Pull from materialsproject [WIP] by mmbliss · Pull Request #10 · molmd/pymatgen

mmbliss · 2024-08-27T16:51:37Z

Summary

Pull updates from materialsproject master to make this branch compatible with python 3.9. Only take commits up until version 2022.1.20 (January 20, 2022).

TODO (if any)

Need to test this branch to ensure it functions and can be installed on python 3.9 (and possible 3.8 and 3.10)

Checklist

Before a pull request can be merged, the following items must be checked:

Code is in the standard Python style. The easiest way to handle this
is to run the following in the correct sequence on your local machine. Start with running
black on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
pycodestyle, followed by
flake8.
Docstrings have been added in the Google docstring format.
Run pydocstyle on your code.
Type annotations are highly encouraged. Run mypy to type check your code.
Tests have been added for any new functionality or bug fixes.
All linting and tests pass.

Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply cp pre-commit .git/hooks and a check will be run prior to allowing commits.

* pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.12 → v0.12.2](astral-sh/ruff-pre-commit@v0.11.12...v0.12.2) - [github.com/pre-commit/mirrors-mypy: v1.16.0 → v1.16.1](pre-commit/mirrors-mypy@v1.16.0...v1.16.1) - [github.com/MarcoGorelli/cython-lint: v0.16.6 → v0.16.7](MarcoGorelli/cython-lint@v0.16.6...v0.16.7) - [github.com/RobertCraigie/pyright-python: v1.1.401 → v1.1.402](RobertCraigie/pyright-python@v1.1.401...v1.1.402) * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…me` (#4454) * remove unit in docstring for density of solid * add unit hatree to "Atomic orbitals" * fix unit for molar volume * maybe recover unit in docstring, need discussion * MN m^-2 -> MPa for Brinell and Vickers hardness

* clean up tests * remove trailing line sensitivity * simplify temp file * lint fix * add test * fix filename Co-authored-by: Aakash Ashok Naik <91958822+naik-aakash@users.noreply.github.com> Signed-off-by: Haoyu (Daniel) YANG 杨浩宇 <yanghaoyu97@outlook.com> * also test default filename * test `_get_lines` --------- Signed-off-by: Haoyu (Daniel) YANG 杨浩宇 <yanghaoyu97@outlook.com> Co-authored-by: Aakash Ashok Naik <91958822+naik-aakash@users.noreply.github.com>

Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.18.8 to 1.18.9. - [Release notes](https://github.com/sparklemotion/nokogiri/releases) - [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md) - [Commits](sparklemotion/nokogiri@v1.18.8...v1.18.9) --- updated-dependencies: - dependency-name: nokogiri dependency-version: 1.18.9 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* unignore PERF401 rule * fix core * fix dev_scripts * fix ext * fix entries * fix symmetry * fix transformations * fix alchemy * fix apps * fix command line * fix phonon * fix lobster * fix vasp * fix io * fix electronic structure * fix analysis * fix typo * fix some mypy error * add test

…atgen/-/commit/dcba4226dfc59789070bd1f7aa40b953e7722651 (#4476)

@shyuep

* Update FHI-aims io to use pyfhiaims * Update si for file format changes consistent number of # * update ref file with blank line in header * Update for new parsers * Replace where AimsParseError is located updating parsers * Add modified converters interface. Move that to pyfhiaims * Update for pyfhiaims parsers * Updates from pyfhiaims cleanups * update tests for new interface restults seemed to have change, so fixing that * fix things for atomate2 * modify pyproject.toml Add optional aims reqirement of pyfhiaims * Add importorskip line for pyfhiaims Should skip aims test without the optional dependency * Remove FHI-aims test files Tests will be done in pyfhiaims as per @shyuep request * fix build errors aims not apart of optional as it's not needed in tests * Add pymatgen-io-aims to the add on's page * FHI-aims now in add on remove copied files from the add on

updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.2 → v0.12.7](astral-sh/ruff-pre-commit@v0.12.2...v0.12.7) - [github.com/pre-commit/mirrors-mypy: v1.16.1 → v1.17.1](pre-commit/mirrors-mypy@v1.16.1...v1.17.1) - [github.com/RobertCraigie/pyright-python: v1.1.402 → v1.1.403](RobertCraigie/pyright-python@v1.1.402...v1.1.403) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* clean up type and docs * remove non-existent interpolation_order arg * clean up comment for arg `spline_options` * clean up doc more * deprecate `spline_options` with a more understandable zero_slope_saddle flag * exact match first for glob * completely deprecate spline_options * completely deprecate spline_options * more doc and type cleanup * a -> an NEB * fix relative energy * fix test

