Bump pymatgen from 2023.7.20 to 2024.1.27

[dependabot[bot]]

Bumps pymatgen from 2023.7.20 to 2024.1.27.

Release notes

Sourced from pymatgen's releases.

v2024.1.27

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2024.1.26...v2024.1.27

v2024.1.26

What's Changed

🐛 Bug Fixes

• Fix label propagation in Symmetry.from_spacegroup by @​stefsmeets in materialsproject/pymatgen#3527
• Bug fix: SpectrumPlotter.add_spectra by @​minhsueh in materialsproject/pymatgen#3529
• Fix bug in SQSTransformation by @​esoteric-ephemera in materialsproject/pymatgen#3541
• Fix failing CI due to broken BoltzTraP2 install by @​janosh in materialsproject/pymatgen#3543
• Enforce zval to be an integer to avoid improper syntax in .cri file by @​wladerer in materialsproject/pymatgen#3502
• Fix MaterialsProjectCompatibility run type handling for GGA+U by @​rkingsbury in materialsproject/pymatgen#3540
• Accept Path objects as filename in IStructure.to() by @​janosh in materialsproject/pymatgen#3553
• Retain Structure.properties in structure_from_abivars()/structure_to_abivars() round trip by @​janosh in materialsproject/pymatgen#3552
• Support magmoms in get_phonopy_structure() by @​tomdemeyere in materialsproject/pymatgen#3555
• Fix ValueError: Invalid fmt with Structure.to(fmt='yml') by @​janosh in materialsproject/pymatgen#3557
• Improve CIF checking, support for isotopes, and correct handling of new VASP 6.4.2 POSCAR format incl. slashes in header by @​esoteric-ephemera in materialsproject/pymatgen#3542
• Deprecate Structure.ntypesp replaced by Structure.n_elems by @​janosh in materialsproject/pymatgen#3562
• Ruff fixes by @​janosh in materialsproject/pymatgen#3564
• Fix highly-nested parens when formula parsing in Composition by @​janosh in materialsproject/pymatgen#3569
• Fix floating point imprecision error in ordering property of CollinearMagneticStructureAnalyzer by @​kaueltzen in materialsproject/pymatgen#3574
• Support parsing of "final_energy" in Q-Chem 6.1.1 by @​Andrew-S-Rosen in materialsproject/pymatgen#3580

🛠 Enhancements

• Add GitHub Issue Templates by @​DanielYang59 in materialsproject/pymatgen#3528
• Improve PhononBandStructure.has_imaginary_gamma_freq() by checking for negative freqs at all q-points close to Gamma by @​janosh in materialsproject/pymatgen#3530
• Add default issue template labels by @​DanielYang59 in materialsproject/pymatgen#3531
• Add functionality to read ASE *.traj file in Trajectory class method from_file() by @​exenGT in materialsproject/pymatgen#3422
• Add PhononDos.r2_score method by @​janosh in materialsproject/pymatgen#3535
• Add codespace container for reproducing issues by @​DanielYang59 in materialsproject/pymatgen#3537
• Phonon convenience imports by @​janosh in materialsproject/pymatgen#3544
• Add diffusive thermal conductivity model proposed by Agne et al. by @​naik-aakash in materialsproject/pymatgen#3546
• Add flag write_site_properties = False in CifWriter for writing Structure.site_properties as _atom_site_{prop} by @​Andrew-S-Rosen in materialsproject/pymatgen#3550
• Add pymatgen.io.pwmat module by @​lhycms in materialsproject/pymatgen#3512
• Lazy import pandas in Structure.as_dataframe() to improve startup speed by @​janosh in materialsproject/pymatgen#3568
• Return self in SiteCollection spin/oxi state add/remove methods by @​janosh in materialsproject/pymatgen#3573
• Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in addition to PR #3574 by @​kaueltzen in materialsproject/pymatgen#3577

🧹 House-Keeping

• Pass file IO modes as kwarg by @​janosh in materialsproject/pymatgen#3560
• Remove deprecated (to|from|as|get)_string methods by @​janosh in materialsproject/pymatgen#3561

🧪 Tests

• Improve handling of Vasprun POTCAR search, expanded fake POTCAR library for VASP I/O tests by @​esoteric-ephemera in materialsproject/pymatgen#3491
• Add test for NEBAnalysis.get_plot() by @​janosh in materialsproject/pymatgen#3570
• tests/io/aims use numpy.testing.assert_allclose and pytest.MonkeyPatch by @​janosh in materialsproject/pymatgen#3575

💥 Breaking Changes

• Breaking: remove single-use PolarizationLattice which inherited from Structure (antipattern) by @​janosh in materialsproject/pymatgen#3585

🤷‍♂️ Other Changes

• Standardise and update VASP input sets by @​utf in materialsproject/pymatgen#3484

... (truncated)

Changelog

Sourced from pymatgen's changelog.

