [ ] Need to fix the EOS test failure on Ubuntu 3.13 (seemingly related to numerical precision but cannot recreate locally)
- [ ] Revert all platforms tested on Python 3.13 in `test.yml` test matrix (c9cc898301a7198488d... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4101 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4101/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4101/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4101/events | https://github.com/materialsproject/pymatgen/pull/4101 | 2,577,733,496 | PR_kwDOACgets5-Ku55 | 4,101 | bump `chgnet` to support numpy 2, skip failing `matgl` test for `torch` 2.4.1 | {
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"[The unit test failure](https://github.com/materialsproject/pymatgen/actions/runs/11269124025/job/31337138014?pr=4101):\r\n> E FileNotFoundError: Cannot find DGL C++ graphbolt library at /home/runner/micromamba/envs/pmg/lib/python3.12/site-packages/dgl/graphbolt/libgraphbolt_pytorch_2.4.1.so\r\n\r\nSeem... | 2024-10-10T06:13:02 | 2024-10-22T03:03:58 | 2024-10-22T02:41:39Z | CONTRIBUTOR | {
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} | ### Summary
- Bump `chgnet` to support Numpy2
### Conflicting `torch` version
- `chgnet 0.4.0` requires `torch > 2.4.1` to be NumPy2 compatible https://github.com/CederGroupHub/chgnet/pull/202#discussion_r1756944575
- `matgl` requires `torch <= 2.2.1` for `dgl` to work correctly https://github.com/materialsp... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4102 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4102/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4102/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4102/events | https://github.com/materialsproject/pymatgen/pull/4102 | 2,578,166,448 | PR_kwDOACgets5-ME_8 | 4,102 | pin python 3.12 in CI and `requires-python` | {
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"The last set of tests never started. Thus, we are stuck here. Any thoughts, @DanielYang59 ?",
"> The last set of tests never started. Thus, we are stuck here. \r\n\r\nI don't know the exact reason, ~~but my guess is the unstarted set is the cached set for our current config (python > 3.10 for Ubuntu). As the fin... | 2024-10-10T09:06:01 | 2024-12-24T12:17:44 | 2024-10-21T20:58:32Z | CONTRIBUTOR | {
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- Pin Python 3.12 in CI for now, as it seems a lot of dependencies don't support Python 3.13 yet #4100 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4103 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4103/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4103/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4103/events | https://github.com/materialsproject/pymatgen/pull/4103 | 2,579,466,913 | PR_kwDOACgets5-QPRE | 4,103 | Support to aims format from Structure instance | {
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"Thanks!"
] | 2024-10-10T17:45:19 | 2024-10-15T10:29:47 | 2024-10-10T18:35:49Z | CONTRIBUTOR | {
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} | ## Summary
This pull request adds support for reading and writing files in FHI-aims `geometry.in` format to the `Structure` objects.
Major changes:
- Support for reading `geometry.in` file in `Structure.from_file` and `Structure.from_str` methods
- Support for writing FHI-aims formatted file in `Structure.to` m... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4104 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4104/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4104/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4104/events | https://github.com/materialsproject/pymatgen/pull/4104 | 2,582,321,414 | PR_kwDOACgets5-YxZo | 4,104 | VASP Bugfixes: Volumetric data and XDATCAR parsing for monatomic structures | {
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"@shyuep and @mkhorton should be ready for review whenever you have time. I had to make some version changes to linting / testing in CI to get the tests to set up correctly and run (newer version of mypy throws a lot of errors that should be handled separately and the linux build failed because of py3.13)",
"Than... | 2024-10-11T23:23:35 | 2024-11-15T18:08:49 | 2024-10-14T18:37:42Z | CONTRIBUTOR | {
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} | Two bug fixes:
- For VASP 6.4.2 and up, all POSCAR-style strings include both the POTCAR symbol (e.g., `Mg_pv` rather than the elemental symbol `Mg`) and part of the POTCAR hash (`Si/79d9987ad87` rather than `Si`). While the hashing is already accounted for, the underscore was not. Fixed here, impacts CONTCAR and all ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4105 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4105/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4105/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4105/events | https://github.com/materialsproject/pymatgen/pull/4105 | 2,582,840,086 | PR_kwDOACgets5-aBSL | 4,105 | Replace deprecated `ExpCellFilter` with `FrechetCellFilter` | {
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"Thanks for this @ab5424, appreciate you expanding the type hint too!",
"Still issues with these ghost tests",
"I minor head up though, the `ExpCellFilter` -> `FrechetCellFilter` change is more than an API migration, but involved behaviour change (sounds more like a bug fix), see [the implementation note](https... | 2024-10-12T11:08:48 | 2024-10-22T21:47:17 | 2024-10-22T03:05:20Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- Replace deprecated `ase` `ExpCellFilter` with `FrechetCellFilter` for structure relaxation.
- `pre-commit` complained about outdated configuration so I updated it.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with... | {
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"Yes this impacts compatibility with the Materials Project entries. You can use the `MPScanRelaxSet` which uses the PBE_54 pseudopotentials and will be compatible with the newer materials project r2SCAN data",
"Ok, thank you. I see. "
] | 2024-10-12T12:46:24 | 2024-10-14T17:05:57 | 2024-10-14T17:05:57Z | NONE | {
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} | ### Feature Requested
When users run MPGGARelax or any other workflow requiring MPRelaxSet, and the structures contain elements like tungsten (W), they encounter a "POTCAR not found" error. This issue arises because the newer PBE 54 pseudopotential set no longer includes W_pv, which is still expected by MPRelaxSet. Ho... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4107 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4107/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4107/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4107/events | https://github.com/materialsproject/pymatgen/pull/4107 | 2,583,693,702 | PR_kwDOACgets5-cJKk | 4,107 | Properly test `ase` not installed error, use single `skip` mark for module level test skip | {
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} | ### Summary
- Properly test `ase` not installed error, the original test would not actually run because `ase` is installed in CI (ideally the test should be independent of whether that package is installed or not)
- Also fix not installed test for `seekpath` in `io.pwmat.inputs`
- Use module level skip when packag... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4108 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4108/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4108/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4108/events | https://github.com/materialsproject/pymatgen/issues/4108 | 2,585,455,312 | I_kwDOACgets6aGurQ | 4,108 | pmg plot --dos ... errs in matplotlib call | {
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"Thanks for reporting this, this should be related to the change in return type from figure to axes in #3237. I would fix this."
] | 2024-10-14T09:47:55 | 2024-10-21T20:52:56 | 2024-10-21T20:52:56Z | CONTRIBUTOR | {
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} | ### Python version
3.12.7
### Pymatgen version
2024.10.3
### Operating system version
_No response_
### Current behavior
```bash
pmg plot -d vasprun.xml --out_file dos.png
```
yields
```bash
Traceback (most recent call last):
File "/home/yantar92/Downloads/Nio.DOS/.venv/bin/pmg", line 8,... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4109 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4109/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4109/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4109/events | https://github.com/materialsproject/pymatgen/pull/4109 | 2,585,503,098 | PR_kwDOACgets5-hFbb | 4,109 | Fix `savefig` in `pmg.cli.plot` | {
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} | ### Summary
- Fix `savefig` in pmg.cli.plot, to close #4108
- [x] Add unit test
- [x] Confirm `matplotlib` versions (oldest supported matplotlib 3.8 works)
- Split tests for `cli` module
- Fix `test_pkg` to use the `src` layout path
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https://api.github.com/repos/materialsproject/pymatgen/issues/4110 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4110/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4110/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4110/events | https://github.com/materialsproject/pymatgen/pull/4110 | 2,585,724,960 | PR_kwDOACgets5-h1Am | 4,110 | Remove all `no_type_check` mark, fix new `mypy` error in `1.12.0` | {
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- Remove all `no_type_check` mark, follow up #4109
- Fix new `mypy` errors in CI after [the `1.12.0` release](https://github.com/python/mypy/releases/tag/v1.12.0)
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https://api.github.com/repos/materialsproject/pymatgen/issues/4111 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4111/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4111/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4111/events | https://github.com/materialsproject/pymatgen/pull/4111 | 2,588,468,088 | PR_kwDOACgets5-qSov | 4,111 | Add support for `use_structure_charge` keyword in FHI-aims input generator | {
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"Looks good to me!",
"Thanks."