* capture expected warning * fix python 3.10 syntaxerror * pre-commit auto-fixes * test 3.10 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Addition of JDFTx set to pymatgen from atomate2. * None structure handling in input set generation --------- Signed-off-by: Cooper <101949243+cote3804@users.noreply.github.com> Co-authored-by: cote3804 <cooyploopy@gmail.com>

* remove deprecated args * loose requests pin * loose further to first version for python 3.10 * fix deprecate warning from numpy.cross /Users/yang/developer/pmg/tests/analysis/test_interface_reactions.py:367: DeprecationWarning: Arrays of 2-dimensional vectors are deprecated. Use arrays of 3-dimensional vectors instead. (deprecated in NumPy 2.0) positions = [np.cross(v1, v2) for v1, v2 in relative_vectors] * fix encoding warning * fix numpy deprecation warning /Users/yang/developer/pmg/src/pymatgen/core/tensors.py:292: DeprecationWarning: __array_wrap__ must accept context and return_scalar arguments (positionally) in the future. (Deprecated NumPy 2.0) * ignore import position * check status before parsing * limit scope of env var * more explicit skip reason * use approx for float * check mp api key length * I don't think we need to set api globally but could be wrong * tweak * Revert "I don't think we need to set api globally but could be wrong" This reverts commit c5493c3. * revert debug change * revert get_entries arg change in test * fix syntax error in python < 3.11 src/pymatgen/io/jdftx/outputs.py:328:45: SyntaxError: Cannot use star expression in index on Python 3.10 (syntax was added in Python 3.11) * match warning * avoid default value in test function * fix pytest-warns-with-multiple-statements (PT031) * ignore PLW1641 fix now * warning order should not matter * Writing numpy-version-dependent code https://numpy.org/doc/stable/numpy_2_0_migration_guide.html#writing-numpy-version-dependent-code * commit uv lock * replace monty copy_r

* fix has_cobi when NcICOBILIST is present * linebreak * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* overwrite default grou * [NEED CONFIRM] remove lock file for PDM * try replace with uv * update guide * maybe we don't need explicit activate * clean up linting workflow * remove dgl/matgl install which doesn't seem to do anything * also remove pdm dev dep * clean up pre-commit guide * Revert "[NEED CONFIRM] remove lock file for PDM" This reverts commit 2f135a1. * Revert "also remove pdm dev dep" This reverts commit c1cec26. * separate dev dep groups * remove ci group * module var all cap * fix pytest as not really using venv from uv, but mamba DEBUG: why moyopy is not available when it's installed? DEBUG: revert some changes Revert "DEBUG: why moyopy is not available when it's installed?" This reverts commit 5036d54. uv run try to remove explicit active again emmm nope, still need manual activation remove manual activate again, but I don't think uv run would re-sync venv? * remove contributing at root * clean up contributing guide * update admin.md * update uv lock * update docs * don't need manual line wrap * clean up usage.md

This reverts commit 117effe.

…nal_energy_components` (#4440) * Filling out `JOutStructure.properties` for feeding to `frame_properties` for `Trajectory` in `JDFTXOutfileSlice.trajectory` * unneccessary line * better comments on joutstructure initialization order * TODOs * Adding missing kinetic_functional option * Removing vestigial function * Vibrations parsing and testing * removing debug comments * removing commented out code * Parsing and testing for vibrational energy components * Add vibrational data to `JDFTXOutfile` to be read from `JDFTXOutfileSlice` --------- Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>

) * fix test method name * use scipy implementation * enhance test

Bumps [pillow](https://github.com/python-pillow/Pillow) from 12.1.1 to 12.2.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@12.1.1...12.2.0) --- updated-dependencies: - dependency-name: pillow dependency-version: 12.2.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Update actions still on Node 20 to their latest Node 24-based releases and pin floating third-party tags to specific versions. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

astral-sh/setup-uv has no floating v8 tag (only v8.0.0/v8.1.0), which broke action resolution after the bump from @v8.0.0 to @v8. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…el packages Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.19.1 to 1.19.3. - [Release notes](https://github.com/sparklemotion/nokogiri/releases) - [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md) - [Commits](sparklemotion/nokogiri@v1.19.1...v1.19.3) --- updated-dependencies: - dependency-name: nokogiri dependency-version: 1.19.3 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [faraday](https://github.com/lostisland/faraday) from 2.14.1 to 2.14.2. - [Release notes](https://github.com/lostisland/faraday/releases) - [Changelog](https://github.com/lostisland/faraday/blob/main/CHANGELOG.md) - [Commits](lostisland/faraday@v2.14.1...v2.14.2) --- updated-dependencies: - dependency-name: faraday dependency-version: 2.14.2 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

pymatgen-core's default branch is main; the depth=1 fetch of master* matched nothing and aborted the Pages build. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

setup-micromamba is broken on Windows runners since ~2026-05-14 (STATUS_DLL_NOT_FOUND, mamba-org/setup-micromamba#306). Mirror the workaround already applied in pymatgen-core: use actions/setup-python on Windows and create a uv venv to host the test install. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Signed-off-by: Sai Asish Y <say.apm35@gmail.com>

