Bump pymatgen from 2024.4.13 to 2024.7.18

[dependabot[bot]]

Bumps pymatgen from 2024.4.13 to 2024.7.18.

Release notes

Sourced from pymatgen's releases.

v2024.7.18

layout: default title: Change Log

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

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.7.18

• Fix setuptools for packaging (#3934)
• Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram (#3900)
• Add electronic structure methods for Species (#3902)
• Migrate spglib to new SpglibDataset format with version 2.5.0 (#3923)
• SpaceGroup changes (#3859)
• Add MD input set to FHI-aims (#3896)

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

... (truncated)

Commits

• 27d90b7 Update docs
• 380d2f2 [Hot Fix] Fix setuptools for pymatgen packaging (#3934)
• 0234182 Improve Keep Redundant Spaces algorithm for PatchedPhaseDiagram (#3900)
• 454aa5e Add electronic structure methods for Species (#3902)
• 58e8a35 Migrate spglib to new SpglibDataset format with version 2.5.0 (#3923)
• 106e8f5 Fix analyzer tests.
• e9e6e34 Set mac test to 3.10.
• f3cd079 Use >3,9
• a1e774b Use 3.x designation in python version to test latest version on ubuntu
• d0ed5d7 Use newer pytjon for linting.
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[dependabot[bot]]

Superseded by #486.