] | 2024-10-15T11:25:30 | 2024-10-22T09:40:52 | 2024-10-21T20:55:12Z | CONTRIBUTOR | {
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} | ## Summary
This PR adds support of `use_structure_charge` keyword to a base FHI-aims input generator to make it more consistent with VASP and `atomate2` common defect workflows.
Major changes:
- support of `use_structure_charge` keyword to a base FHI-aims input generator
## Checklist
- [X] Google format ... | {
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} | ### Python version
python 3.10
### Pymatgen version
2024.10.3
### Operating system version
ubuntu 20.04lts
### Current behavior
pymatgen/analysis/magnetism/heisenberg.py:323: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4113 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4113/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4113/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4113/events | https://github.com/materialsproject/pymatgen/pull/4113 | 2,591,802,407 | PR_kwDOACgets5-04qu | 4,113 | Fix arg passing in `inverse` property of `SymmOp` | {
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} | ### Summary
- Fix arg passing in `inverse` property of `SymmOp`, to fix #4023
- Replace some `np.array` with `np.asarray` for efficiency where we don't rely on creating a copy
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https://api.github.com/repos/materialsproject/pymatgen/issues/4114 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4114/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4114/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4114/events | https://github.com/materialsproject/pymatgen/issues/4114 | 2,593,386,431 | I_kwDOACgets6ak--_ | 4,114 | `io.pwscf.PWInput.from_file()` incorrectly reads decimal numbers and the `K_POINTS` card in `automatic` mode | {
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"Seems there is one more bug in parsing `K_POINTS` card, adding that to this issue"
] | 2024-10-17T01:38:04 | 2024-10-21T20:54:32 | 2024-10-21T20:54:32Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.4
### Pymatgen version
2024.10.3
### Operating system version
Ubuntu 22.04.5 LTS
### Current behavior
The `io.pwscf.PWInput.from_file()` method fails to correctly parse:
- decimal numbers written in scientific notation with exponent part prefixed with `e` or `E` (not... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4115 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4115/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4115/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4115/events | https://github.com/materialsproject/pymatgen/pull/4115 | 2,593,393,947 | PR_kwDOACgets5-53uc | 4,115 | Bugfix: Parsing bugs in `io.pwscf.PWInput` | {
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"Thanks."
] | 2024-10-17T01:46:36 | 2024-10-21T20:54:35 | 2024-10-21T20:54:31Z | CONTRIBUTOR | {
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} | ## Summary
A quick regexp fixes + strengthened test cases to close #4114
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https://api.github.com/repos/materialsproject/pymatgen/issues/4116 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4116/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4116/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4116/events | https://github.com/materialsproject/pymatgen/pull/4116 | 2,593,490,202 | PR_kwDOACgets5-6LhP | 4,116 | bump `networkx` to 2.7 to fix intermittent CI failure when `torch` install failed: `ImportError: cannot import name 'Mapping' from 'collections'` | {
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"Happened again in https://github.com/materialsproject/pymatgen/actions/runs/11383942907/job/31670629571",
"Looks like networkx 2.7 [causes test failure in MacOS CI](https://github.com/materialsproject/pymatgen/actions/runs/11432515352/job/31803122891) (if `torch` install failed of course), might need to bump it ... | 2024-10-17T03:08:29 | 2024-10-22T05:46:56 | 2024-10-21T20:52:35Z | CONTRIBUTOR | {
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} | ### Summary
- Bump `networkx` to resolve [the following intermittent CI failure](https://github.com/materialsproject/pymatgen/actions/runs/11377302114/job/31651207689):
```
../../../micromamba/envs/pmg/lib/python3.11/site-packages/networkx/__init__.py:100: in <module>
import networkx.classes.filters
../../..... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4117 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4117/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4117/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4117/events | https://github.com/materialsproject/pymatgen/pull/4117 | 2,594,383,971 | PR_kwDOACgets5-861J | 4,117 | Migrate `ext.COD` from `mysql` to REST API | {
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"Thanks.",
"No problem, thanks for reviewing and for original bringing up the idea to migrate to REST API"
] | 2024-10-17T11:03:58 | 2024-10-22T02:08:11 | 2024-10-21T20:54:02Z | CONTRIBUTOR | {
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} | ### Summary
- Migrate `ext.COD` from `mysql` to REST API, to close #4016
- [**Deprecation**] Deprecate `timeout` arg from `get_structure_by_id` method and use a single class level `timeout`
- [x] suppress timeout error in CI | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4118 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4118/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4118/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4118/events | https://github.com/materialsproject/pymatgen/pull/4118 | 2,594,611,793 | PR_kwDOACgets5-9ppQ | 4,118 | Support Pymatgen Species object in aims | {
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} | ## Summary
As of now, the basis set for the site in FHI-aims input files got chosen according to the site element. This PR enables the support of Species object when present in the structure, which should make setting up heterogeneous calculations with FHI-aims and Pymatgen easier.
Major changes:
- Suppor... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4119 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4119/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4119/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4119/events | https://github.com/materialsproject/pymatgen/issues/4119 | 2,594,639,289 | I_kwDOACgets6apw25 | 4,119 | VaspInput setter and Incar.check_params() are inconsistent | {
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"Thanks for reporting this, I believe the warning on `GGA=PS` is owing to: https://github.com/materialsproject/pymatgen/blob/4f7aa35f15cb17a89209b955903c64b39e2fa922/src/pymatgen/io/vasp/inputs.py#L988\r\n\r\nI.e. any keyword not included inside the following and is not `boolean/float/int` (`str`) would be capitali... | 2024-10-17T12:46:59 | 2024-12-19T08:13:47 | 2024-10-21T19:05:19Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.4
### Pymatgen version
2024.7.18
### Operating system version
_No response_
### Current behavior
When I set INCAR parametrs via `vasp_input['INCAR']['PARAM']=value`, they do not always pass `Incar.check_params()` checks.
Using the example below, I am getting:
``... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4120 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4120/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4120/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4120/events | https://github.com/materialsproject/pymatgen/issues/4120 | 2,595,606,238 | I_kwDOACgets6atc7e | 4,120 | `AseAtomsAdaptor` conversions fail to preserve 1D or 2D PBC | {
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} | ### Python version
Python 3.12.4
### Pymatgen version
2024.10.3
### Operating system version
Ubuntu 22.04.5 LTS
### Current behavior
The `get_atoms()` and `get_structure()` methods defined in `pymatgen.io.ase.AseAtomsAdaptor` class both set PBC of output objects to `True` (i.e., periodic in all 3 directions) whe... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4121 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4121/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4121/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4121/events | https://github.com/materialsproject/pymatgen/pull/4121 | 2,595,611,095 | PR_kwDOACgets5_AyvM | 4,121 | Bugfix: Preserve PBC info in `AseAtomsAdaptor` | {
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"Thanks."
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The `get_atoms()` and `get_structure()` methods of the `pymatgen.io.ase.AseAtomsAdaptor` class now preserve PBC value of their input.
