Bump pymatgen from 2024.3.1 to 2024.4.13

[dependabot[bot]]

Bumps pymatgen from 2024.3.1 to 2024.4.13.

Release notes

Sourced from pymatgen's releases.

v2024.4.13

Hot fix release for v2024.4.12 to be yanked on PyPI due to materialsproject/pymatgen#3751.

🐛 Bug Fixes

• Revert mistaken Cohp.has_antibnd_states_below_efermi rename by @​JaGeo in materialsproject/pymatgen#3750
• Fix typing_extension ImportError in downstream packages by @​janosh in materialsproject/pymatgen#3752
• Update some of the OPTIMADE aliases by @​ml-evs in materialsproject/pymatgen#3754

🧹 House-Keeping

• Remove duplicate ruff rule in pyproject.toml by @​Andrew-S-Rosen in materialsproject/pymatgen#3755

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.4.12...v2024.4.13

v2024.4.12

What's Changed

🎉 New Features

• Add pymatgen.io.openff module by @​orionarcher in materialsproject/pymatgen#3729

🐛 Bug Fixes

• Fix blank line bug in io.res.ResWriter by @​stefsmeets in materialsproject/pymatgen#3671
• Reset label for sites changed by Structure.replace_species() by @​stefsmeets in materialsproject/pymatgen#3672
• Fix phonopy.get_pmg_structure site_properties key for magmoms by @​JonathanSchmidt1 in materialsproject/pymatgen#3679
• Improve Bandoverlaps parser by @​naik-aakash in materialsproject/pymatgen#3689
• Convert some staticmethod to classmethod by @​DanielYang59 in materialsproject/pymatgen#3710
• Correct units of Element.atomic_orbitals by @​esoteric-ephemera in materialsproject/pymatgen#3714
• Add a fix for if a parameter is None in AimsControlIn by @​tpurcell90 in materialsproject/pymatgen#3727
• Replace general raise Exception and add missing raise keyword by @​DanielYang59 in materialsproject/pymatgen#3728
• Fix ChemicalPotentialDiagram 2D plot not respecting formal_chempots setting by @​uliaschauer in materialsproject/pymatgen#3734
• Update ENCUT type to float in incar_parameters.json by @​yuuukuma in materialsproject/pymatgen#3741
• Clean up core.surface comments and docstrings by @​DanielYang59 in materialsproject/pymatgen#3691
• Fix io.cp2k.input.DataFile by @​DanielYang59 in materialsproject/pymatgen#3745

🛠 Enhancements

• Ensure MSONAtoms is indeed MSONable when Atoms.info is loaded with goodies by @​Andrew-S-Rosen in materialsproject/pymatgen#3670
• Generalize fatband plots from Lobster by @​JaGeo in materialsproject/pymatgen#3688
• Plotting of Multicenter COBIs by @​JaGeo in materialsproject/pymatgen#2926
• Support appending vectors to positions in XSF format by @​mturiansky in materialsproject/pymatgen#3704
• Define needs_u_correction(comp: CompositionLike) -> set[str] utility function by @​janosh in materialsproject/pymatgen#3703
• Add more flexibility to PhononDOSPlotter and PhononBSPlotter by @​ab5424 in materialsproject/pymatgen#3700
• Define ElementType enum in core/periodic_table.py by @​janosh in materialsproject/pymatgen#3726

📖 Documentation

• Reformat docstrings to Google style and add type annotations by @​DanielYang59 in materialsproject/pymatgen#3694

🧹 House-Keeping

• Breaking: all plot methods return plt.Axes by @​janosh in materialsproject/pymatgen#3749
• Clean up test files: VASP outputs by @​DanielYang59 in materialsproject/pymatgen#3653
• Clean up test files: VASP inputs by @​DanielYang59 in materialsproject/pymatgen#3674
• Clean up test files: dedicated VASP directories, xyz, mcif, cssr, exciting, wannier90 by @​DanielYang59 in materialsproject/pymatgen#3681
• Remove exception printing when importing phonopy by @​lan496 in materialsproject/pymatgen#3696

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.4.13

Hot fix release for v2024.4.12 to be yanked on PyPI due to materialsproject/pymatgen#3751.

