Pymatgen

🐛 Bug Fixes

* Hot fix: `pymatgen` package missing `potcar-summary-stats.json.bz2` by janosh in https://github.com/materialsproject/pymatgen/pull/3468

🛠 Enhancements

* Add `Composition.charge` and `charge_balanced` properties by janosh in https://github.com/materialsproject/pymatgen/pull/3471

🐛 Bug Fixes

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

🛠 Enhancements

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

🧹 House-Keeping

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

🤷‍♂️ Other Changes

* Create jekyll-gh-pages.yml by shyuep in https://github.com/materialsproject/pymatgen/pull/3410
* Make `from_(str|file)` `(static->class)methods` by janosh in https://github.com/materialsproject/pymatgen/pull/3429

New Contributors

* RedStar-Iron made their first contribution in https://github.com/materialsproject/pymatgen/pull/3430
* tawe141 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3452
* tpurcell90 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3435

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.10.11...v2023.11.10

🐛 Bug Fixes

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

🛠 Enhancements

* New class to handle `NcICOBILIST.lobster` files by QuantumChemist in <https://github.com/materialsproject/pymatgen/pull/2878>
* Add `inplace: bool=True` arg to `Structure.apply_strain()` by janosh in <https://github.com/materialsproject/pymatgen/pull/3376>
* Add `Structure.to_(conventional|primitive|cell)` methods by janosh in <https://github.com/materialsproject/pymatgen/pull/3384>
* Add `SiteCollection.to_ase_atoms()` by janosh in <https://github.com/materialsproject/pymatgen/pull/3389>
* Add `mode: Literal["w", "a", "wt", "at"] = "w"` keyword to `CifWriter.write_file()` by janosh in <https://github.com/materialsproject/pymatgen/pull/3399>

📖 Documentation

* Add `docs/fetch_pmg_contributors.py` script by janosh in <https://github.com/materialsproject/pymatgen/pull/3387>

🧹 House-Keeping

* Fix ruff `FURB` violations by janosh in <https://github.com/materialsproject/pymatgen/pull/3382>
* Remove deprecated module `pymatgen/util/convergence.py` by janosh in <https://github.com/materialsproject/pymatgen/pull/3388>
* Remove `pylint: disable` comments by janosh in <https://github.com/materialsproject/pymatgen/pull/3390>
* Fix `ruff` `N806` by janosh in <https://github.com/materialsproject/pymatgen/pull/3394>

🧪 Tests

* Update `incar_parameters.json` to allow `ISIF=8` by matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3381>
* Add `test_potcar_summary_stats()` by janosh in <https://github.com/materialsproject/pymatgen/pull/3395>
* Mirror atomate2 fix and improve `MPScanRelaxSet.test_kspacing` edge case coverage by janosh in <https://github.com/materialsproject/pymatgen/pull/3396>

💥 Breaking Changes

* Breaking: snake_case `FiestaInput` keywords and class attributes by janosh in <https://github.com/materialsproject/pymatgen/pull/3386>
* Ion: default hydrates=False in reduced_formula by rkingsbury in <https://github.com/materialsproject/pymatgen/pull/3350>

🏷️ Type Hints

* Add type annotations to io/lammps by ab5424 in <https://github.com/materialsproject/pymatgen/pull/3379>
* Add type annotations to phonon by ab5424 in <https://github.com/materialsproject/pymatgen/pull/3393>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.10.4...v2023.10.11>

🐛 Bug Fixes

* Fix missing `potcar_summary_stats.json.gz` in `setup.package_data` by janosh in <https://github.com/materialsproject/pymatgen/pull/3372>
* Bug fixes for MPRester and packaged data by shyuep

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.10.3...v2023.10.4>

🐛 Bug Fixes

* Revert `openbabel.OBAlign()` in `molecule_matcher.py` to use positional args for `includeH`, `symmetry` by janosh in <https://github.com/materialsproject/pymatgen/pull/3353>
* Fix MPMD set bug by MichaelWolloch in <https://github.com/materialsproject/pymatgen/pull/3355>
* Fix `TestMPResterNewBasic` + `AseAtomsAdaptor` test errors and `TransformedStructure.from_snl` overwriting `hist` variable by janosh in <https://github.com/materialsproject/pymatgen/pull/3362>
* Fix `TypeError`: can only join an iterable with AECCAR in `VolumetricData.write_file` by chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3343>

🛠 Enhancements

* Don't rely on `jsanitize` in `Atoms` <--> `Structure` object interconversion by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3359>
* Breaking: New method of POTCAR validation by esoteric-ephemera in <https://github.com/materialsproject/pymatgen/pull/3351>
* Add alias `.to_file()` for `.to()` method of structures and molecules by QuantumChemist in <https://github.com/materialsproject/pymatgen/pull/3356>

🧹 House-Keeping

* Chargemol minor refactor by janosh in <https://github.com/materialsproject/pymatgen/pull/3357>
* Breaking typo fix: `Targe(tt->t)edPenaltiedAbundanceChemenvStrategy` by janosh in <https://github.com/materialsproject/pymatgen/pull/3360>
* Fix undiscovered tests by janosh in <https://github.com/materialsproject/pymatgen/pull/3369>

🏥 Package Health

* Bump min `numpy` to v1.25.0 by janosh in <https://github.com/materialsproject/pymatgen/pull/3352>

New Contributors

* esoteric-ephemera made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3351>
* QuantumChemist made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3356>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.25...v2023.10.3>

* New basic MPRester implemented that supports the most common use cases without having to install mp-api. mp-api is no longer a dependency of pymatgen.
* Breaking: rename get_ax3d_fig_plt->get_ax3d_fig and get_ax_fig_plt->get_ax_fig plus no longer return plt
* Misc bug fixes.