Intended to close #4120 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4122 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4122/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4122/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4122/events | https://github.com/materialsproject/pymatgen/pull/4122 | 2,596,307,690 | PR_kwDOACgets5_C8Eb | 4,122 | Make `Incar` keys case insensitive, fix init `Incar` from dict val processing for str/float/int | {
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"ping the true expert @esoteric-ephemera in case you have any comments (perhaps deserve a separate PR):\r\n\r\n- ~~Do we want to cast INCAR keys to upper case (to be consistent with VASP behaviour, but potentially breaking)~~\r\n- ~~Do we want to automatically filter duplicated INCAR keys (with a warning of course)... | 2024-10-18T03:28:51 | 2024-10-26T11:42:11 | 2024-10-21T19:05:18Z | CONTRIBUTOR | {
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} | ### Summary
- Fix `Incar.check_params` handling of case sensitivity, to fix #4119, also add unit tests
- [x] Issue warning if duplicated keys found when init `Incar`
### Make more operations (get/update/setdefault) in `Incar` case insensitive
- [x] Init `Incar` from dict (also the `from_dict` method) doesn't ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4123 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4123/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4123/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4123/events | https://github.com/materialsproject/pymatgen/pull/4123 | 2,597,908,305 | PR_kwDOACgets5_H4gt | 4,123 | fix: preserve site properties over cell transform | {
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"Thanks"
] | 2024-10-18T16:05:50 | 2024-10-21T20:51:12 | 2024-10-21T20:51:08Z | CONTRIBUTOR | {
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} | Make sure site properties are properly transferred from the original cell to the primitive or refined one.
## Summary
Major changes:
- fix 1: in `SpacegroupAnalyzer.get_refined_cell`, the flag `keep_site_properties` (used notably by `get_conventional_standard_structure`) would not behave as expected before b... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4124 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4124/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4124/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4124/events | https://github.com/materialsproject/pymatgen/pull/4124 | 2,597,915,949 | PR_kwDOACgets5_H6J7 | 4,124 | doc: make the test procedure explicit | {
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"I don't think we need to do both:\r\n- either we install pymatgen in editable mode to make the test files available (as test files are not included inside the distribution), OR\r\n- if for whatever reason you don't want to install in editable mode (test the distribution content for example), set `PMG_TEST_FILES_DI... | 2024-10-18T16:10:23 | 2024-10-19T16:06:45 | 2024-10-19T16:06:45Z | CONTRIBUTOR | {
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} | The most common usual workflow with `pytest` is just `pip install . && pytest`, but this doesn't apply to pymatgen because of the test files.
Since I had to dig (just a bit) in the sources to get `pytest` to run I figured I could help the next contributor by making it clear how to point to the files using an environme... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4125 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4125/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4125/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4125/events | https://github.com/materialsproject/pymatgen/issues/4125 | 2,599,513,999 | I_kwDOACgets6a8W-P | 4,125 | Add CUDA functionality to `parse_lammps_dumps` to allow for NVIDIA GPU support when analyzing large dump files. | {
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} | ### Feature Requested
I'd like to add GPU support for NVIDIA A100 GPUs for using `parse_lammps_dumps` from `pymatgen.io.lammps.outputs`.
### Proposed Solution
Use `cudf` instead of `pandas` to read and parse LAMMPS dump file.
### Relevant Information
Can increase efficiency of LAMMPS dump file reading ... | {
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"Dear @hongyi-zhao ,\r\n\r\nI think the different kpath scheme implementations have been made as a part of this publication: https://doi.org/10.1038/s41524-020-00383-7\r\n\r\nHistorically, MP used the scheme by 'setyawan_curtarolo first. That's why the prinitive and content cells are implemented like this. I assume... | 2024-10-20T04:06:06 | 2024-10-20T08:26:02 | 2024-10-20T08:26:02Z | CONTRIBUTOR | {
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} | Hello pymatgen developers,
I've been examining the documentation for [`get_conventional_standard_structure`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmetry.analyzer.SpacegroupAnalyzer.get_conventional_standard_structure) and [`HighSymmKpath`](https://pymatgen.org/pymatgen.symmetry.html#pymatgen.symmet... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4127 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4127/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4127/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4127/events | https://github.com/materialsproject/pymatgen/pull/4127 | 2,602,528,146 | PR_kwDOACgets5_UetE | 4,127 | Fix gaussian input parser, and add test | {
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"Thanks"
] | 2024-10-21T13:15:22 | 2024-10-22T00:42:37 | 2024-10-21T20:50:53Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Major changes:
- fix 1: In src/pymatgen/io/gaussian.py, within the from_str() method, the variable route_index is initially set to None and later assigned an integer representing the line number in the file. The code used `if route_index:` to check if route_index was set to a value other than None. How... | {
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"Strange, I cannot [recreate this CI failure](https://github.com/materialsproject/pymatgen/actions/runs/11454074042/job/31867593537?pr=4128) on Ubuntu 22.04, python 3.12.7 (still trying) and h5py==3.11.0:\r\n\r\nMight be https://stackoverflow.com/questions/49317927/errno-101-netcdf-hdf-error-when-opening-netcdf-fil... | 2024-10-22T03:52:11 | 2024-11-14T03:35:11 | 2024-11-13T17:49:45Z | CONTRIBUTOR | {
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} | ## Summary
- Organize optional dependencies in `pyproject.toml` to avoid duplicate
- Bump `sympy >= 1.3` to resolve https://github.com/materialsproject/pymatgen/pull/4116#issuecomment-2428308320
- Avoid `from numpy.testing import assert_allclose` in production code
---
- bump `monty` to use [the latest json ... | {
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"Thanks for reporting this, yes I could confirm this. \r\n\r\nMeanwhile it seems comments are not passed for some other modes as well, I would fix this.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/3ee17e2c346dea6e9248eb04c989e58880914650/src/pymatgen/io/vasp/inputs.py#L1594\r\n\r\nhttps://github.com/ma... | 2024-10-23T13:26:20 | 2024-10-25T21:25:23 | 2024-10-25T21:25:23Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.4
### Pymatgen version
Version: 2024.10.22
### Operating system version
_No response_
### Current behavior
Given the following example KPOINTS file
```
pymatgen with grid density = 10000 / number of atoms
0
Gamma
19 19 6
```
Upon reading it, I am getting kpt.comment value '... | {
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"@yantar92 Thanks again for reporting, am I missing anything here?\r\n\r\nUpdate: I changed my mind, I would change the methods to take a `comment` arg instead of hard coding the comments.",
"> Thanks again for reporting, am I missing anything here?\r\n\r\nLooks reasonable from a quick glance. Thanks!",
"No pro... | 2024-10-23T13:55:34 | 2024-10-27T03:15:53 | 2024-10-25T21:25:22Z | CONTRIBUTOR | {
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} | ### Summary
- Fix comment pass in `Kpoints` in auto/gamma/Monkhorst modes, to close #4130
- [x] Add unit test | {
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"Thanks for reporting this and your investigation. I could confirm this issue.\r\n\r\nOn top of the issue you discovered, there's another subtle bug in: https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/apps/borg/hive.py#L229-L239\r\n\r\nWhen `files` has no matc... | 2024-10-23T15:39:18 | 2024-11-12T18:01:08 | 2024-11-12T18:01:08Z | NONE | {
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} | ### Python version
Python 3.12.3
### Pymatgen version
2024.10.22
### Operating system version
Ubuntu 22.04 LTS
### Current behavior
assimilate method in apps.borg.hive.SimpleVaspToComputedEntryDrone is not raising the ValueError when checking if all the necessary files are present ("INCAR", "POTCAR", "CONTCAR", ... | {
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"@anyangml I hope this looks good to you, with this patch your example would terminate gracefully:\r\n```python\r\n/Users/yang/developer/pymatgen/src/pymatgen/io/cif.py:1318: UserWarning: No structure parsed for section 1 in CIF.\r\nlattice.volume=2.2009330203855426e-06 ų below threshold, double check your structu... | 2024-10-25T10:26:50 | 2024-11-14T03:30:59 | 2024-11-13T17:49:17Z | CONTRIBUTOR | {
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} | ### Summary
- Add min thickness check in `CifParser` to filter invalid structure which leads to infinite loop, to fix #4028
- [x] Add unit test
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} | ### Summary
- Minor clean up `neighbors.pyx` variable name, remnant from #4028, **I don't expect any functional changes**