🐛 Bug Fixes

• Revert mistaken Cohp.has_antibnd_states_below_efermi rename by @​JaGeo in materialsproject/pymatgen#3750
• Fix typing_extension ImportError in downstream packages by @​janosh in materialsproject/pymatgen#3752
• Update some of the OPTIMADE aliases by @​ml-evs in materialsproject/pymatgen#3754

🧹 House-Keeping

• Remove duplicate ruff rule in pyproject.toml by @​Andrew-S-Rosen in materialsproject/pymatgen#3755

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.4.12...v2024.4.13

v2024.4.12

🎉 New Features

• Add pymatgen.io.openff module by @​orionarcher in materialsproject/pymatgen#3729

🐛 Bug Fixes

• Fix blank line bug in io.res.ResWriter by @​stefsmeets in materialsproject/pymatgen#3671
• Reset label for sites changed by Structure.replace_species() by @​stefsmeets in materialsproject/pymatgen#3672
• Fix phonopy.get_pmg_structure site_properties key for magmoms by @​JonathanSchmidt1 in materialsproject/pymatgen#3679
• Improve Bandoverlaps parser by @​naik-aakash in materialsproject/pymatgen#3689
• Convert some staticmethod to classmethod by @​DanielYang59 in materialsproject/pymatgen#3710
• Correct units of Element.atomic_orbitals by @​esoteric-ephemera in materialsproject/pymatgen#3714
• Add a fix for if a parameter is None in AimsControlIn by @​tpurcell90 in materialsproject/pymatgen#3727
• Replace general raise Exception and add missing raise keyword by @​DanielYang59 in materialsproject/pymatgen#3728
• Fix ChemicalPotentialDiagram 2D plot not respecting formal_chempots setting by @​uliaschauer in materialsproject/pymatgen#3734
• Update ENCUT type to float in incar_parameters.json by @​yuuukuma in materialsproject/pymatgen#3741
• Clean up core.surface comments and docstrings by @​DanielYang59 in materialsproject/pymatgen#3691
• Fix io.cp2k.input.DataFile by @​DanielYang59 in materialsproject/pymatgen#3745

🛠 Enhancements

• Ensure MSONAtoms is indeed MSONable when Atoms.info is loaded with goodies by @​Andrew-S-Rosen in materialsproject/pymatgen#3670
• Generalize fatband plots from Lobster by @​JaGeo in materialsproject/pymatgen#3688
• Plotting of Multicenter COBIs by @​JaGeo in materialsproject/pymatgen#2926
• Support appending vectors to positions in XSF format by @​mturiansky in materialsproject/pymatgen#3704
• Define needs_u_correction(comp: CompositionLike) -> set[str] utility function by @​janosh in materialsproject/pymatgen#3703
• Add more flexibility to PhononDOSPlotter and PhononBSPlotter by @​ab5424 in materialsproject/pymatgen#3700
• Define ElementType enum in core/periodic_table.py by @​janosh in materialsproject/pymatgen#3726

🚧 CI

• Migrate CI dependency installation from pip to uv by @​janosh in materialsproject/pymatgen#3675

... (truncated)

Commits

• 585bb67 v2024.4.13
• a4e033a Remove duplicate ruff rule in pyproject.toml (#3755)
• 9aacf65 Update some of the OPTIMADE aliases (#3754)
• f81535f Fix typing_extension ImportError in downstream packages (#3752)
• 4adc00f Fix breaking changes in cohp module of pymatgen (#3750)
• 696aace v2024.4.12
• 48860fb Breaking: all plot methods return plt.Axes (#3749)
• 9337a4e Fix io.cp2k.input.DataFile (#3745)
• 7064c43 Add pymatgen.io.openff module (#3729)
• 55869a1 Clean up core.surface comments and docstrings (#3691)
• Additional commits viewable in compare view

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Superseded by #271.