---

layout: default title: Change Log nav_order: 4

Changelog

v2024.1.26

🐛 Bug Fixes

• Fix label propagation in Symmetry.from_spacegroup by @​stefsmeets in materialsproject/pymatgen#3527
• Bug fix: SpectrumPlotter.add_spectra by @​minhsueh in materialsproject/pymatgen#3529
• Fix bug in SQSTransformation by @​esoteric-ephemera in materialsproject/pymatgen#3541
• Fix failing CI due to broken BoltzTraP2 install by @​janosh in materialsproject/pymatgen#3543
• Enforce zval to be an integer to avoid improper syntax in .cri file by @​wladerer in materialsproject/pymatgen#3502
• Fix MaterialsProjectCompatibility run type handling for GGA+U by @​rkingsbury in materialsproject/pymatgen#3540
• Accept Path objects as filename in IStructure.to() by @​janosh in materialsproject/pymatgen#3553
• Retain Structure.properties in structure_from_abivars()/structure_to_abivars() round trip by @​janosh in materialsproject/pymatgen#3552
• Support magmoms in get_phonopy_structure() by @​tomdemeyere in materialsproject/pymatgen#3555
• Fix ValueError: Invalid fmt with Structure.to(fmt='yml') by @​janosh in materialsproject/pymatgen#3557
• Improve CIF checking, support for isotopes, and correct handling of new VASP 6.4.2 POSCAR format incl. slashes in header by @​esoteric-ephemera in materialsproject/pymatgen#3542
• Deprecate Structure.ntypesp replaced by Structure.n_elems by @​janosh in materialsproject/pymatgen#3562
• Ruff fixes by @​janosh in materialsproject/pymatgen#3564
• Fix highly-nested parens when formula parsing in Composition by @​janosh in materialsproject/pymatgen#3569
• Fix floating point imprecision error in ordering property of CollinearMagneticStructureAnalyzer by @​kaueltzen in materialsproject/pymatgen#3574
• Support parsing of "final_energy" in Q-Chem 6.1.1 by @​Andrew-S-Rosen in materialsproject/pymatgen#3580

🛠 Enhancements

• Add GitHub Issue Templates by @​DanielYang59 in materialsproject/pymatgen#3528
• Improve PhononBandStructure.has_imaginary_gamma_freq() by checking for negative freqs at all q-points close to Gamma by @​janosh in materialsproject/pymatgen#3530
• Add default issue template labels by @​DanielYang59 in materialsproject/pymatgen#3531
• Add functionality to read ASE *.traj file in Trajectory class method from_file() by @​exenGT in materialsproject/pymatgen#3422
• Add PhononDos.r2_score method by @​janosh in materialsproject/pymatgen#3535
• Add codespace container for reproducing issues by @​DanielYang59 in materialsproject/pymatgen#3537
• Phonon convenience imports by @​janosh in materialsproject/pymatgen#3544
• Add diffusive thermal conductivity model proposed by Agne et al. by @​naik-aakash in materialsproject/pymatgen#3546
• Add flag write_site_properties = False in CifWriter for writing Structure.site_properties as _atom_site_{prop} by @​Andrew-S-Rosen in materialsproject/pymatgen#3550
• Add pymatgen.io.pwmat module by @​lhycms in materialsproject/pymatgen#3512
• Lazy import pandas in Structure.as_dataframe() to improve startup speed by @​janosh in materialsproject/pymatgen#3568
• Return self in SiteCollection spin/oxi state add/remove methods by @​janosh in materialsproject/pymatgen#3573
• Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in addition to PR #3574 by @​kaueltzen in materialsproject/pymatgen#3577

🧹 House-Keeping

• Pass file IO modes as kwarg by @​janosh in materialsproject/pymatgen#3560
• Remove deprecated (to|from|as|get)_string methods by @​janosh in materialsproject/pymatgen#3561

... (truncated)

Commits

• ac8a7e9 Update docs
• 5137111 Fix monty version.
• 575f404 v2024.1.26
• e9cc87a remove unneeded unittest tearDown methods
• 9a0eb81 Breaking: remove single-use PolarizationLattice which inherited from `Struc...
• f345f2f test nested square bracket in formula strings
• 9604d75 Allow square brackets in composition. Fixes #3583.
• c0c40dd fix variable clash "dist" in zero_d_graph_to_molecule_graph() introduced in 7...
• cb2f490 Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in a...
• 0b8be98 Support parsing of "final_energy" in Q-Chem 6.1.1 (#3580)
• Additional commits viewable in compare view

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Superseded by #197.