v2024.5.1

What's Changed

🐛 Bug Fixes

• Fix OPTIMADE rester URL contruction and improve testing by @ml-evs in #3756
• Add fix for SFAC writer by @stefsmeets in #3779
• Fix LobsterSet by @naik-aakash in #3771
• Update vasprun.converged_ionic logic when EDIFFG=0, REDO of PR #3765 by @matthewkuner in #3783
• Fix for incorrect file path in tests/io/test_zeopp.py by @AntObi in #3784
• Fix for writing non-unique site labels in CifWriter by @stefsmeets in #3767
• Homogenize return type of Lattice.get_points_in_sphere to always be np.array(s) by @janosh in #3797

📖 Documentation

• Add note to documentation for usage of CrystalNN by @JaGeo in #3764
• Update to average Grüneisen documentation by @JaGeo in #3773
• Format doc strings by @janosh in #3790
• Imperative doc strings by @janosh in #3792

🧹 House-Keeping

• pyright fixes for ext/io/phonon/symmetry/transformations/util/vis/dev_scripts and improve io.lobster by @DanielYang59 in #3757
• Separate test files by modules and collect test files csv/cif into folders by @DanielYang59 in #3746

🚧 CI

• Officially support Python 3.12 and test in CI by @janosh in #3685

🏥 Package Health

• Remove gulp from package data, code base and CI tests by @DanielYang59 in #3789

🏷️ Type Hints

• Add type annotations for io.vasp.inputs/optics by @DanielYang59 in #3740
• pyright fixes by @DanielYang59 in #3777
• Convert kpts in Kpoints to Sequence[tuple] and set it as property by @DanielYang59 in #3758

🤷‍♂️ Other Changes

• add get_string->get_str alias for Poscar by @timurbazhirov in #3763
• Fix ruff FURB192 by @janosh in #3785

New Contributors

• @timurbazhirov made their first contribution in #3763
• @AntObi made their first contribution in #3784

Full Changelog: v2024.4.13...2024.5.1

v2024.4.13

Hot fix release for v2024.4.12 to be yanked on PyPI due to #3751.

🐛 Bug Fixes

• Revert mistaken Cohp.has_antibnd_states_below_efermi rename by @JaGeo in #3750
• Fix typing_extension ImportError in downstream packages by @janosh in #3752
• Update some of the OPTIMADE aliases by @ml-evs in #3754

🧹 House-Keeping

• Remove duplicate ruff rule in pyproject.toml by @Andrew-S-Rosen in #3755

Full Changelog: v2024.4.12...v2024.4.13

v2024.4.12

What's Changed

🎉 New Features

• Add pymatgen.io.openff module by @orionarcher in #3729

🐛 Bug Fixes

• Fix blank line bug in io.res.ResWriter by @stefsmeets in #3671
• Reset label for sites changed by Structure.replace_species() by @stefsmeets in #3672
• Fix phonopy.get_pmg_structure site_properties key for magmoms by @JonathanSchmidt1 in #3679
• Improve Bandoverlaps parser by @naik-aakash in #3689
• Convert some staticmethod to classmethod by @DanielYang59 in #3710
• Correct units of Element.atomic_orbitals by @esoteric-ephemera in #3714
• Add a fix for if a parameter is None in AimsControlIn by @tpurcell90 in #3727
• Replace general raise Exception and add missing raise keyword by @DanielYang59 in #3728
• Fix ChemicalPotentialDiagram 2D plot not respecting formal_chempots setting by @uliaschauer in #3734
• Update ENCUT type to float in incar_parameters.json by @yuuukuma in #3741
• Clean up core.surface comments and docstrings by @DanielYang59 in #3691
• Fix io.cp2k.input.DataFile by @DanielYang59 in #3745

🛠 Enhancements

• Ensure MSONAtoms is indeed MSONable when Atoms.info is loaded with goodies by @Andrew-S-Rosen in #3670
• Generalize fatband plots from Lobster by @JaGeo in #3688
• Plotting of Multicenter COBIs by @JaGeo in #2926
• Support appending vectors to positions in XSF format by @mturiansky in #3704
• Define needs_u_correction(comp: CompositionLike) -> set[str] utility function by @janosh in #3703
• Add more flexibility to PhononDOSPlotter and PhononBSPlotter by @ab5424 in #3700
• Define ElementType enum in core/periodic_table.py by @janosh in #3726

