Bump pymatgen from 2024.6.10 to 2024.8.9

[dependabot[bot]]

Bumps pymatgen from 2024.6.10 to 2024.8.9.

Release notes

Sourced from pymatgen's releases.

v2024.8.9

• Revert bad split of sets.py, which broke downstream code.

v2024.8.8

🎉 New Features

• Add multiwfn QTAIM parsing capabilities by @​espottesmith in materialsproject/pymatgen#3926

🐛 Bug Fixes

• Fix chemical system method for different oxidation states by @​danielzuegner in materialsproject/pymatgen#3915
• Fix coordination number bug by @​jmmshn in materialsproject/pymatgen#3954
• Fix Ion formula parsing bug; add more special formulas by @​rkingsbury in materialsproject/pymatgen#3942
• Dedup numpydependency in pyproject by @​janosh in materialsproject/pymatgen#3970
• test_graph: add filename only to pdf list by @​drew-parsons in materialsproject/pymatgen#3972
• Bugfix: io.pwscf.PWInput.from_str() by @​jsukpark in materialsproject/pymatgen#3931
• Fix d2k function by @​tpurcell90 in materialsproject/pymatgen#3932
• Assign frame properties to molecule/structure when indexing trajectory by @​CompRhys in materialsproject/pymatgen#3979

🛠 Enhancements

• Element/Species: order full_electron_structure by energy by @​rkingsbury in materialsproject/pymatgen#3944
• Extend CubicSupercell transformation to also be able to look for orthorhombic cells by @​JaGeo in materialsproject/pymatgen#3938
• Allow custom .pmgrc.yaml location via new PMG_CONFIG_FILE env var by @​janosh in materialsproject/pymatgen#3949
• Fix MPRester tests and access phonon properties from the new API without having mp-api installed. by @​AntObi in materialsproject/pymatgen#3950
• Adding Abinit magmoms from netCDF files to Structure.site_properties by @​gbrunin in materialsproject/pymatgen#3936
• Parallel Joblib Process Entries by @​CompRhys in materialsproject/pymatgen#3933
• Add OPTIMADE adapter by @​ml-evs in materialsproject/pymatgen#3876
• Check Inputs to Trajectory. by @​CompRhys in materialsproject/pymatgen#3978

📖 Documentation

• Replace expired BoltzTraP link by @​DanielYang59 in materialsproject/pymatgen#3929
• Correct method get_projection_on_elements docstring under Procar class by @​DanielYang59 in materialsproject/pymatgen#3945

🧹 House-Keeping

• Split VASP input sets into submodules by @​janosh in materialsproject/pymatgen#3865

🚧 CI

• Install some optional dependencies in CI by @​DanielYang59 in materialsproject/pymatgen#3786

💡 Refactoring

• Fix Incar check_params for Union type by @​DanielYang59 in materialsproject/pymatgen#3958

🏥 Package Health

• build against NPY2 by @​njzjz in materialsproject/pymatgen#3894

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.8.9

• Revert bad split of sets.py, which broke downstream code.

v2024.8.8

🎉 New Features

• Add multiwfn QTAIM parsing capabilities by @​espottesmith in materialsproject/pymatgen#3926

🐛 Bug Fixes

• Fix chemical system method for different oxidation states by @​danielzuegner in materialsproject/pymatgen#3915
• Fix coordination number bug by @​jmmshn in materialsproject/pymatgen#3954
• Fix Ion formula parsing bug; add more special formulas by @​rkingsbury in materialsproject/pymatgen#3942
• Dedup numpydependency in pyproject by @​janosh in materialsproject/pymatgen#3970
• test_graph: add filename only to pdf list by @​drew-parsons in materialsproject/pymatgen#3972
• Bugfix: io.pwscf.PWInput.from_str() by @​jsukpark in materialsproject/pymatgen#3931
• Fix d2k function by @​tpurcell90 in materialsproject/pymatgen#3932
• Assign frame properties to molecule/structure when indexing trajectory by @​CompRhys in materialsproject/pymatgen#3979

🛠 Enhancements

• Element/Species: order full_electron_structure by energy by @​rkingsbury in materialsproject/pymatgen#3944
• Extend CubicSupercell transformation to also be able to look for orthorhombic cells by @​JaGeo in materialsproject/pymatgen#3938
• Allow custom .pmgrc.yaml location via new PMG_CONFIG_FILE env var by @​janosh in materialsproject/pymatgen#3949
• Fix MPRester tests and access phonon properties from the new API without having mp-api installed. by @​AntObi in materialsproject/pymatgen#3950
• Adding Abinit magmoms from netCDF files to Structure.site_properties by @​gbrunin in materialsproject/pymatgen#3936
• Parallel Joblib Process Entries by @​CompRhys in materialsproject/pymatgen#3933
• Add OPTIMADE adapter by @​ml-evs in materialsproject/pymatgen#3876
• Check Inputs to Trajectory. by @​CompRhys in materialsproject/pymatgen#3978

📖 Documentation

• Replace expired BoltzTraP link by @​DanielYang59 in materialsproject/pymatgen#3929
• Correct method get_projection_on_elements docstring under Procar class by @​DanielYang59 in materialsproject/pymatgen#3945

🧹 House-Keeping

• Split VASP input sets into submodules by @​janosh in materialsproject/pymatgen#3865

🚧 CI

• Install some optional dependencies in CI by @​DanielYang59 in materialsproject/pymatgen#3786

💡 Refactoring

• Fix Incar check_params for Union type by @​DanielYang59 in materialsproject/pymatgen#3958

🏥 Package Health

... (truncated)

Commits

• 1ac6c68 Update docs
• d3526bc Update changelog.
• 636165b Add back missing sets.py file.
• f1eb364 Revert "Split VASP input sets into submodules (#3865)" (#3989)
• 6db6111 Revert "Add fdint install."
• aab9092 Add fdint install.
• 9703a1c Bypass COD for Structure.from_id when COD is down.
• a277a54 Fix timeout error checking.
• 2adfe8f Skip openff tests if openbabel is not present.
• 289d281 Updating Ternary and Quaternary Plots (#3948)
• Additional commits viewable in compare view

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Superseded by #979.