Bump pymatgen from 2024.3.1 to 2024.5.31

[dependabot[bot]]

Bumps pymatgen from 2024.3.1 to 2024.5.31.

Release notes

Sourced from pymatgen's releases.

v2024.5.31

What's Changed

🐛 Bug Fixes

• Make Beautifulsoup optional by @​ab5424 in materialsproject/pymatgen#3774
• Fix overlayed subplots in BSPlotterProjected.get_projected_plots_dots() by @​janosh in materialsproject/pymatgen#3798
• Fix _get_dipole_info for DDEC6 ChargemolAnalysis and add test case by @​JonathanSchmidt1 in materialsproject/pymatgen#3801
• Cp2kOutput.parse_initial_structure() use regex for line matching to allow arbitrary white space between Atom/Kind/Element/... by @​janosh in materialsproject/pymatgen#3810
• Fix the minor document error in POTCAR Setup. by @​hongyi-zhao in materialsproject/pymatgen#3834
• Use isclose over == for overlap position check in SlabGenerator.get_slabs by @​DanielYang59 in materialsproject/pymatgen#3825
• [Deprecation] Replace Element property is_rare_earth_metal with is_rare_earth to include Y and Sc by @​DanielYang59 in materialsproject/pymatgen#3817

🛠 Enhancements

• Add is_radioactive property to Element class by @​AntObi in materialsproject/pymatgen#3804
• Add a from_ase_atoms() method to Structure by @​Andrew-S-Rosen in materialsproject/pymatgen#3812
• Adapt to the latest version of PWmat output file by @​lhycms in materialsproject/pymatgen#3823
• Update VASP sets to transition atomate2 to use pymatgen input sets exclusively by @​esoteric-ephemera in materialsproject/pymatgen#3835

📖 Documentation

• Imperative get_... method and @property doc strings by @​janosh in materialsproject/pymatgen#3802
• Doc string standardization by @​janosh in materialsproject/pymatgen#3805

🧹 House-Keeping

• Add types for core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc) by @​DanielYang59 in materialsproject/pymatgen#3829
• Move test structures out of util directory by @​DanielYang59 in materialsproject/pymatgen#3831

🧪 Tests

• Improve type annotations for core.(trajectory/units) by @​DanielYang59 in materialsproject/pymatgen#3832

🏷️ Type Hints

• More type annotations by @​janosh in materialsproject/pymatgen#3800
• Add types for core.periodic_table/bonds/composition/ion/lattice/libxcfunc, new type MillerIndex and fix Lattice hash by @​DanielYang59 in materialsproject/pymatgen#3814
• Guard TYPE_CHECKING only imports by @​DanielYang59 in materialsproject/pymatgen#3827
• Improve type annotations and comments for io.cif by @​DanielYang59 in materialsproject/pymatgen#3820
• Improve type annotations for core.structure by @​DanielYang59 in materialsproject/pymatgen#3837
• Add type annotations for io.vasp.outputs by @​DanielYang59 in materialsproject/pymatgen#3776

🤷‍♂️ Other Changes

• mixing scheme: change default for verbose by @​tschaume in materialsproject/pymatgen#3806
• ruff 0.4.3 auto-fixes by @​janosh in materialsproject/pymatgen#3808
• Re-enable some useful ruff rules by @​DanielYang59 in materialsproject/pymatgen#3813
• pandas.read_csv: replace deprecated delim_whitespace=True with sep="\s+" by @​ab5424 in materialsproject/pymatgen#3846
• Improve unphysical (greater than 1) occupancy handling in CifParser and add missing site label if not check_occu by @​DanielYang59 in materialsproject/pymatgen#3819

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31

v2024.5.1

What's Changed

🐛 Bug Fixes

• Fix OPTIMADE rester URL contruction and improve testing by @​ml-evs in materialsproject/pymatgen#3756
• Add fix for SFAC writer by @​stefsmeets in materialsproject/pymatgen#3779
• Fix LobsterSet by @​naik-aakash in materialsproject/pymatgen#3771

... (truncated)

Changelog

Sourced from pymatgen's changelog.