Addresses dependabot alerts: - idna < 3.15 (CVE-2024-3651 bypass, medium) - urllib3 < 2.7.0 (sensitive header forwarding on proxied redirects, high) - urllib3 2.6.x decompression-bomb safeguards bypass (high) Lock and requirements.txt regenerated via `uv lock --upgrade-package idna --upgrade-package urllib3` and `uv pip compile`, which also pulled in incidental updates to monty, plotly, tqdm, etc. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

mmbliss self-assigned this Aug 27, 2024

pre-commit-ci Bot and others added 29 commits July 29, 2025 09:19

Add comment.

00bf636

Merge branch 'master' of github.com:materialsproject/pymatgen

0d708d6

patch ReDOS vulnerability: https://salsa.debian.org/debichem-team/pym…

0f5c4af

…atgen/-/commit/dcba4226dfc59789070bd1f7aa40b953e7722651 (#4476)

Comment out alloys API test. Because MP API changes.

1797d0c

Add alloys to optional.

ebd8fea

Fix jdftx.outputs usage of 3.11+ only syntax (#4484)

38997ee

* capture expected warning * fix python 3.10 syntaxerror * pre-commit auto-fixes * test 3.10 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Move JDFTx sets from atomate2 to pymatgen (#4479)

4f30bfa

* Addition of JDFTx set to pymatgen from atomate2. * None structure handling in input set generation --------- Signed-off-by: Cooper <101949243+cote3804@users.noreply.github.com> Co-authored-by: cote3804 <cooyploopy@gmail.com>

Fix has_cobicar when NcICOBILIST is present (#4447)

fd41fd1

* fix has_cobi when NcICOBILIST is present * linebreak * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Fix tests for lower.

117effe

Revert "Fix tests for lower."

3e06c93

This reverts commit 117effe.

Fix MPRester tests without alloys installed.

90c3e59

Use importlib find_spec.

5b7273b

Guess we have to use the old method.

74ff64b

Fix TranslateSitesTransformation (#4487)

d2454dc

Update uv.lock.

7225790

Merge branch 'master' of github.com:materialsproject/pymatgen

e715742

Fix type errors.

937115d

Replace linear_assignment with scipy linear_sum_assignment (#4490

b622498

) * fix test method name * use scipy implementation * enhance test

dependabot Bot and others added 30 commits May 5, 2026 05:13

Updated changelog.

0b69105

Merge branch 'master' of github.com:materialsproject/pymatgen

4198b24

Fix pagination bug on MPRester.

2a89a89

Fix failing tasks MPRester test.

a2a48aa

Update docs

8495e94

Fix doc version.

ce95fe5

chore: bump GitHub Actions to Node 24 majors

0f281d8

Update actions still on Node 20 to their latest Node 24-based releases and pin floating third-party tags to specific versions. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

fix: pin setup-uv to v8.1.0 in Jekyll workflow

406d8d9

astral-sh/setup-uv has no floating v8 tag (only v8.0.0/v8.1.0), which broke action resolution after the bump from @v8.0.0 to @v8. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

chore: bump setup-uv to v8.1.0 in lint and test workflows

9bd5fff

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Update pymatgen-core submodule.

e2bba33

docs: limit api toctree maxdepth so landing page lists only first-lev…

c20f52c

…el packages Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

docs: limit sphinx-apidoc maxdepth to 1 in pages workflow

8ec9d2f

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Update pymatgen-core

5228fbc

Merge branch 'master' of github.com:materialsproject/pymatgen

caf9717

algin toml wth core

999e9cf

Update docs and fix tests.

2455a14

Update pymatgen-core submodule.

dd0dd11

Fix doc deploy: checkout pymatgen-core main, not master.

fc74ebe

pymatgen-core's default branch is main; the depth=1 fetch of master* matched nothing and aborted the Pages build. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

fix: strip H/O from PourbaixDiagram comp_dict (#4657) (#4658)

c14a699

Signed-off-by: Sai Asish Y <say.apm35@gmail.com>

Updated README.

1d43eb0

Merge branch 'master' of github.com:materialsproject/pymatgen

8c10222

Update submodule.

27f2297

Remove req.txt.

2934bc2

Update submodule.

3dac345

Update source links.

6d5733b

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Pull from materialsproject [WIP]#10

Pull from materialsproject [WIP]#10
mmbliss wants to merge 4866 commits into
molmd:molmd_fix_3-9from
materialsproject:master

mmbliss commented Aug 27, 2024

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mmbliss commented Aug 27, 2024

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