- Use `unsigned int` (`npy_uint32`) over `int` for variables that we're certain would not be negative (counter, index when looping through "number of points/dimensions") | {
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"@yantar92 Hope this looks good to you\r\n\r\nThe issue with `incar_parameters.json` is not completely resolved as we cannot reply on manual upgrade of tags and values, a script is certainly needed but I don't have time to work on this at this moment.\r\n",
"> a script is certainly needed but I don't have time to... | 2024-10-26T02:25:03 | 2024-11-13T01:46:18 | 2024-11-12T18:08:52Z | CONTRIBUTOR | {
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} | ### Summary
- Manually update `incar_parameters.json`, to fix https://github.com/materialsproject/pymatgen/issues/4119#issuecomment-2431859839, need a more systematic script to update `incar_parameters.json` in the long run
- `check_params` use `proc_val`
- Remove some unnecessary casting in INCAR values as we're ... | {
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"Hi @mkhorton, This PR aims to enhance the performance of `AflowPrototypeMatcher` with a similar approach to `StructureMatcher.group_structures` (see https://github.com/materialsproject/pymatgen/pull/2490). It might be of interest to you. Could you please review this PR?\r\n",
"Merged. Thanks,"
] | 2024-10-26T03:01:55 | 2024-11-12T18:03:38 | 2024-11-12T18:03:30Z | CONTRIBUTOR | {
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The `AflowPrototypeMatcher` matches a structure against predefined AFLOW prototype structures using `StructureMatcher`. `StructureMatcher` requires preprocessing via lattice reduction and primitive-cell conversion. This commit optimizes performance by preprocessing AFLOW prototype structures during the in... | {
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} | ### Summary
- Show `FutureWarning` and `DeprecationWarning` for `pytest`, https://docs.pytest.org/en/stable/how-to/capture-warnings.html
- [x] Fix #4112
- [x] **For replacement of external APIs, double check the minimal version requirement** (scipy, phonopy and pandas)
- [ ] Are there alternatives for deprecated ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4139 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4139/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4139/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4139/events | https://github.com/materialsproject/pymatgen/issues/4139 | 2,615,897,934 | I_kwDOACgets6b629O | 4,139 | How to transform elastic constants after a change of basis with the help of pymatgen? | {
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"Based on the related documentation [here](https://docs.materialsproject.org/methodology/materials-methodology/elasticity#derived-elastic-properties) and [here](https://materialsproject.github.io/atomate2/user/codes/vasp.html#elastic-constant), I got the following solution based on the method [here](https://pymatge... | 2024-10-26T14:23:50 | 2024-11-05T14:11:46 | 2024-10-28T02:43:31Z | CONTRIBUTOR | {
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} | Hi there,
I have a question about transforming elastic constants when changing the basis/coordinate system. Does pymatgen provide functionality for this kind of transformation?
Specifically, I want to:
1. Take a 6x6 elastic constant matrix in Voigt notation
2. Apply a basis transformation
3. Get the transform... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4140 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4140/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4140/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4140/events | https://github.com/materialsproject/pymatgen/issues/4140 | 2,615,951,966 | I_kwDOACgets6b7EJe | 4,140 | Poscar.from_file throws a cryptic error for VASP5-like POSCARs when POTCAR does not contain all the present elements | {
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"Thanks for reporting again. Yes I agree this error message is not semantic, and I'm happy to have a closer look later.\r\n\r\n> Ideally, I'd like Poscar.from_file fall back to using POSCAR symbols if POTCAR does not specify them all and throw a warning.\r\n\r\nI believe this \"not failing back to POSCAR symbol\" b... | 2024-10-26T15:44:23 | 2024-11-13T17:48:18 | 2024-11-13T17:48:18Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.7
### Pymatgen version
Version: 2024.10.22
### Operating system version
_No response_
### Current behavior
Consider the following scenario:
1. We have a POSCAR file in VASP5 format with, say, C and Na sites
2. We have an obsolete POTCAR file only specifying C potentials
3. We tr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4141 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4141/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4141/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4141/events | https://github.com/materialsproject/pymatgen/pull/4141 | 2,616,444,673 | PR_kwDOACgets6AAhvz | 4,141 | VaspDoc.get_incar_tags: Use Mediawiki API | {
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"Thanks!"
] | 2024-10-27T09:24:17 | 2024-10-29T00:06:01 | 2024-10-29T00:05:56Z | CONTRIBUTOR | {
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} | * src/pymatgen/io/vasp/help.py (VaspDoc.get_incar_tags): Use Mediawiki API instead of parsing the HTML source directly. The old approach is not stable against changes in the tag list because of the way URLs are constructed. pagefrom= parameters start from certain tag, which is not guaranteed to provide the complete t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4142 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4142/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4142/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4142/events | https://github.com/materialsproject/pymatgen/pull/4142 | 2,616,898,493 | PR_kwDOACgets6ABkYE | 4,142 | Add a coerce formal charges method to openff code | {
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"Please add a unittest for the new method. Thanks."
] | 2024-10-27T21:55:45 | 2024-11-16T16:42:52 | CONTRIBUTOR | {
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} | ## Summary
Major changes:
Add a `coerce_formal_charges` method to the `pymatgen.io.openff` code, allowing molecules with formal charges to be more accurately parsed.
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new f... | {
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"@yantar92 This situation seems a bit trickier than I thought (I don't have much experience handling an incompatible POTCAR). I'm still finding a cleaner way to handle this.\r\n\r\n`check_for_potcar` doesn't really check the content (elements matching) of a POTCAR, but more likely: \r\n1. check existence (by callin... | 2024-10-28T03:50:41 | 2024-11-14T03:30:46 | 2024-11-13T17:48:17Z | CONTRIBUTOR | {
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} | ### Summary
- The glob logic of POTCAR matching might need some attention, as files other than `POTCAR` might take higher priority than `POTCAR`
- Suppress a lot of expected warning in VASP.inputs tests, to avoid warning pollution
### For element mismatch in POTCAR and POSCAR, to fix #4140:
- If is able to ove... | {
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"Perhaps just copy the source code (and include the BSD license) as they're used only once. The original implementation just use `numpy`:\r\n\r\n\r\nhttps://github.com/scipy/scipy/blob/ea916c6f7f487bd53e98de082649d542cc6106ed/scipy/_lib/_finite_differences.py#L1-L144"
] | 2024-10-28T11:48:51 | 2024-10-29T08:10:38 | 2024-10-29T05:01:42Z | CONTRIBUTOR | {
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} | The following two code pieces use deprecated `scipy.misc` API, but `scipy` doesn't provide replacement.
These API should have been removed ([1.12.0 was out in Jan 2024](https://pypi.org/project/scipy/#history)) but perhaps they postponed the removal?
```python
import scipy.misc
print(scipy.__version__) #... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4145 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4145/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4145/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4145/events | https://github.com/materialsproject/pymatgen/pull/4145 | 2,618,370,800 | PR_kwDOACgets6AGTrG | 4,145 | Fixed execution of packmol in relative path. | {
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"Thanks."
] | 2024-10-28T13:04:28 | 2024-10-29T00:04:07 | 2024-10-29T00:04:03Z | CONTRIBUTOR | {
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Major changes:
- fix 1: One could not do packmol_input_set.run("randomdirectory"). Code would fail.
This PR fixes this small issue. Added (actually adapted) a unit test to make sure it continues to work. | {
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"Here is a test with `memory_profiler`:\r\n\r\n```python\r\nfrom memory_profiler import profile\r\nfrom monty.serialization import loadfn\r\n\r\n@profile\r\ndef test():\r\n for _ in range(100):\r\n loadfn(\"mp-1000005.json.gz\")\r\n\r\nif __name__ == \"__main__\":\r\n test()\r\n```\r\n\r\nDoing one ite... | 2024-10-28T18:22:11 | 2024-10-28T22:48:58 | 2024-10-28T22:48:31Z | NONE | {
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} | ### Python version
Python 3.12.4
### Pymatgen version
2024.10.27
### Operating system version
Linux
### Current behavior
I'm working with Professor Andrew Rosen @Andrew-S-Rosen. We found what appears to be a memory leak associated with `Chgcar.from_dict`. Even when deleting the object from memory w... | {
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} | Bumps [rexml](https://github.com/ruby/rexml) from 3.3.6 to 3.3.9.
