v2024.1.27

Full Changelog: v2024.1.26...v2024.1.27

v2024.1.26

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

v2023.12.18

What's Changed

🐛 Bug Fixes

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

🛠 Enhancements

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

📖 Documentation

• QCInput: add docstrings for svp and pcm_nonels by @rkingsbury in #3522

🚀 Performance

• Avoid redirects in MPRester requests by @tschaume in #3496

🧪 Tests

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

🏷️ Type Hints

• ruff automatic type annotations by @janosh in #3498

New Contributors

• @kyledmiller made their first contribution in #3467

Full Changelog: v2023.11.12...v2023.12.18

v2023.11.12

🐛 Bug Fixes

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

🛠 Enhancements

• Add Composition.charge and charge_balanced properties by @janosh in #3471

v2023.11.10

🐛 Bug Fixes

• Fix LobsterMatrices calculated incorrectly by @naik-aakash in #3407
• Fix test_relax_chgnet by @janosh in #3417
• Breaking: return sum of Species with matching Element in Composition.__getitem__ by @janosh in #3427
• Update inputs.py by @RedStar-Iron in #3430
• Fix lattice velocities formatting by @gpetretto in #3433
• Fix lobsterin dict inheritance and treat \t in lobsterins correctly by @JaGeo in #3439
• Fix BSPlotterProjected.get_elt_projected_plots by @janosh in #3451
• Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms by @kaifengZheng in #3426
• Write test-created files to temporary directory, don't pollute test dir by @janosh in #3454
• Issue stronger warning if bader is run without the AECCARs by @janosh in #3458
• Fix Vasprun not interpreting float overflow as nan by @tawe141 in #3452
• Aims bug fixes by @tpurcell90 in #3466

🛠 Enhancements

• Add LobsterMatrices parser to lobster.io.outputs by @naik-aakash in #3361
• Propagate site labels in SymmetrizedStructure() by @stefsmeets in #3423
• Add lattice velocities to Poscar by @gpetretto in #3428
• Add summary_stats key to Vasprun.potcar_spec by @esoteric-ephemera in #3434
• Deprecate CifParser.get_structures() in favor of new parse_structures in which primitive defaults to False by @janosh in #3419
• FHI-aims IO Parsers by @tpurcell90 in #3435

🧹 House-Keeping

• Rename Poscar.from_file() check_for_POTCAR to check_for_potcar by @janosh in #3406
• Remove warning in cohp module by @JaGeo in #3418
• Drop black for ruff format by @janosh in #3420
• Refresh OPTIMADE aliases and update docstrings by @ml-evs in #3447
• Use convenience exports from pymatgen/core/__init__.py where no risk of circular imports by @janosh in #3461
• Move needlessly function-scoped imports to module scope by @janosh in #3462
• Module-scoped imports by @janosh in #3464

🤷‍♂️ Other Changes

• Create jekyll-gh-pages.yml by @shyuep in #3410
• Make from_(str|file) (static->class)methods by @janosh in #3429

New Contributors

• @RedStar-Iron made their first contribution in #3430
• @tawe141 made their first contribution in #3452
• @tpurcell90 made their first contribution in #3435

v2023.10.11

🐛 Bug Fixes

• Fix outdated setup.py find_namespace_packages and add test_egg_sources_txt_is_complete by @janosh in #3374
• release.yml add option to publish to TestPyPI by @janosh in #3375
• Fix wrong unit=eV in get_band_(skewness|kurtosis) doc string by @janosh in #3383
• Further updating POTCAR validation / identification by @esoteric-ephemera in #3392
• MatPESStaticSet.yaml set LMAXMIX: 6 by @janosh in #3400
• Fix type annotations in phonon/ and lammps/ by @ab5424 in #3401
• Fix OBAlign(includeH=False, symmetry=False) can't take keywords by @janosh in #3403

🛠 Enhancements

• New class to handle NcICOBILIST.lobster files by @QuantumChemist in #2878
• Add inplace: bool=True arg to Structure.apply_strain() by @janosh in #3376
• Add Structure.to_(conventional|primitive|cell) methods by @janosh in #3384
• Add SiteCollection.to_ase_atoms() by @janosh in #3389
• Add mode: Literal["w", "a", "wt", "at"] = "w" keyword to CifWriter.write_file() by @janosh in #3399

📖 Documentation

• Add docs/fetch_pmg_contributors.py script by @janosh in #3387

🧹 House-Keeping

• Fix ruff FURB violations by @janosh in #3382
• Remove deprecated module pymatgen/util/convergence.py by @janosh in #3388
• Remove pylint: disable comments by @janosh in #3390
• Fix ruff N806 by @janosh in #3394

🧪 Tests

• Update incar_parameters.json to allow ISIF=8 by @matthewkuner in #3381
• Add test_potcar_summary_stats() by @janosh in #3395
• Mirror atomate2 fix and improve MPScanRelaxSet.test_kspacing edge case coverage by @janosh in #3396

