Bump pymatgen from 2024.4.13 to 2024.6.10

[dependabot[bot]]

Bumps pymatgen from 2024.4.13 to 2024.6.10.

Release notes

Sourced from pymatgen's releases.

v2024.6.10

layout: default title: Change Log

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

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.6.10

• Fix bug in update_charge_from_potcar (#3866)
• Fix bug in VASP parameter parsing (@​mkhorton)
• Add strict_anions option to MaterialsProject2020Compatibility (@​mkhorton)
• Slightly more robust MSONAtoms handling (@​Andrew-S-Rosen)
• Bug fix: handle non-integer oxidation states in Species (@​esoteric-ephemera)
• Revert change that removed test structure files from pymatgen source.

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

... (truncated)

Commits

• d136109 Update docs
• 0d695c9 Update changelog.
• 5144d8b Revert "move structures out of util dir (#3831)" (#3875)
• 624e6eb Add SymmetryUndetermined(ValueError) exception type (#3872)
• 735db5b Fix bug in update_charge_from_potcar (#3866)
• b0d9946 Fix bug in VASP parameter parsing (#3870)
• 85e0f34 Add strict_anions option to MaterialsProject2020Compatibility (#3803)
• 024fce1 Slightly more robust MSONAtoms handling (#3869)
• f545d58 Simplify case handling in lobster.inputs (#3848)
• 36cde41 np.newaxis -> None
• Additional commits viewable in compare view

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Superseded by #480.