<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 3.3.9 - 2024-10-24</h2>
<h3>Improvements</h3>
<ul>
<li>Improved performance.
<ul>
<li><a... | {
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- [ ] update documentation
- [ ] completely solve the translation question (i.e., figuring out the direction and origin)
- [ ] add a test case where this plays a role | {
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| Metric | Average | Median | 90th percentile |
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| Time to first response | 11:32:34 | 2:26:24 | 1 day, 7:53:28 |
| Time to close | 2 days, 14:34:21 | 2 days, 4:19:33 | 5 days, 8:02:11 |
| Time to answer | None | None | None |
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"Merged. Thanks."
] | 2024-11-01T22:09:45 | 2024-12-23T16:38:19 | 2024-11-12T18:04:27Z | CONTRIBUTOR | {
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} | # New flag for `AutoOxiStateDecorationTransformation`
The situation we have in mind is `AutoOxiStateDecorationTransformation` -> `OrderDisorderedStructureTransformation` pipeline.
The `OrderDisorderedStructureTransformation` expects oxidation numbers to help rank the structure guesses. However, if you have metal... | {
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- Reverse breaking `analysis.local_env` `default_op_params/cn_opt_params` rename, reported in https://github.com/materialsproject/pymatgen-analysis-defects/pull/206 and https://github.com/materialsproject/atomate2/pull/1030
- [x] Add unit test
- Minor format tweak
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updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.9...v0.7.2)
- [github.com/pre-commit/mirrors-mypy: v1.12.0 → v1.13.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.12.0...v1.13.0)
- [github.com/adamchainz/bla... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4154 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4154/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4154/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4154/events | https://github.com/materialsproject/pymatgen/pull/4154 | 2,635,374,676 | PR_kwDOACgets6A7QT7 | 4,154 | Fix `borg.hive.SimpleVaspToComputedEntryDrone.assimilate` ValueError when core file missing | {
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} | ### Summary
- Fix `borg.hive.SimpleVaspToComputedEntryDrone.assimilate` ValueError when core file missing, to fix #4132
- Add unit test
- Improve type annotation
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https://api.github.com/repos/materialsproject/pymatgen/issues/4155 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4155/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4155/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4155/events | https://github.com/materialsproject/pymatgen/pull/4155 | 2,635,884,618 | PR_kwDOACgets6A83rv | 4,155 | Add informative error message to `SymmetryUndeterminedError` | {
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"Appreciate the improvement, thanks @kavanase !",
"Sorry for the delay in merging, auto-merge was broken and I hadn't realised. Should be fixed now."
] | 2024-11-05T16:07:50 | 2024-11-17T23:25:00 | 2024-11-17T23:24:47Z | CONTRIBUTOR | {
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} | After pulling my hair out for a little while, trying to figure out why I was getting `SymmetryUndeterminedError`s when trying to initialise `SpacegroupAnalyzer` with a particular structure (which currently don't come with any message), I realised that `spglib.get_error_message()` can be called to get an error message f... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4158 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4158/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4158/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4158/events | https://github.com/materialsproject/pymatgen/issues/4158 | 2,643,731,180 | I_kwDOACgets6dlCLs | 4,158 | tests use equality to compare floating point numbers | {
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"Thanks for reporting, would fix this."
] | 2024-11-08T11:20:50 | 2025-01-24T15:21:29 | 2025-01-24T15:21:28Z | CONTRIBUTOR | {
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} | Floating point numbers (angles) are compared in transformation tests at
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/tests/transformations/test_advanced_transformations.py#L840
Using equality to compare floating point numbers inevitably fails
e.g. https://buildd.debi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4159 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4159/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4159/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4159/events | https://github.com/materialsproject/pymatgen/pull/4159 | 2,645,529,341 | PR_kwDOACgets6BYpAL | 4,159 | Avoid using full equality (`==`) to compare float, avoid `assert_array_equal` compare float array | {
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} | ### Summary
- Avoid using full equality `==` to compare float, to fix #4158
- Avoid [`assert_array_equal` on int array](https://numpy.org/doc/stable/reference/generated/numpy.testing.assert_array_equal.html):
> Assert fails with numerical imprecision with floats:
> Use [assert_allclose](https://numpy.org/... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4160 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4160/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4160/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4160/events | https://github.com/materialsproject/pymatgen/pull/4160 | 2,645,870,841 | PR_kwDOACgets6BZKnC | 4,160 | Clean up `io.vasp.outputs.Outcar` docstring | {
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} | ### Clean up `io.vasp.outputs.Outcar` docstring/comment
- Greatly enhance type annotation for parsers in `Outcar` with more specific types, clarify docstring: `Renders accessible from self.data` (the internal `self.data` dictionary) vs `Renders accessible from attributes` (instance attributes)
- Other docstring/com... | {
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"Hi @drew-parsons thanks for reporting this and the analysis, sorry for the trouble caused.\r\n\r\nWe explicitly cast `int` to `int64` in a previous migration to NumPy 2.x #3992, as NumPy 2.x changed the default NumPy/Cython integer on 64-bit Windows platform to `int64` (was previously `int32`). Also `np.intp` was ... | 2024-11-09T17:17:11 | 2024-12-11T02:03:15 | 2024-12-11T02:03:15Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.7
### Pymatgen version
2024.10.29
### Operating system version
Debian unstable
### Current behavior
pymatgen coordination geometry sets an explicit `int64` for separation indices at
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pyma... | {
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} | Using `float` as `dict` keys can be prone to precision issues (especially when `float` is not rounded), a few functions operate on such `dict[float, Any]` (could be more not annotated):
### `core.bonds.obtain_all_bond_lengths`
https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2... | {
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} | ### Summary
- [ ] Should `formula_double_format` return string instead of float?
- Clarify `util.string.formula_double_format` return type as `Literal[""] | float`
- Add types for `util.string`
- **Bug fix**: `int` would not round to nearest int (but truncate decimal part): https://github.com/materialsproject/pym... | {
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- Replace some hard-coded `np.allclose/isclose`
- Replace hard-coded `abs(a-b)<= tol` with`isclose` for **complex expressions**, **rationale**:
- better readability as `isclose` is more declarative, especially for complex expressions like `if abs(p1 - pos2[idx]) > tolerance[idx] and abs(p1 - pos2[... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4165 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4165/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4165/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4165/events | https://github.com/materialsproject/pymatgen/issues/4165 | 2,648,294,170 | I_kwDOACgets6d2cMa | 4,165 | [BUG] Missing `()` in `electronic_structure.boltztrap.BoltztrapAnalyzer.get_extreme.is_isotropic` | {
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} | Seemingly missing `()` in 744c7db9780a301e2f5fcdf1948a1b7a4d36a404: https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/electronic_structure/boltztrap.py#L1457-L1473
```diff
- and (abs(st[2] - st[0]) / st[2] <= isotropy_tolerance)
+ and (abs((st[2] - st[0]) / st... | {
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"@naik-aakash Could you kindly check this (after Thursday ;))? Thanks a lot. ",
"Hi @DanielYang59 , thanks for pointing this out. Indeed there seems to have been an error with comparison logic here. Using np.any should be preferable here as you suggested I think.\r\n\r\nI assume you have already started working o... | 2024-11-11T06:41:47 | 2024-11-18T13:32:59 | 2024-11-18T13:32:59Z | CONTRIBUTOR | {
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} | The following method: https://github.com/materialsproject/pymatgen/blob/bd9fba9ec62437b5b62fbd0b2c2c723216cc5a2c/src/pymatgen/io/lobster/outputs.py#L1694-L1737
Used a pattern like `np.array().all() > tolerance` with the intention to perform element-wise value comparison, however [this seems to be misused as `all()`]... | {
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"And I also have a question, why we need run this\r\n\r\n```python\r\nelif len(dictio[elt][0]) > 1:\r\n```\r\nfor example code, the len(\"dxy\") = 3, what's meaning of this?"