📖 Documentation

• Reformat docstrings to Google style and add type annotations by @DanielYang59 in #3694

🧹 House-Keeping

• Breaking: all plot methods return plt.Axes by @janosh in #3749
• Clean up test files: VASP outputs by @DanielYang59 in #3653
• Clean up test files: VASP inputs by @DanielYang59 in #3674
• Clean up test files: dedicated VASP directories, xyz, mcif, cssr, exciting, wannier90 by @DanielYang59 in #3681
• Remove exception printing when importing phonopy by @lan496 in #3696
• Standardize test names: e.g. LatticeTestCase -> TestLattice by @janosh in #3693
• Clean up tests by @janosh in #3713
• Fix import order for if TYPE_CHECKING: block by @DanielYang59 in #3711
• Use Self type in Method Signatures by @DanielYang59 in #3705
• Remove deprecated analysis.interface, rename classes to PascalCase and rename with_* to from_* by @DanielYang59 in #3725
• Test EntrySet.ground_states and CIF writing in NEBSet.write_input by @janosh in #3732

🚀 Performance

• Migrate CI dependency installation from pip to uv by @janosh in #3675
• Dynamic __hash__ for BalancedReaction by @DanielYang59 in #3676

🚧 CI

• Prevent GitHub Actions from running docs-related CI on forks by @lan496 in #3697

🧪 Tests

• Clean up tests 2 by @janosh in #3716
• Remove unnecessary unittest.TestCase subclassing by @janosh in #3718

🔒 Security Fixes

• Avoid using exec in code by @DanielYang59 in #3736
• Avoid using eval, replace manual offset in enumerate and rename single letter variables by @DanielYang59 in #3739

🏷️ Type Hints

• Self return type on from_dict methods by @janosh in #3702
• Return self from Structure methods replace, substitute, remove_species, remove_sites by @janosh in #3706
• Self return type on Lattice methods by @janosh in #3707

🤷‍♂️ Other Changes

• os.path.(exists->isfile) by @janosh in #3690

New Contributors

• @JonathanSchmidt1 made their first contribution in #3679
• @uliaschauer made their first contribution in #3734

Full Changelog: v2024.3.1...v2024.4.12

v2024.3.1

What's Changed

🐛 Bug Fixes

• Fix BSPlotterProjected.get_projected_plots_dots_patom_pmorb fix set & list intersect by @janosh in #3651
• Remove rounding during FEFF writing by @matthewcarbone in #3345
• Fix get_niggli_reduced_lattice if entering A1 case by @packer-jp in #3657
• Remove BadPoscarWarning when POSCAR elements set by POTCAR by @esoteric-ephemera in #3662
• Fix RuntimeError triggered in CI of downstream packages by @janosh in #3664

🛠 Enhancements

• Kpoint.__eq__ and PhononBandStructureSymmLine.__eq__ methods + tests by @janosh in #3650
• LOBSTER IO improvements by @naik-aakash in #3649

📖 Documentation

• Lobsterout update doc-string to match renamed class variable by @naik-aakash in #3655
• Fix installation.md formatting by @Andrew-S-Rosen in #3661

🧹 House-Keeping

• Use np.eye(3) instead of [[1, 0, 0], [0, 1, 0], [0, 0, 1]] for identies by @janosh in #3659

🧪 Tests

• Deprecate _parse_atomic_densities in BaderAnalysis and fix Bader test setup by @DanielYang59 in #3656

🏷️ Type Hints

• Improve INCAR tag check by @DanielYang59 in #3621

🤷‍♂️ Other Changes

• Avoid bader_caller from altering compressed file in place by @DanielYang59 in #3660

New Contributors

• @matthewcarbone made their first contribution in #3345
• @packer-jp made their first contribution in #3657

