v2024.7.18

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title: Change Log

v2024.6.10

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title: Change Log

v2024.6.4

What's Changed

🐛 Bug Fixes

• Run CI with two different uv resolution strategies: highest and lowest-direct by @janosh in #3852
• Fix filter condition for warn msg of unphysical site occupancy in io.cif by @DanielYang59 in #3853

🛠 Enhancements

• Add new .pmgrc.yaml setting PMG_VASP_PSP_SUB_DIRS: dict[str, str] by @janosh in #3858

📖 Documentation

• Clarify argument shift for SlabGenerator.get_slab by @DanielYang59 in #3748

🚧 CI

• Add CI run without 'optional' deps installed by @janosh in #3857

Full Changelog: v2024.5.31...v2024.6.4

v2024.5.31

What's Changed

🐛 Bug Fixes

• Make Beautifulsoup optional by @ab5424 in #3774
• Fix overlayed subplots in BSPlotterProjected.get_projected_plots_dots() by @janosh in #3798
• Fix _get_dipole_info for DDEC6 ChargemolAnalysis and add test case by @JonathanSchmidt1 in #3801
• Cp2kOutput.parse_initial_structure() use regex for line matching to allow arbitrary white space between Atom/Kind/Element/... by @janosh in #3810
• Fix the minor document error in POTCAR Setup. by @hongyi-zhao in #3834
• Use isclose over == for overlap position check in SlabGenerator.get_slabs by @DanielYang59 in #3825
• [Deprecation] Replace Element property is_rare_earth_metal with is_rare_earth to include Y and Sc by @DanielYang59 in #3817

🛠 Enhancements

• Add is_radioactive property to Element class by @AntObi in #3804
• Add a from_ase_atoms() method to Structure by @Andrew-S-Rosen in #3812
• Adapt to the latest version of PWmat output file by @lhycms in #3823
• Update VASP sets to transition atomate2 to use pymatgen input sets exclusively by @esoteric-ephemera in #3835 (slightly breaking, see #3860 for details)

📖 Documentation

• Imperative get_... method and @property doc strings by @janosh in #3802
• Doc string standardization by @janosh in #3805

🧹 House-Keeping

• Add types for core.(molecular_orbitals|operations|sites|spectrum|tensor|xcfunc) by @DanielYang59 in #3829
• Move test structures out of util directory by @DanielYang59 in #3831

🧪 Tests

• Improve type annotations for core.(trajectory/units) by @DanielYang59 in #3832

🏷️ Type Hints

• More type annotations by @janosh in #3800
• Add types for core.periodic_table/bonds/composition/ion/lattice/libxcfunc, new type MillerIndex and fix Lattice hash by @DanielYang59 in #3814
• Guard TYPE_CHECKING only imports by @DanielYang59 in #3827
• Improve type annotations and comments for io.cif by @DanielYang59 in #3820
• Improve type annotations for core.structure by @DanielYang59 in #3837
• Add type annotations for io.vasp.outputs by @DanielYang59 in #3776

🤷‍♂️ Other Changes

• mixing scheme: change default for verbose by @tschaume in #3806
• ruff 0.4.3 auto-fixes by @janosh in #3808
• Re-enable some useful ruff rules by @DanielYang59 in #3813
• pandas.read_csv: replace deprecated delim_whitespace=True with sep="\s+" by @ab5424 in #3846
• Improve unphysical (greater than 1) occupancy handling in CifParser and add missing site label if not check_occu by @DanielYang59 in #3819

Full Changelog: v2024.5.1...v2024.5.31

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