] | 2024-11-12T07:35:01 | 2024-11-24T12:22:51 | NONE | {
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} | **Fix**: Ensure BSPlotterProjected._Orbitals_SumOrbitals() checks if sum_morbs is not None, as a NoneType object cannot be iterated.
## Summary
### Major changes:
- Fixed the BSPlotterProjected._Orbitals_SumOrbitals() method to handle cases where sum_morbs is None.
## Description
When running the following c... | {
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} | ### Summary
- I don't think we need `PMG_VASP_PSP_DIR` in editable mode
- [`matplotlib` test use non-interactive `agg` backend](https://matplotlib.org/stable/users/explain/figure/backends.html), as the [tk install for github windows runner seems pretty flaky](https://github.com/matplotlib/matplotlib/issues/29119#is... | {
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"Merged. Thanks. One option is to break this out as an add-on for separate management."
] | 2024-11-13T00:11:13 | 2024-11-13T02:11:34 | 2024-11-13T02:05:11Z | MEMBER | {
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} | this PR fixes several bugs encountered trying to use the `cp2k` modules in `pymatgen` which don't seem to have seen active development over the last 4 years (so some errors from upstream breaking changes expected)
## Key Changes
1. **Default Verbosity**: change `Keyword` + `Section` `verbose` default to `False` t... | {
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} | `DftSet` in `src/pymatgen/io/cp2k/sets.py` gets a new `element_defaults: dict[str, dict[str, Any]] | None = None` keyword (format is `{element: {key: value}}`). includes new tests for this feature
`element_defaults` allows specifying e.g. initial magmoms/spins via the "magnetization" key for each element
this PR ... | {
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"Hi @yurivict thanks for asking.\r\n\r\nLooks like you installed `pymatgen` in non-editable mode, **`pymatgen` doesn't include test files as package data**, so you have to get the test files (usually by cloning the repo), and use one of the two ways to make test files available:\r\n- Install `pymatgen` in editable ... | 2024-11-14T22:17:26 | 2025-01-24T07:36:23 | 2025-01-24T07:36:21Z | NONE | {
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} | ### Python version
Python-3.11
### Pymatgen version
2024.11.13
### Operating system version
FreeBSD 14.1
### Current behavior
```
========================================================================================== ERRORS ======================================================================... | {
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"@hongyi-zhao , this is more of an atomate2 question, but the critical thing here is that the line `flow = update_user_incar_settings(flow, incar_settings)` is not needed. The `MPGGADoubleRelaxMaker` is constructed to use MP's settings by default\r\n\r\nIf you want to use the magmoms from the MP structure as the st... | 2024-11-15T00:30:18 | 2024-12-24T00:40:02 | 2024-12-24T00:40:01Z | CONTRIBUTOR | {
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```python
from mp_api.client import MPRester
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from atomate2.vasp.flows.mp import MPGGADoubleRelaxMaker
from atomate2.vasp.powerups i... | {
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} | - [I believe this would not be breaking] The default value as `False` over `None` might be more conventional (we [should not use truthy to check `None`](https://docs.quantifiedcode.com/python-anti-patterns/readability/comparison_to_none.html)):
```diff
# When the `_is_named_isotope` doesn't have `_is_named_isotop... | {
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"Thanks! Currently `codespell` doesn't seem to support block/file level support with pattern, I would update once they do."
] | 2024-11-15T13:08:39 | 2024-11-16T13:40:42 | 2024-11-16T13:37:02Z | CONTRIBUTOR | {
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} | ## Cleanup `codespell` ignore patterns
Currently a lot of global ignore patterns are very specific to a certain module (or even one line), there's no good reason to ignore a pattern globally for such cases. Admittedly it will be a balance between convenience (no one want to insert a `# codespell:ignore` tag every li... | {
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"Thanks @esoteric-ephemera, appreciate the context with the matsci.org thread too",
"Thanks."
] | 2024-11-15T20:31:54 | 2024-11-18T18:15:42 | 2024-11-18T13:35:12Z | CONTRIBUTOR | {
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} | The XAS spectrum class used to not throw a `ValueError` when more than 5% of the user-input intensities are non-positive (cverified this was still the behavior as of v2020.4.29). More, the warning that is thrown is misleading, as it suggests that the majority of intensities are non-positive.
This change in behavior... | {
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"@ansobolev Does this work for your things?",
"@tpurcell90 This seems to work for the defect workflow, thanks; however, as aims accepts anything in the `species` line (it's just a label), I would rather use something like `site.label` for site description in `geometry.in`. This will allow more precise accounting ... | 2024-11-15T20:59:32 | 2024-12-11T20:31:24 | 2024-12-11T14:46:30Z | CONTRIBUTOR | {
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} | FHI-aims does not read spin from the species and that causes issues with magnetic calculations
## Summary
Major changes:
- fix 1: Don't use species_string for FHI-aims
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests ... | {
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"Hey Zhao,\r\nCould you elaborate a little bit why exactly this warning is inappropriate? ",
"I mean, this warning should be triggered by something like [`update_user_potcar_functional`](https://materialsproject.github.io/atomate2/reference/atomate2.vasp.powerups.update_user_potcar_functional.html#update-user-pot... | 2024-11-17T02:11:24 | 2024-11-19T07:05:02 | 2024-11-19T07:05:02Z | CONTRIBUTOR | {
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```shell
In [7]: flow = update_user_incar_settings(flow, { 'ALGO': 'Normal', 'EDIFF': 1e-06, 'ENCUT':700})
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/pymatgen/io/vasp/sets.py:288: BadInputSetWarning: Overriding th... | {
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"I agree isotopes shouldn't appear as part of default behavior.",
"That was an oversight on my part, thanks for the fix! Also agree that enumerating over elements shouldn't list isotopes. Maybe adding a method to `Element` to show people which isotopes are available would be useful tho?",
"> That was an oversig... | 2024-11-17T06:14:48 | 2025-01-10T02:27:51 | 2025-01-09T20:38:24Z | CONTRIBUTOR | {
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} | ### Summary
- Skip isotopes when iterating through `core.Element`, to fix #4178, rationale:
- I might expect looping through `Element` to behave similarly to looping through the periodic table, i.e. isotopes should not sneak in here, do you like this idea @esoteric-ephemera?
- Implementation based on https://d... | {
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"@naik-aakash could you add a few more tests here next week (not today) and make sure it is working as intended? ",
"> @naik-aakash could you add a few more tests here next week (not today) and make sure it is working as intended?\r\n\r\nSure can do this 😄 ",
"Forgive me, I'm going slightly off-topic again (Ha... | 2024-11-17T11:42:37 | 2024-11-18T13:33:03 | 2024-11-18T13:32:58Z | CONTRIBUTOR | {
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} | ## Closes #4166
## Changes
Based on the suggestions form @QuantumChemist ( https://github.com/materialsproject/pymatgen/issues/4166#issuecomment-2480508677) and @DanielYang59 (https://github.com/materialsproject/pymatgen/issues/4166#issuecomment-2480925279) , the code has been fixed to correctly evaluate whethe... | {
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"Thanks."
] | 2024-11-18T09:31:09 | 2024-11-18T13:32:23 | 2024-11-18T13:32:20Z | CONTRIBUTOR | {
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} | ## Summary
`NUPDOWN` key in Incar can be set to floating point values in VASP (see https://gitlab.com/ase/ase/-/merge_requests/2580).
However, it is current treated as an int in `Incar.proc_val`.
This PR treats `NUPDOWN` as a float instead.
