Bump pymatgen from 2024.7.18 to 2024.9.10

[dependabot[bot]]

Bumps pymatgen from 2024.7.18 to 2024.9.10.

Release notes

Sourced from pymatgen's releases.

v2024.9.10

💥 Breaking: NumPy/Cython integer type changed from np.long/np.int_ to int64 on Windows to align with NumPy 2.x, changing the default integer type to int64 on Windows 64-bit systems in favor of the platform-dependent np.int_ type. Recommendation: Please explicitly declare dtype=np.int64 when initializing a NumPy array if it's passed to a Cythonized pymatgen function like find_points_in_spheres. You may also want to test downstream packages with NumPy 1.x on Windows in CI pipelines.

🛠 Enhancements

• Formatting customization for PWInput by @​jsukpark in materialsproject/pymatgen#4001
• DOS Fingerprints enhancements by @​naik-aakash in materialsproject/pymatgen#3946
• Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. by @​hongyi-zhao in materialsproject/pymatgen#3955
• Add VASP setting for the dftd4 vdW functional and extend PBE_64 support. by @​hongyi-zhao in materialsproject/pymatgen#3967
• Add SOC & multiple PROCAR parsing functionalities by @​kavanase in materialsproject/pymatgen#3890
• Add modification to aims input to match atomate2 magnetic order script by @​tpurcell90 in materialsproject/pymatgen#3878

🐛 Bug Fixes

• Ion: fix CO2- and I3- parsing errors; enhance tests by @​rkingsbury in materialsproject/pymatgen#3991
• Fix ruff PD901 and prefer sum over len+if by @​janosh in materialsproject/pymatgen#4012
• Explicitly use int64 in Numpy/cython code to avoid OS inconsistency by @​DanielYang59 in materialsproject/pymatgen#3992
• Update FermiDos.get_doping() to be more robust by @​kavanase in materialsproject/pymatgen#3879
• Fix missing /src in doc links to source code by @​DanielYang59 in materialsproject/pymatgen#4032
• Fix LNONCOLLINEAR match in Outcar parser by @​DanielYang59 in materialsproject/pymatgen#4034
• Fix in-place VaspInput.incar updates having no effect if incar is dict (not Incar instance) by @​janosh in materialsproject/pymatgen#4052
• Fix typo in Cp2kOutput.parse_hirshfeld add_site_property("hirshf[i->'']eld") by @​janosh in materialsproject/pymatgen#4055
• Fix apply_operation(fractional=True) by @​kavanase in materialsproject/pymatgen#4057

💥 Breaking Changes

• Pascal-case PMG_VASP_PSP_DIR_Error by @​janosh in materialsproject/pymatgen#4048

📖 Documentation

• Docstring tweaks for io.vasp.inputs and format tweaks for some other parts by @​DanielYang59 in materialsproject/pymatgen#3996
• Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark by @​DanielYang59 in materialsproject/pymatgen#4021
• Fix incorrect attribute name in Lobster.outputs.Cohpcar docstring by @​DanielYang59 in materialsproject/pymatgen#4039

🧹 House-Keeping

• Use strict=True with zip to ensure length equality by @​DanielYang59 in materialsproject/pymatgen#4011

🚀 Performance

• add LRU cache to structure matcher by @​kbuma in materialsproject/pymatgen#4036

🚧 CI

• Install optional boltztrap, vampire and openbabel in CI by @​DanielYang59 in materialsproject/pymatgen#3985

💡 Refactoring

• Make AimsSpeciesFile a dataclass by @​tpurcell90 in materialsproject/pymatgen#4054

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.9.10

💥 Breaking: NumPy/Cython integer type changed from np.long/np.int_ to int64 on Windows to align with NumPy 2.x, changing the default integer type to int64 on Windows 64-bit systems in favor of the platform-dependent np.int_ type. Recommendation: Please explicitly declare dtype=np.int64 when initializing a NumPy array if it's passed to a Cythonized pymatgen function like find_points_in_spheres. You may also want to test downstream packages with NumPy 1.x on Windows in CI pipelines.