💥 Breaking Changes

• Breaking: snake_case FiestaInput keywords and class attributes by @janosh in #3386
• Ion: default hydrates=False in reduced_formula by @rkingsbury in #3350

🏷️ Type Hints

• Add type annotations to io/lammps by @ab5424 in #3379
• Add type annotations to phonon by @ab5424 in #3393

Full Changelog: v2023.10.4...v2023.10.11

v2023.10.4

What's Changed

🐛 Bug Fixes

• Fix missing potcar_summary_stats.json.gz in setup.package_data by @janosh in #3372

Full Changelog: v2023.10.3...v2023.10.4

v2023.10.3

What's Changed

🐛 Bug Fixes

• Revert openbabel.OBAlign() in molecule_matcher.py to use positional args for includeH, symmetry by @janosh in #3353
• Fix MPMD set bug by @MichaelWolloch in #3355
• Fix TestMPResterNewBasic + AseAtomsAdaptor test errors and TransformedStructure.from_snl overwriting hist variable by @janosh in #3362
• Fix TypeError: can only join an iterable with AECCAR in VolumetricData.write_file by @chiang-yuan in #3343

🛠 Enhancements

• Don't rely on jsanitize in Atoms <--> Structure object interconversion by @Andrew-S-Rosen in #3359
• Breaking: New method of POTCAR validation by @esoteric-ephemera in #3351
• Add alias .to_file() for .to() method of structures and molecules by @QuantumChemist in #3356
• Update POTCAR summary stats to include 6.4 POTCARs and add dev_script utils for future updates by @esoteric-ephemera in #3370

🧹 House-Keeping

• Chargemol minor refactor by @janosh in #3357
• Breaking typo fix: Targe(tt->t)edPenaltiedAbundanceChemenvStrategy by @janosh in #3360
• Fix undiscovered tests by @janosh in #3369

🏥 Package Health

• Bump min numpy to v1.25.0 by @janosh in #3352

New Contributors

• @esoteric-ephemera made their first contribution in #3351
• @QuantumChemist made their first contribution in #3356

Full Changelog: v2023.9.25...v2023.10.3

v2023.9.25

What's Changed

🐛 Bug Fixes

• Fix MPSOCSet raising ValueError on structure=None by @janosh in #3310
• Fix AttributeError in BSPlotter.get_plot() by @janosh in #3327
• Use ax = fig.add_subplot(projection='3d') to create Axes3D by @janosh in #3330
• Fix breaking change to CoherentInterfaceBuilder.get_interfaces by @janosh in #3337
• Add properties @property/docstring to IStructure by @mkhorton in #3338
• Always return 0 for Composition.oxi_state_guesses() of diatomic molecules by @janosh in #3332
• Fix: TestMITMPRelaxSet.test_nelect claimed to but wasn't testing disordered structure by @janosh in #3344

🛠 Enhancements

• Allow usage of calculate_ng with a custom ENCUT and PREC values for VASP input sets by @matthewkuner in #3314
• Fix TestPotcar.test_write polluting git repo on failure by @janosh in #3347

📖 Documentation

• Update @arosen93 to @Andrew-S-Rosen by @Andrew-S-Rosen in #3311
• Google-style doc strings for class attributes by @janosh in #3320
• More Google-style class attribute doc strings by @janosh in #3323
• Readme notice regarding updated pymatgen publication by @janosh in #3325
• Breaking: rename get_ax3d_fig_plt->get_ax3d_fig and get_ax_fig_plt->get_ax_fig plus no longer return plt by @janosh in #3329

🧹 House-Keeping

• Fix internal SymmOp.from_xyz_string and MagSymmOp.from_xyzt_string deprecation warnings by @janosh in #3315
• Fix ruff A001 violations: Variable is shadowing a Python builtin by @janosh in #3331
• Delete unused or numpy-provided routines from pymatgen.util.num by @janosh in #3333
• fix ruff FBT003: Boolean positional value in function call by @janosh in #3335
• Snake case test method names by @janosh in #3339

🤷‍♂️ Other Changes

• Fix atomic mass for Og by @mkhorton in #3317

Full Changelog: v2023.9.10...v2023.9.25

v2023.9.10

What's Changed

🐛 Bug Fixes

• Fix code comment in ASE adapter by @Andrew-S-Rosen in #3298
• Fix IndexError when parsing Hessian from Gaussian frequency job by @janosh in #3308

🛠 Enhancements

• Add an input arg check for Kpoints.automatic_density_by_lengths by @Andrew-S-Rosen in #3299

🏥 Package Health

• Remove pydantic < 2 from setup.py and bump monty in requirements.txt by @Andrew-S-Rosen in #3303
• Move py.typed to package root by @Andrew-S-Rosen in #3307
• Consistent casing setup->setUp across test classes by @janosh in #3305

🤷‍♂️ Other Changes

• v2023.9.10 by @janosh in #3309

Full Changelog: v2023.9.2...v2023.9.10