Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis

<!-- Release notes generated using configuration in .github/release.yml at v2023.12.18 -->

What's Changed

🐛 Bug Fixes

• Improve doc strings substitution_probability.py by @JaGeo in https://github.com/materialsproject/pymatgen/pull/3477
• Convert all FHI-aims stresses to be 3x3 instead of Voigt notation by @tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3476
• Revert pymatgen/symmetry/groups.py module-scoped SymmOp import causing circular import by @janosh in https://github.com/materialsproject/pymatgen/pull/3486
• fix reciprocal_density in MPHSEBSSet and tests by @fraricci in https://github.com/materialsproject/pymatgen/pull/3499
• fix TypeError when attr force_field not exists by @xjf729 in https://github.com/materialsproject/pymatgen/pull/3495
• Fix pdplotter.show with matplotlib backend by @lbluque in https://github.com/materialsproject/pymatgen/pull/3493
• Fix legend label order in PhononBSPlotter.plot_compare() by @janosh in https://github.com/materialsproject/pymatgen/pull/3510

🛠 Enhancements

• Define PBE64Base.yaml for new VASP PBE_64 POTCARs by @janosh in https://github.com/materialsproject/pymatgen/pull/3470
• (Structure|Molecule).alphabetical_formula by @janosh in https://github.com/materialsproject/pymatgen/pull/3478
• Improvements to PhononDosPlotter and PhononBSPlotter by @janosh in https://github.com/materialsproject/pymatgen/pull/3479
• PhononDosPlotter.plot_dos() add support for existing plt.Axes by @janosh in https://github.com/materialsproject/pymatgen/pull/3487
• Allow Structure.interpolate to extrapolate by @kyledmiller in https://github.com/materialsproject/pymatgen/pull/3467
• Updates for Vasprun with MD simulations by @gpetretto in https://github.com/materialsproject/pymatgen/pull/3489
• Add gradient, Hessian, and orbital coeffs scratch file parsers to pymatgen.io.qchem.outputs by @Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3483
• Add multipole parsing for Q-Chem IO by @espottesmith in https://github.com/materialsproject/pymatgen/pull/3490
• CifParser only warn about primitive default value change to False if not passed to parse_structures explicitly by @janosh in https://github.com/materialsproject/pymatgen/pull/3505
• PhononBSPlotter.plot_compare() add legend labels by @janosh in https://github.com/materialsproject/pymatgen/pull/3507
• Define arithmetic ops __add__ __sub__ __mul__ __neg__ __eq__ for PhononDos with tests by @janosh in https://github.com/materialsproject/pymatgen/pull/3511
• Equalize Phonon(Dos|BS)Plotter colors, allow custom plot settings per-DOS by @janosh in https://github.com/materialsproject/pymatgen/pull/3514
• Add bold flag to latexify by @janosh in https://github.com/materialsproject/pymatgen/pull/3516
• Composition raise ValueError if formula string is only numbers and spaces by @janosh in https://github.com/materialsproject/pymatgen/pull/3517
• Raise ValueError for float('NaN') in Composition by @janosh in https://github.com/materialsproject/pymatgen/pull/3519
• Add PhononDos.mae() and PhononBandStructure.has_imaginary_gamma_freq() methods by @janosh in https://github.com/materialsproject/pymatgen/pull/3520
• PhononDos.get_smeared_densities return unchanged for sigma=0 by @janosh in https://github.com/materialsproject/pymatgen/pull/3524
• Add PhononDos.get_last_peak() by @janosh in https://github.com/materialsproject/pymatgen/pull/3525

📖 Documentation

• QCInput: add docstrings for svp and pcm_nonels by @rkingsbury in https://github.com/materialsproject/pymatgen/pull/3522

🚀 Performance

• Avoid redirects in MPRester requests by @tschaume in https://github.com/materialsproject/pymatgen/pull/3496

🧪 Tests

• Fix weak __str__ tests across pymatgen by @janosh in https://github.com/materialsproject/pymatgen/pull/3472
• Test improvements by @janosh in https://github.com/materialsproject/pymatgen/pull/3497

🏷️ Type Hints

• ruff automatic type annotations by @janosh in https://github.com/materialsproject/pymatgen/pull/3498

New Contributors

• @kyledmiller made their first contribution in https://github.com/materialsproject/pymatgen/pull/3467

Full Changelog: https://github.com/materialsproject/pymatgen/compare/v2023.11.12...v2023.12.18