- [x] Google format doc strings added. Check with `ruff`.
- [x] Ty... | {
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"Thanks. Merged."
] | 2024-11-18T20:07:06 | 2024-11-18T20:46:36 | 2024-11-18T20:41:04Z | CONTRIBUTOR | {
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https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/analysis/magnetism/analyzer.py#L657
The update method will overwrite the values in the keys of the 'transformation_kwargs' coming from the input, e.g. timeout cannot be chang... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4185 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4185/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4185/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4185/events | https://github.com/materialsproject/pymatgen/issues/4185 | 2,675,649,523 | I_kwDOACgets6feyvz | 4,185 | Timeout in MagneticStructureEnumerator (and EnumlibAdaptor) does not work | {
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} | ### Python version
3.11.5
### Pymatgen version
2024.11.13
### Operating system version
_No response_
### Current behavior
`enum = MagneticStructureEnumerator(structure)` should stop after 5 minutes by default,
but it does not. Passing a different timeout does not change anything. I'm now making su... | {
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"I should add that I am using an older Pymatgen and older CP2K but this is the exact same error with newest Pymatgen and newest CP2K data directory."
] | 2024-11-20T15:48:22 | 2024-11-20T15:49:42 | NONE | {
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} | ### Python version
3.12
### Pymatgen version
v2024.9.17.1
### Operating system version
MacOSX
### Current behavior
Git clone cp2k v2022 for the data directory
Performed pmg config --cp2k /path/to/cp2k/data /path/to/pmg/cp2kdata
Doing any compounds mixed with In, O as species gives this error (also with other... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4187 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4187/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4187/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4187/events | https://github.com/materialsproject/pymatgen/pull/4187 | 2,680,993,344 | PR_kwDOACgets6Cut2P | 4,187 | Addition of "valences" property to ElementBase and Species for mixed-valence ions | {
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"closing this until I make those fixes"
] | 2024-11-21T21:23:22 | 2024-12-12T22:47:18 | 2024-11-26T22:47:19Z | CONTRIBUTOR | {
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} | ## Summary
Note: This code change is **no longer required for #4078** and the `valences` property does **not** return `(idx, ne)` for every valence subshell but only **every partially filled valence subshell** (unless all subshells are filled, which causes only the last subshell to be returned). I don't see a use fo... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4188 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4188/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4188/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4188/events | https://github.com/materialsproject/pymatgen/issues/4188 | 2,681,078,401 | I_kwDOACgets6fzgKB | 4,188 | Poscar.get_str() cartesian vs direct coords | {
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"Erm, I am not sure what you mean. I don't think you can use 0, 0, 0 as the example. Those coordinates are the same whether in direct or cartesian coords by definition. Also, your code is confusing because your comment says \"Position of the atom in Cartesian coordinates\" and yet you set `coords_are_cartesian` to ... | 2024-11-21T21:46:19 | 2025-03-13T19:32:40 | 2025-03-13T19:32:39Z | NONE | {
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} | First of all, thank you for this incredible library!
### Python version
Python 3.12.7
### Pymatgen version
2024.11.13
### Operating system version
Pop!_OS 22.04 LTS
### Current behavior
**Steps to reproduce**
- define structure in cartesian coords
- create Poscar object from structure
- wirt... | {
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"@mkhorton , are you OK with merging this change?\r\n\r\n@shyuep I am not sure why some of the optional checks are not running, I started the tests a couple of days ago.\r\n\r\nLooks like all changes are restricted to the io/jdftx module, so not much likelihood of things breaking",
"Thanks for your patience with ... | 2024-11-21T23:20:36 | 2025-01-24T17:48:18 | 2025-01-24T00:21:07Z | CONTRIBUTOR | {
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} | ## Summary
Major changes:
- feature 1: `inputs.py` module containing `JDFTXInfile` class to give pythonic representation to the inputs for a JDFTx calculation
- feature 2: "helper" module `generic_tags.py` holding "Tag" objects (`AbstractTag` and inheritors of `AbstractTag`) to represent the different data struc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4190 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4190/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4190/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4190/events | https://github.com/materialsproject/pymatgen/pull/4190 | 2,681,419,754 | PR_kwDOACgets6CvqIx | 4,190 | Outputs - JDFTx IO Module | {
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"@mkhorton , are you OK with merging this change?\r\n\r\n@shyuep I am not sure why some of the optional checks are not running, I started the tests a couple of days ago.\r\n\r\nLooks like all changes are restricted to the io/jdftx module, so not much likelihood of things breaking",
"I’ll try and review this later... | 2024-11-22T00:34:16 | 2025-01-24T17:48:09 | 2025-01-24T15:05:39Z | CONTRIBUTOR | {
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Major changes:
-feature 0: hierarchy of class objects used to represent the data contained within a JDFTx out file. Hierarchy here is used to represent where each class object is stored - none of these classes inherit the class below it. Classes stored within a list in its parent are indicated by "[i]"... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4192 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4192/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4192/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4192/events | https://github.com/materialsproject/pymatgen/pull/4192 | 2,685,285,242 | PR_kwDOACgets6C5MEq | 4,192 | Clean up `util.num.make_symmetric_matrix_from_upper_tri` and `util.io_util.micro_pyawk`, fix new `ruff` errors | {
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} | ### Simplify/clarify `util.num.make_symmetric_matrix_from_upper_tri` and add tests
> [!CAUTION]
> `make_symmetric_matrix_from_upper_tri` now raise `ValueError` for non 3x3 array
I believe `utils.num.make_symmetric_matrix_from_upper_tri` is designed to [work on 3x3 matrix alone](https://github.com/materialsprojec... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4193 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4193/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4193/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4193/events | https://github.com/materialsproject/pymatgen/pull/4193 | 2,685,388,332 | PR_kwDOACgets6C5WmV | 4,193 | Remove unnecesary isotope conversion in `core.periodic_table.get_el_sp` | {
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"@esoteric-ephemera Do we have further concerns on this change here? If not I might mark as ready?",
"If you mark as ready I'm happy to merge @DanielYang59, thank you!",
"Good to go from my side, not sure these lines are needed anymore. Thanks for checking!",
"No problem guys, happy holiday :)"
] | 2024-11-23T05:20:49 | 2025-01-10T02:27:23 | 2025-01-09T20:34:32Z | CONTRIBUTOR | {
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} | To close #4171.
This isotope conversion may not be working as we expected as the `name` of an isotope `Element/Species` is the "isotope name" (e.g. `"D"` for `Element.D` and `Species("D")` instead of `"H"`):
https://github.com/materialsproject/pymatgen/blob/31f1e1fb8cc1bb517d59ea8e484965bb641c42a0/src/pymatgen/core... | {
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"@drew-parsons I believe this resolved the index dtype issue in 32-bit systems (tested on Debian 12 32-bit with NumPy 1.26.4 and Python 3.11), let me know if you notice any issues :)",
"Thanks. This patch seems to be working well, applied to debian build 2024.10.29+dfsg1-4\t\r\nhttps://buildd.debian.org/status/p... | 2024-11-24T10:39:52 | 2024-12-11T02:29:36 | 2024-12-11T02:03:14Z | CONTRIBUTOR | {
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} | ### Summary
- Fix NumPy array indexing in 32-bit system, to close #4161
> https://numpy.org/doc/1.21/reference/arrays.scalars.html
I may use `intp` instead of `uintp` as I'm not 100% sure if the indexes could be negative or not in the code design.