Full Changelog: v2024.2.23...v2024.3.1

v2024.2.23

What's Changed

🐛 Bug Fixes

• Modify BadInputSetWarning logic for relaxations of a likely metal by @Andrew-S-Rosen in #3634
• Fix Lobsterenv Bug by @naik-aakash in #3637
• [BugFix] Subclass Construction Locpot<:VolumetricData by @jmmshn in #3639
• Guard MSONAtoms definition behind ASE package availability by @ml-evs in #3645
• Remove properties from abivars dict as this breaks the interface with… by @gmatteo in #3642

🛠 Enhancements

• Add interface to icet SQS tools through SQSTransformation by @esoteric-ephemera in #3593
• Modified CifParser.check() as one possible solution for issue #3626 by @kaueltzen in #3628
• Add capability for Vasprun to read KPOINTS_OPT data by @bfield1 in #3509

🧪 Tests

• Compress test vasprun.xml files by @DanielYang59 in #3648

🤷‍♂️ Other Changes

• Alias VaspInputSet to VaspInputGenerator by @janosh in #3566

New Contributors

• @bfield1 made their first contribution in #3509

Full Changelog: v2024.2.20...v2024.2.23

v2024.2.20

What's Changed

This release addresses an important security issue that might affect some users of pymatgen who are parsing untrusted user input, for example a server using pymatgen to parse a user-uploaded CIF file. More information is available in the associated CVE. Thank you to William Khem-Marquez (@SteakEnthusiast) for the discovery and responsible disclosure of this issue.

🐛 Bug Fixes

• Revert back TransformedStructure.__getattr__ by @mjwen in #3617
• Fixed Incar object to allow for ML_MODE vasp tag by @davidwaroquiers in #3625
• Add missing MPSCANRelaxSet.yaml parameters and alphabetize by @Andrew-S-Rosen in #3615
• Fix bader_analysis_from_path using warning as file path and reinstate test by @janosh in #3632

🛠 Enhancements

• Breaking: fix SubstrateAnalyzer film + substrate vectors not using original crystal coordinates by @jinlhr542 in #3572
• Handle invalid selective dynamics info in POSCAR by @DanielYang59 in #3539
• Return self from all SiteCollection/Structure/Molecule in-place modification methods by @janosh in #3623
• Make the POTCAR setup instructions clearer by @Andrew-S-Rosen in #3630

🧹 House-Keeping

• Refactors + types + fix doc string returns to use Google format by @janosh in #3620

🚀 Performance

• Speeding up get_nn_info in local_env.py by @ftherrien in #3635

💥 Breaking Changes

• Lobsterenv improvements by @naik-aakash in #3624

🤷‍♂️ Other Changes

• Fix URL joining in OptimadeRester by @rdamaral in #3613
• Create a CODEOWNERS by @Andrew-S-Rosen in #3616
• Adds support for an MSONAtoms class that's an MSONable form of an ASE Atoms object by @Andrew-S-Rosen in #3619
• Lobster io improvements by @naik-aakash in #3627

New Contributors

• @jinlhr542 made their first contribution in #3572
• @rdamaral made their first contribution in #3613
• @ftherrien made their first contribution in #3635

Full Changelog: v2024.2.8...v2024.2.20

v2024.2.8

What's Changed

🐛 Bug Fixes

• Fix Vasprun.get_potcars search method; tweak fake POTCARs by @esoteric-ephemera in #3587

🛠 Enhancements

• Aims input sets by @tpurcell90 in #3482
• Add SiteCollection.reduced_formula property by @janosh in #3610
• Add Entry.(formula|reduced_formula) by @janosh in #3611
• VASP IO copy() methods by @janosh in #3602

📖 Documentation

• Adding FHI-aims inputs developers by @tpurcell90 in #3592

🧹 House-Keeping

• chore: fix a typo by @VsevolodX in #3609

🧪 Tests

• Add tests for the New Vasp input sets by @Zhuoying in #3576

🏥 Package Health

• Switch macOS wheel building to new M1 runners by @janosh in #3596

🤷‍♂️ Other Changes

• Fix text formatting in bug_report.yaml by @Andrew-S-Rosen in #3589
• Minor update to avoid deprecation warning by @kavanase in #3601

New Contributors

• @VsevolodX made their first contribution in #3609

Full Changelog: v2024.1.27...v2024.2.8

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