🛠 Enhancements

• Formatting customization for PWInput by @​jsukpark in materialsproject/pymatgen#4001
• DOS Fingerprints enhancements by @​naik-aakash in materialsproject/pymatgen#3946
• Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. by @​hongyi-zhao in materialsproject/pymatgen#3955
• Add VASP setting for the dftd4 vdW functional and extend PBE_64 support. by @​hongyi-zhao in materialsproject/pymatgen#3967
• Add SOC & multiple PROCAR parsing functionalities by @​kavanase in materialsproject/pymatgen#3890
• Add modification to aims input to match atomate2 magnetic order script by @​tpurcell90 in materialsproject/pymatgen#3878

🐛 Bug Fixes

• Ion: fix CO2- and I3- parsing errors; enhance tests by @​rkingsbury in materialsproject/pymatgen#3991
• Fix ruff PD901 and prefer sum over len+if by @​janosh in materialsproject/pymatgen#4012
• Explicitly use int64 in Numpy/cython code to avoid OS inconsistency by @​DanielYang59 in materialsproject/pymatgen#3992
• Update FermiDos.get_doping() to be more robust by @​kavanase in materialsproject/pymatgen#3879
• Fix missing /src in doc links to source code by @​DanielYang59 in materialsproject/pymatgen#4032
• Fix LNONCOLLINEAR match in Outcar parser by @​DanielYang59 in materialsproject/pymatgen#4034
• Fix in-place VaspInput.incar updates having no effect if incar is dict (not Incar instance) by @​janosh in materialsproject/pymatgen#4052
• Fix typo in Cp2kOutput.parse_hirshfeld add_site_property("hirshf[i->'']eld") by @​janosh in materialsproject/pymatgen#4055
• Fix apply_operation(fractional=True) by @​kavanase in materialsproject/pymatgen#4057

💥 Breaking Changes

• Pascal-case PMG_VASP_PSP_DIR_Error by @​janosh in materialsproject/pymatgen#4048

📖 Documentation

• Docstring tweaks for io.vasp.inputs and format tweaks for some other parts by @​DanielYang59 in materialsproject/pymatgen#3996
• Replace HTTP URLs with HTTPS, avoid from pytest import raises/mark by @​DanielYang59 in materialsproject/pymatgen#4021
• Fix incorrect attribute name in Lobster.outputs.Cohpcar docstring by @​DanielYang59 in materialsproject/pymatgen#4039

🧹 House-Keeping

• Use strict=True with zip to ensure length equality by @​DanielYang59 in materialsproject/pymatgen#4011

🚀 Performance

• add LRU cache to structure matcher by @​kbuma in materialsproject/pymatgen#4036

🚧 CI

• Install optional boltztrap, vampire and openbabel in CI by @​DanielYang59 in materialsproject/pymatgen#3985

💡 Refactoring

... (truncated)

Commits

• 1ff1ba5 Use distinct names for artifacts (#4059)
• 48e7c98 fix cibuildwheel: No build identifiers selected: BuildSelector(build_config='...
• c469dd8 update docs/CHANGES.md with notes for v2024.9.10 and v2024.8.9
• 6012a68 v2024.9.10
• ed4de1d Fix apply_operation(fractional=True) (#4057)
• dc6a292 Fix typo in Cp2kOutput.parse_hirshfeld `add_site_property("hirshf[i->'']eld...
• f6b4073 Fix ruff PLC0206 and PLR6104 (#4035)
• 13182c5 Avoid importing namespace package pymatgen directly (#4053)
• 326beb9 Make AimsSpeciesFile a dataclass (#4054)
• 149e115 fix typos in AimsSpeciesFile and AimsOutCalcChunk
• Additional commits viewable in compare view

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[dependabot[bot]]

The following labels could not be found: dependency_updates.

[davidwaroquiers]

@dependabot rebase

[dependabot[bot]]

Superseded by #55.