### Run unit tests locally as GitHub doesn't provide 32-... | {
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"@Andrew-S-Rosen Is currently implementation looking good to you? :)",
"Due to time commitments, I can just say that I trust you. 👍 Happy to report if something comes up. ",
"Thanks for saying that, I tested on multiple VASP versions (included in unit test) and didn't find any issue for now, do let me know if ... | 2024-11-25T03:27:47 | 2024-12-11T02:29:56 | 2024-12-11T02:01:55Z | CONTRIBUTOR | {
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} | ### Summary
- Read NBANDS in `io.vasp.outputs.Outcar` init, to close #3843
- Add overwriting tests and test file (355 KB), I didn't find any reusable file (`zgrep 'I found NBANDS' OUTCAR*` returns nothing)
#### VASP version stability
- 5.2.11 (unit test)
- 5.4.4 (unit test)
- 6.3.0 (unit test)
- 6.3.2 (unit ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4196 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4196/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4196/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4196/events | https://github.com/materialsproject/pymatgen/pull/4196 | 2,689,508,698 | PR_kwDOACgets6C_OFX | 4,196 | Change `get` default from empty list (`[]`) to `False` when used as `bool` or condition check for `Outcar` parsing methods | {
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} | ### Summary
- Change `get` default from empty list (`[]`) to `False` when used as `bool` or condition check for `Outcar` parsing methods
This is slightly more readable as `bool([])` is `False`, also this would not be breaking as the evaluation result is not assigned (condition check only)
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https://api.github.com/repos/materialsproject/pymatgen/issues/4197 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4197/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4197/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4197/events | https://github.com/materialsproject/pymatgen/issues/4197 | 2,689,903,538 | I_kwDOACgets6gVKuy | 4,197 | Structure.merge_sites fails when selective_dynamics is property present | {
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"Thanks for reporting and for including a code snippet again, I would take care of this"
] | 2024-11-25T09:13:34 | 2025-01-09T20:35:17 | 2025-01-09T20:35:17Z | CONTRIBUTOR | {
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} | ### Python version
Python 3.12.7
### Pymatgen version
Version: 2024.10.22
### Operating system version
_No response_
### Current behavior
Error is thrown when I try to run merge_sites.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/yantar92/.venv/lib/python3.12/site-p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4198 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4198/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4198/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4198/events | https://github.com/materialsproject/pymatgen/pull/4198 | 2,690,320,806 | PR_kwDOACgets6DBRvD | 4,198 | Fix array comparison in `core.Structure.merge_sites`, also allow `int` property to be merged instead of `float` alone, `mode` only allow full name | {
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} | ### Summary
- Fix array comparison in `core.Structure.merge_sites`, to fix #4197
- [x] Test for property reset warning is missing
- [x] Add test for `is_np_dict_equal ` for custom `__eq__`
- Add check for illegal `mode` initials (not starting with `a/s/d`, currently don't check full name yet)
---
> [!WARNI... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4199 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4199/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4199/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4199/events | https://github.com/materialsproject/pymatgen/pull/4199 | 2,692,885,273 | PR_kwDOACgets6DHyo7 | 4,199 | Fix `py.typed` usage for namespace packages | {
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"Still I would prefer closing this and let maintainers take over, esp. around the migration from namespace system to entry points."
] | 2024-11-26T02:54:26 | 2024-12-01T07:50:34 | 2024-12-01T07:50:05Z | CONTRIBUTOR | {
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} | - [ ] [Fix `py.typed` marker file placement](https://typing.readthedocs.io/en/latest/spec/distributing.html#packaging-typed-libraries) to close #3413:
> For namespace packages (see [PEP 420](https://peps.python.org/pep-0420/)), the py.typed file should be in the submodules of the namespace, to avoid conflicts and ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4200 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4200/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4200/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4200/events | https://github.com/materialsproject/pymatgen/issues/4200 | 2,695,618,108 | I_kwDOACgets6gq948 | 4,200 | Parsing Failure of vasprun.xml from MD Simulations Using MLFF | {
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} | ### Python version
Python 3.10.14
### Pymatgen version
Version: 2024.11.13
### Operating system version
Red Hat Enterprise Linux Ver 8.6
### Current behavior
When trying to parse the `vasprun.xml` file generated from calculations using MLFF with the `Vasprun` class, an `IndexError: list index out of range` is ra... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4201 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4201/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4201/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4201/events | https://github.com/materialsproject/pymatgen/pull/4201 | 2,700,801,454 | PR_kwDOACgets6DbBlq | 4,201 | Fix VASP/ABINIT link in main `README.md` | {
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"Seems the following is now recommended https://github.com/gaurav-nelson/github-action-markdown-link-check: \r\n\r\n> 🚨 Update (May 2024)\r\n\r\n>I have developed a new tool called [Linkspector](https://github.com/UmbrellaDocs/linkspector), which offers improved functionality and reduced false positives. I recomme... | 2024-11-28T05:09:21 | 2024-12-11T02:29:42 | 2024-12-11T02:02:11Z | CONTRIBUTOR | {
"total": 0,
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} | ### Summary
- Fix VASP/ABINIT hyperlink in main `README.md`
Can someone help me double check to **make sure this is not my network issue**?
```diff
# VASP
- https://cms.mpi.univie.ac.at/vasp
+ https://www.vasp.at/
# ABINIT
- https://abinit.org
+ https://abinit.github.io/abinit_web/
```
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4202 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4202/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4202/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4202/events | https://github.com/materialsproject/pymatgen/issues/4202 | 2,701,218,120 | I_kwDOACgets6hAVFI | 4,202 | [Dev/Test] Migrate `PymatgenTest` from `unittest.TestCase` to `pytest` | {
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} | Current [`pytest` framework isn't fully compatible with `unittest.TestCase`](https://docs.pytest.org/en/stable/how-to/unittest.html#pytest-features-in-unittest-testcase-subclasses), we should consider migrate to `pytest` framework:
> The following pytest features do not work, and probably never will due to different d... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4203 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4203/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4203/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4203/events | https://github.com/materialsproject/pymatgen/pull/4203 | 2,701,820,296 | PR_kwDOACgets6DdZdG | 4,203 | Remove redundant `total_ordering` decorator usage | {
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} | ### Summary
- Remove redundant `total_ordering` decorator usage, as `total_ordering` is already applied on superclasses and child classes did not redefine any rich comparison operations.
- Clean up comment of equality definition of `core.IStructure`
- Minor import clean up (avoid `from io import StringIO` when it... | {
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"Admittedly the behaviour is surprising, but I believe this is expected, I had the same question in https://github.com/materialsproject/pymatgen/pull/3895\r\n\r\nThis comparison operation is not defined to really \"compare\" `Composition` (it might not make chemical sense to order compositions in the first place), ... | 2024-11-28T12:19:45 | 2024-11-28T15:48:21 | NONE | {
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} | ### Python version
Python 3.9
### Pymatgen version
2024.3.1
### Operating system version
macos
### Current behavior
<img width="455" alt="image" src="https://github.com/user-attachments/assets/cbf2053e-5d93-4157-abc9-9124fc4ee1ba">
### Expected Behavior
The second one should output False.
### Minimal exampl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4205 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4205/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4205/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4205/events | https://github.com/materialsproject/pymatgen/pull/4205 | 2,704,006,459 | PR_kwDOACgets6Dh8vq | 4,205 | Fix `assert_str_content_equal`, add tests for testing utils | {
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} | ### Summary
- Fix `assert_str_content_equal` not raising `AssertionError`
- Add unit tests for `util.testing` as it's intended for public usage (and [quite some external code use `PymatgenTest`](https://github.com/search?q=%22%28PymatgenTest%29%3A%22&type=code))
- More human-readable error messages for assert met... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/4206 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/4206/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/4206/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/4206/events | https://github.com/materialsproject/pymatgen/issues/4206 | 2,704,244,274 | I_kwDOACgets6hL34y | 4,206 | `test_str` and `test_mul` for `TestStructureGraph` of `analysis.graphs` are failing | {
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} | After fixing `assert_str_content_equal` implementations in #4205, noticed the following tests for `TestStructureGraph` of `analysis.graphs` are failing.
cc @mkhorton
### `pytest tests/analysis/test_graphs.py::TestStructureGraph::test_str`
```
E AssertionError: Strings are not equal (whitespaces ignored):
E... | {
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