pymatgen 2024.1.26

v2024.1.26

on Python PyPI

What's Changed

🐛 Bug Fixes

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

🛠 Enhancements

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

🧹 House-Keeping

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

🧪 Tests

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

💥 Breaking Changes

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

🤷‍♂️ Other Changes

• Standardise and update VASP input sets by @utf in #3484

New Contributors

• @DanielYang59 made their first contribution in #3528
• @minhsueh made their first contribution in #3529
• @exenGT made their first contribution in #3422
• @wladerer made their first contribution in #3502
• @tomdemeyere made their first contribution in #3555
• @lhycms made their first contribution in #3512

Full Changelog: v2023.12.18...v2024.1.26