Bump pymatgen from 2023.9.10 to 2023.12.18

[dependabot[bot]]

Bumps pymatgen from 2023.9.10 to 2023.12.18.

Release notes

Sourced from pymatgen's releases.

v2023.12.18

What's Changed

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

• QCInput: add docstrings for svp and pcm_nonels by @​rkingsbury in materialsproject/pymatgen#3522

🚀 Performance

• Avoid redirects in MPRester requests by @​tschaume in materialsproject/pymatgen#3496

🧪 Tests

• Fix weak __str__ tests across pymatgen by @​janosh in materialsproject/pymatgen#3472
• Test improvements by @​janosh in materialsproject/pymatgen#3497

🏷️ Type Hints

• ruff automatic type annotations by @​janosh in materialsproject/pymatgen#3498

New Contributors

• @​kyledmiller made their first contribution in materialsproject/pymatgen#3467

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

v2023.11.12

🐛 Bug Fixes

• Hot fix: pymatgen package missing potcar-summary-stats.json.bz2 by @​janosh in materialsproject/pymatgen#3468

... (truncated)

Changelog

Sourced from pymatgen's changelog.

v2023.12.18

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

• QCInput: add docstrings for svp and pcm_nonels by @​rkingsbury in materialsproject/pymatgen#3522

🚀 Performance

• Avoid redirects in MPRester requests by @​tschaume in materialsproject/pymatgen#3496

🧪 Tests

• Fix weak __str__ tests across pymatgen by @​janosh in materialsproject/pymatgen#3472
• Test improvements by @​janosh in materialsproject/pymatgen#3497

🏷️ Type Hints

• ruff automatic type annotations by @​janosh in materialsproject/pymatgen#3498

... (truncated)

Commits

• 36e289c v2023.12.18
• b29a0a6 Add PhononDos.get_last_peak() (#3525)
• 4e40e57 PhononDos.get_smeared_densities return density unchanged for sigma=0 (#3524)
• 0caa466 QCInput: add docstrings for svp and pcm_nonels (#3522)
• b45666b Add PhononDos.mae() and PhononBandStructure.has_imaginary_gamma_freq() me...
• 131c455 Update docstring
• f31d6ab Raise ValueError for float('NaN') in Composition (#3519)
• 11714b9 only show legend in PhononDosPlotter if there are non-empty labels
• d5d750f Add strict parameter to _parse_formula method and raise ValueError if formula...
• 4a94f9c Add bold flag to latexify (#3516)
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