Pymatgen

Latest version: v2024.4.13

Safety actively analyzes 621173 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 1 of 59

2024.4.13

Hot fix release for [v2024.4.12](v2024412) to be yanked on PyPI due to https://github.com/materialsproject/pymatgen/issues/3751.

πŸ› Bug Fixes

* Revert mistaken `Cohp.has_antibnd_states_below_efermi` rename by JaGeo in https://github.com/materialsproject/pymatgen/pull/3750
* Fix `typing_extension` `ImportError` in downstream packages by janosh in https://github.com/materialsproject/pymatgen/pull/3752
* Update some of the OPTIMADE aliases by ml-evs in https://github.com/materialsproject/pymatgen/pull/3754

🧹 House-Keeping

* Remove duplicate ruff rule in `pyproject.toml` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3755

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.4.12...v2024.4.13

2024.4.12

πŸŽ‰ New Features

* Add `pymatgen.io.openff` module by orionarcher in https://github.com/materialsproject/pymatgen/pull/3729

πŸ› Bug Fixes

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

πŸ›  Enhancements

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

🚧 CI

* Migrate CI dependency installation from `pip` to `uv` by janosh in https://github.com/materialsproject/pymatgen/pull/3675
* Prevent GitHub Actions from running docs-related CI on forks by lan496 in https://github.com/materialsproject/pymatgen/pull/3697

πŸ“– Documentation

* Reformat docstrings to Google style and add type annotations by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3694
* Breaking: all plot methods return `plt.Axes` by janosh in https://github.com/materialsproject/pymatgen/pull/3749

🧹 House-Keeping

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

πŸš€ Performance

* Dynamic `__hash__` for `BalancedReaction` by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3676

πŸ§ͺ Tests

* Clean up tests 2 by janosh in https://github.com/materialsproject/pymatgen/pull/3716
* Remove unnecessary `unittest.TestCase` subclassing by janosh in https://github.com/materialsproject/pymatgen/pull/3718

πŸ”’ Security Fixes

* Avoid using `exec` in code by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3736
* Avoid using `eval`, replace manual offset in `enumerate` and rename single letter variables by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3739

🏷️ Type Hints

* `Self` return type on `from_dict` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3702
* Return `self` from `Structure` methods `replace`, `substitute`, `remove_species`, `remove_sites` by janosh in https://github.com/materialsproject/pymatgen/pull/3706
* `Self` return type on `Lattice` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3707

πŸ€·β€β™‚οΈ Other Changes

* `os.path.(exists->isfile)` by janosh in https://github.com/materialsproject/pymatgen/pull/3690

New Contributors

* JonathanSchmidt1 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3679
* uliaschauer made their first contribution in https://github.com/materialsproject/pymatgen/pull/3734

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.3.1...v2024.4.12

2024.3.1

What's Changed

πŸ› Bug Fixes

* Fix `BSPlotterProjected.get_projected_plots_dots_patom_pmorb` fix set & list intersect by janosh in https://github.com/materialsproject/pymatgen/pull/3651
* Remove rounding during FEFF writing by matthewcarbone in https://github.com/materialsproject/pymatgen/pull/3345
* Fix `get_niggli_reduced_lattice` if entering A1 case by packer-jp in https://github.com/materialsproject/pymatgen/pull/3657
* Remove BadPoscarWarning when POSCAR elements set by POTCAR by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3662
* Fix RuntimeError triggered in CI of downstream packages by janosh in https://github.com/materialsproject/pymatgen/pull/3664

πŸ›  Enhancements

* `Kpoint.__eq__` and `PhononBandStructureSymmLine.__eq__` methods + tests by janosh in https://github.com/materialsproject/pymatgen/pull/3650
* LOBSTER IO improvements by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3649

πŸ“– Documentation

* Lobsterout update doc-string to match renamed class variable by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3655
* Fix installation.md formatting by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3661

🧹 House-Keeping

* Use `np.eye(3)` instead of `[[1, 0, 0], [0, 1, 0], [0, 0, 1]]` for identies by janosh in https://github.com/materialsproject/pymatgen/pull/3659

πŸ§ͺ Tests

* Deprecate `_parse_atomic_densities` in `BaderAnalysis` and fix `Bader` test setup by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3656

🏷️ Type Hints

* Improve INCAR tag check by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3621

πŸ€·β€β™‚οΈ Other Changes

* Avoid `bader_caller` from altering compressed file in place by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3660

New Contributors

* matthewcarbone made their first contribution in https://github.com/materialsproject/pymatgen/pull/3345
* packer-jp made their first contribution in https://github.com/materialsproject/pymatgen/pull/3657

