Sync #100
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Sync #100
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* remove deprecated mypy plugin /Users/yang/.cache/pre-commit/reposlddsc8t/py_env-python3.13/bin/mypy:8: DeprecationWarning: `numpy.typing.mypy_plugin` is deprecated, and will be removed in a future release. Please remove `plugins = numpy.typing.mypy_plugin` in your mypy config.(deprecated in NumPy 2.3) sys.exit(console_entry()) * fix comment handling * add test * explicit None when no comment instead of empty str
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.2.3 to 2.5.0. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst) - [Commits](urllib3/urllib3@2.2.3...2.5.0) --- updated-dependencies: - dependency-name: urllib3 dependency-version: 2.5.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* add hacky s3 requests * undo qchem input change * status code change * correct type annotations for bandstructure objects * revert es kpoints typing - only phonon ones are wrong * more mypy * more mypy * revert typing changes
Missing a letter "s" for `site.species` in pymatgen.symmetry.analyser.SpacegroupAnalyzer.get_primitive_standard_structure() Signed-off-by: boyoungzheng <boyoungzheng@users.noreply.github.com>
* enable orjson.OPT_SERIALIZE_NUMPY * np.array -> np.asarray * remove tolist * safer deprecation replacement * rename * better deprecation * put structure related ops together * add test * str -> PathLike for filename * clean up * also enable OPT_SERIALIZE_NUMPY for molecule * overwrite default grou * ignore arg-type, fix needed from monty * Revert "overwrite default grou" This reverts commit 409d954.
… `mcsqs/pyzeo` tests (#4455) * separate optional dep install script * disable wget cert check for now * try dependency cache * optional dep needed before pyzeo install * Revert "optional dep needed before pyzeo install" This reverts commit 10543b9. * install zeopp in optional dep * skip pyzeo on windows * tyep annotation * install mcsqs * fix mcsqs runtime error * fix mcsqs caller test * declare global opt bin dir * skip failing test for now * reuse zeo_found * more readable cache key * pytext skip -> xfail * fix test class naming * remove unnecessary test file dir check
* 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
* 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>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.11](astral-sh/ruff-pre-commit@v0.12.7...v0.12.11) - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](pre-commit/pre-commit-hooks@v5.0.0...v6.0.0) - [github.com/RobertCraigie/pyright-python: v1.1.403 → v1.1.404](RobertCraigie/pyright-python@v1.1.403...v1.1.404) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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