Bump pymatgen from 2023.5.10 to 2024.6.4

[dependabot[bot]]

Bumps pymatgen from 2023.5.10 to 2024.6.4.

Release notes

Sourced from pymatgen's releases.

v2024.6.4

What's Changed

🐛 Bug Fixes

• Run CI with two different uv resolution strategies: highest and lowest-direct by @​janosh in materialsproject/pymatgen#3852
• Fix filter condition for warn msg of unphysical site occupancy in io.cif by @​DanielYang59 in materialsproject/pymatgen#3853

🛠 Enhancements

• Add new .pmgrc.yaml setting PMG_VASP_PSP_SUB_DIRS: dict[str, str] by @​janosh in materialsproject/pymatgen#3858

📖 Documentation

• Clarify argument shift for SlabGenerator.get_slab by @​DanielYang59 in materialsproject/pymatgen#3748

🚧 CI

• Add CI run without 'optional' deps installed by @​janosh in materialsproject/pymatgen#3857

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.5.31...v2024.6.4

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 (slightly breaking, see #3860 for details)

📖 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

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.6.4

🐛 Bug Fixes

• Run CI with two different uv resolution strategies: highest and lowest-direct by @​janosh in materialsproject/pymatgen#3852
• Fix filter condition for warn msg of unphysical site occupancy in io.cif by @​DanielYang59 in materialsproject/pymatgen#3853

🛠 Enhancements

• Add new .pmgrc.yaml setting PMG_VASP_PSP_SUB_DIRS: dict[str, str] by @​janosh in materialsproject/pymatgen#3858

📖 Documentation

• Clarify argument shift for SlabGenerator.get_slab by @​DanielYang59 in materialsproject/pymatgen#3748

🚧 CI

• Add CI run without 'optional' deps installed by @​janosh in materialsproject/pymatgen#3857

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.5.31...v2024.6.4

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 (slightly breaking, see #3860 for details)

📖 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

... (truncated)

Commits

• 163cc01 v2024.6.4
• d38aee2 update tests/files/.pytest-split-durations
• c55e056 Add new .pmgrc.yaml setting PMG_VASP_PSP_SUB_DIRS: dict[str, str] (#3858)
• eed8403 Clarify argument shift for SlabGenerator.get_slab (#3748)
• d1fac20 Add CI run without 'optional' deps installed (#3857)
• 1a5af18 Fix filter condition for warn msg of unphysical site occupancy in io.cif (#...
• eccf075 Run CI with two different uv resolution strategies: highest and `lowest-d...
• 2982968 v2024.5.31
• c70e5b8 Add type annotations for io.vasp.outputs (#3776)
• cd8846b Update reqs.
• Additional commits viewable in compare view

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:point_left: Launch a binder notebook on branch pyiron/ironflow/dependabot/pip/pymatgen-2024.6.4