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.23...v2024.3.1

2024.2.23

πŸ› Bug Fixes

* Remove properties from abivars dict as this breaks the interface with… by gmatteo in https://github.com/materialsproject/pymatgen/pull/3642

πŸ›  Enhancements

* Modified CifParser.check() as one possible solution for issue 3626 by kaueltzen in https://github.com/materialsproject/pymatgen/pull/3628
* Add capability for Vasprun to read KPOINTS_OPT data by bfield1 in https://github.com/materialsproject/pymatgen/pull/3509

πŸ§ͺ Tests

* Compress test vasprun.xml files by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3648

πŸ€·β€β™‚οΈ Other Changes

* Modify `BadInputSetWarning` logic for relaxations of a likely metal by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3634
* Fix Lobsterenv Bug by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3637
* [BugFix] Subclass Construction Locpot<:VolumetricData by jmmshn in https://github.com/materialsproject/pymatgen/pull/3639
* Add interface to icet SQS tools through SQSTransformation by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3593
* Guard `MSONAtoms` definition behind ASE package availability by ml-evs in https://github.com/materialsproject/pymatgen/pull/3645
* Alias `VaspInputSet` to `VaspInputGenerator` by janosh in https://github.com/materialsproject/pymatgen/pull/3566

New Contributors

* bfield1 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3509

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.20...v2024.2.23

2024.2.20

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](https://github.com/materialsproject/pymatgen/security/advisories/GHSA-vgv8-5cpj-qj2f). Thank you to [William Khem-Marquez (SteakEnthusiast)](https://github.com/SteakEnthusiast) for the discovery and responsible disclosure of this issue.

πŸ› Bug Fixes

* Revert back `TransformedStructure.__getattr__` by mjwen in https://github.com/materialsproject/pymatgen/pull/3617
* Fixed Incar object to allow for ML_MODE vasp tag by davidwaroquiers in https://github.com/materialsproject/pymatgen/pull/3625
* Add missing `MPSCANRelaxSet.yaml` parameters and alphabetize by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3615
* Fix `bader_analysis_from_path` using warning as file path and reinstate test by janosh in https://github.com/materialsproject/pymatgen/pull/3632

πŸ›  Enhancements

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

🧹 House-Keeping

* Refactors + types + fix doc string returns to use Google format by janosh in https://github.com/materialsproject/pymatgen/pull/3620

πŸš€ Performance

* Speeding up `get_nn_info` in local_env.py by ftherrien in https://github.com/materialsproject/pymatgen/pull/3635

πŸ’₯ Breaking Changes

* Lobsterenv improvements by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3624

πŸ€·β€β™‚οΈ Other Changes

* Fix URL joining in OptimadeRester by rdamaral in https://github.com/materialsproject/pymatgen/pull/3613
* Create a `CODEOWNERS` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3616
* Adds support for an `MSONAtoms` class that's an `MSONable` form of an ASE `Atoms` object by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3619
* Lobster io improvements by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3627

New Contributors

* jinlhr542 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3572
* rdamaral made their first contribution in https://github.com/materialsproject/pymatgen/pull/3613
* ftherrien made their first contribution in https://github.com/materialsproject/pymatgen/pull/3635

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.2.8...v2024.2.20

2024.2.8

Not secure
πŸ› Bug Fixes

* Fix `Vasprun.get_potcars` search method; tweak fake POTCARs by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3587

πŸ›  Enhancements

* Aims input sets by tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3482
* Add `SiteCollection.reduced_formula` property by janosh in https://github.com/materialsproject/pymatgen/pull/3610
* Add `Entry.(formula|reduced_formula)` by janosh in https://github.com/materialsproject/pymatgen/pull/3611
* VASP IO `copy()` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3602

πŸ“– Documentation

* Adding FHI-aims inputs developers by tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3592

🧹 House-Keeping

* chore: fix a typo by VsevolodX in https://github.com/materialsproject/pymatgen/pull/3609

πŸ§ͺ Tests

* Add tests for the New Vasp input sets by Zhuoying in https://github.com/materialsproject/pymatgen/pull/3576

πŸ₯ Package Health

* Switch macOS wheel building to new M1 runners by janosh in https://github.com/materialsproject/pymatgen/pull/3596

πŸ€·β€β™‚οΈ Other Changes

* Fix text formatting in `bug_report.yaml` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3589
* Minor update to avoid deprecation warning by kavanase in https://github.com/materialsproject/pymatgen/pull/3601

New Contributors

* VsevolodX made their first contribution in https://github.com/materialsproject/pymatgen/pull/3609

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2024.1.27...v2024.2.8

Page 1 of 59

Links

Releases

Has known vulnerabilities

Β© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.