Bump pymatgen from 2024.8.9 to 2024.9.17.1

[dependabot[bot]]

Bumps pymatgen from 2024.8.9 to 2024.9.17.1.

Release notes

Sourced from pymatgen's releases.

v2024.9.17.1

• Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @​yang-ruoxi for fixing.)

v2024.9.17

• Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @​yang-ruoxi for fixing.)

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

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2024.9.17.1

• Emergency release No. 2 to fix yet another regression in chempot diagram. (Thanks @​yang-ruoxi for fixing.)

v2024.9.17

• Emergency release to fix broken phase diagram plotting due to completely unnecessary refactoring. (Thanks @​yang-ruoxi for fixing.)

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

... (truncated)

Commits

• 25efe6f Update docs
• d6204d9 fix chempot_diagram (#4072)
• 150f816 Update docs
• b373410 Updated changelog.
• 96b3284 fix phase diagram break from 41e6d99 (#4070)
• ebfc7a0 improve and test PmgVaspPspDirError msg in PotcarSingle.from_symbol_and_funct...
• 60464fd Fix all ruff DOC202 (#4067)
• 7743ac7 (Not) Use setup-uv in CI tests workflow (#4063)
• 6bb2938 Fix lll_reduce for slab generation (#3927)
• 1ff1ba5 Use distinct names for artifacts (#4059)
• Additional commits viewable in compare view

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[github-actions[bot]]

:point_left: Launch a binder notebook on branch _pyiron/pyironnodes/dependabot/pip/pymatgen-2024.9.17.1

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Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
:white_check_mark: +0.00% (target: -1.00%)	:white_check_mark: ∅

Coverage variation details

| | Coverable lines | Covered lines | Coverage | | ------------- | ------------- | ------------- | ------------- | | Common ancestor commit (2bf23d0623c8a0b6bf80781c6b0b77b173b2e771) | 1554 | 519 | 33.40% | | | Head commit (09238e9c9f16bdc14f9acf0c925fcd85b4417550) | 1554 (+0) | 519 (+0) | 33.40% (**+0.00%**) | **Coverage variation** is the difference between the coverage for the head and common ancestor commits of the pull request branch: ` - `

Diff coverage details

| | Coverable lines | Covered lines | Diff coverage | | ------------- | ------------- | ------------- | ------------- | | Pull request (#82) | 0 | 0 | **∅ (not applicable)** | **Diff coverage** is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: `/ * 100%`

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[coveralls]

Pull Request Test Coverage Report for Build 10962993600

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 33.398%

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Totals
Change from base Build 10962972642:	0.0%
Covered Lines:	519
Relevant Lines:	1554

---

💛 - Coveralls

[dependabot[bot]]

Superseded by #91.