2024.5.31

🐛 Bug Fixes

• Make Beautifulsoup optional by @​ab5424 in materialsproject/pymatgen#3774
• Fix overlayed subplots in BSPlotterProjected.get_projected_plots_dots() by @​janosh in materialsproject/pymatgen#3798
• Fix _get_dipole_info for DDEC6 ChargemolAnalysis and add test case by @​JonathanSchmidt1 in materialsproject/pymatgen#3801
• Cp2kOutput.parse_initial_structure() use regex for line matching to allow arbitrary white space between Atom/Kind/Element/... by @​janosh in materialsproject/pymatgen#3810
• Fix the minor document error in POTCAR Setup. by @​hongyi-zhao in materialsproject/pymatgen#3834
• Use isclose over == for overlap position check in SlabGenerator.get_slabs by @​DanielYang59 in materialsproject/pymatgen#3825
• [Deprecation] Replace Element property is_rare_earth_metal with is_rare_earth to include Y and Sc by @​DanielYang59 in materialsproject/pymatgen#3817

🛠 Enhancements

• Add is_radioactive property to Element class by @​AntObi in materialsproject/pymatgen#3804
• Add a from_ase_atoms() method to Structure by @​Andrew-S-Rosen in materialsproject/pymatgen#3812
• Adapt to the latest version of PWmat output file by @​lhycms in materialsproject/pymatgen#3823
• Update VASP sets to transition atomate2 to use pymatgen input sets exclusively by @​esoteric-ephemera in materialsproject/pymatgen#3835

📖 Documentation

• Imperative get_... method and @property doc strings by @​janosh in materialsproject/pymatgen#3802
• Doc string standardization by @​janosh in materialsproject/pymatgen#3805

🧹 House-Keeping

• Add types for core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc) by @​DanielYang59 in materialsproject/pymatgen#3829
• Move test structures out of util directory by @​DanielYang59 in materialsproject/pymatgen#3831

🧪 Tests

• Improve type annotations for core.(trajectory/units) by @​DanielYang59 in materialsproject/pymatgen#3832

🏷️ Type Hints

• More type annotations by @​janosh in materialsproject/pymatgen#3800
• Add types for core.periodic_table/bonds/composition/ion/lattice/libxcfunc, new type MillerIndex and fix Lattice hash by @​DanielYang59 in materialsproject/pymatgen#3814
• Guard TYPE_CHECKING only imports by @​DanielYang59 in materialsproject/pymatgen#3827
• Improve type annotations and comments for io.cif by @​DanielYang59 in materialsproject/pymatgen#3820
• Improve type annotations for core.structure by @​DanielYang59 in materialsproject/pymatgen#3837

🤷‍♂️ Other Changes

• mixing scheme: change default for verbose by @​tschaume in materialsproject/pymatgen#3806
• ruff 0.4.3 auto-fixes by @​janosh in materialsproject/pymatgen#3808
• Re-enable some useful ruff rules by @​DanielYang59 in materialsproject/pymatgen#3813
• pandas.read_csv: replace deprecated delim_whitespace=True with sep="\s+" by @​ab5424 in materialsproject/pymatgen#3846
• Improve unphysical (greater than 1) occupancy handling in CifParser and add missing site label if not check_occu by @​DanielYang59 in materialsproject/pymatgen#3819

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.5.1...v2024.5.31

... (truncated)

Commits

• 2982968 v2024.5.31
• c70e5b8 Add type annotations for io.vasp.outputs (#3776)
• cd8846b Update reqs.
• cec7d35 Update reqs.
• f214a5c [Deprecation] Replace Element property is_rare_earth_metal with `is_rare_...
• a772ddb Improve unphysical (greater than 1) occupancy handling in CifParser and add...
• 0c9ff40 Use isclose over == for overlap position check in `SlabGenerator.get_slab...
• 8c853cf --- (#3842)
• 541b58b Fix regression.
• 594f189 Add unittests for NotImplementedError.
• Additional commits viewable in compare view

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