Pymatgen

🐛 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.

🐛 Bug Fixes

* Fix code comment in ASE adapter by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3298>
* Fix IndexError when parsing Hessian from Gaussian frequency job by janosh in <https://github.com/materialsproject/pymatgen/pull/3308>

🛠 Enhancements

* Add an input arg check for `Kpoints.automatic_density_by_lengths` by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3299>

🏥 Package Health

* Remove pydantic < 2 from `setup.py` and bump monty in `requirements.txt` by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3303>
* Move `py.typed` to package root by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3307>
* Consistent casing `setup->setUp` across test classes by janosh in <https://github.com/materialsproject/pymatgen/pull/3305>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10>

🛠 Enhancements

* Add an input arg check for `Kpoints.automatic_density_by_lengths` by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3299>

🏥 Package Health

* Remove pydantic < 2 from `setup.py` and bump monty in `requirements.txt` by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3303>
* Move `py.typed` to package root by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3307>
* Consistent casing `setup->setUp` across test classes by janosh in <https://github.com/materialsproject/pymatgen/pull/3305>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.9.2...v2023.9.10>

* Add `Lattice` property `params_dict` by janosh in <https://github.com/materialsproject/pymatgen/pull/3239>
* Generate SupercellTransformation from minimum boundary distance by JiQi535 in <https://github.com/materialsproject/pymatgen/pull/3238>
* More concise `test_from_boundary_distance` by janosh in <https://github.com/materialsproject/pymatgen/pull/3242>
* Breaking: remove deprecated keyword `properties` from `Species` by janosh in <https://github.com/materialsproject/pymatgen/pull/3243>
* Typo in Docs for PeriodicsSite by jmmshn in <https://github.com/materialsproject/pymatgen/pull/3249>
* Fix `Vasprun.converged_electronic` check if `ALGO=CHI` in `INCAR` by janosh in <https://github.com/materialsproject/pymatgen/pull/3250>
* Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module by janosh in <https://github.com/materialsproject/pymatgen/pull/3237>
* Fix `ruff` D212 by janosh in <https://github.com/materialsproject/pymatgen/pull/3251>
* Fix some Kpoints generated using wrong mesh types by matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3245>
* read `mag` from OSZICAR by chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3146>
* Use `numpy.testing.assert_allclose` over `assert np.allclose` by janosh in <https://github.com/materialsproject/pymatgen/pull/3253>
* Don't let tests pollute the `pymatgen` repo by janosh in <https://github.com/materialsproject/pymatgen/pull/3255>
* Update `compatibility.md` by mbercx in <https://github.com/materialsproject/pymatgen/pull/3260>
* Google-style doc string return types by janosh in <https://github.com/materialsproject/pymatgen/pull/3258>
* Quasi-RRHO Thermochemistry Analysis Module by arepstein in <https://github.com/materialsproject/pymatgen/pull/2028>
* Add keyword `check_occu: bool = True` to `CifParser.get_structures()` by jonathanjdenney in <https://github.com/materialsproject/pymatgen/pull/2836>
* Fix bug in feff inputs.py by kaifengZheng in <https://github.com/materialsproject/pymatgen/pull/3256>
* Cancel concurrent CI runs to save budget by janosh in <https://github.com/materialsproject/pymatgen/pull/3263>
* Fix `Procar.get_projection_on_elements` for structures with multiple same-element ionic sites by Na-Kawa in <https://github.com/materialsproject/pymatgen/pull/3261>
* Fix `TestMPScanStaticSet.test_as_from_dict()` by janosh in <https://github.com/materialsproject/pymatgen/pull/3266>
* Bump activesupport from 7.0.6 to 7.0.7.2 in /docs by dependabot in <https://github.com/materialsproject/pymatgen/pull/3267>
* Fix `TestMPStaticSet` using `MPRelaxSet` in `test_user_incar_kspacing` and `test_kspacing_override` by janosh in <https://github.com/materialsproject/pymatgen/pull/3268>
* Fix `nelectrons` not updating when replacing species in `Molecule` by janosh in <https://github.com/materialsproject/pymatgen/pull/3269>
* Add `properties` to Structure and Molecule by gpetretto in <https://github.com/materialsproject/pymatgen/pull/3264>
* Fix `CifParser.get_structures(check_occu=False)` by janosh in <https://github.com/materialsproject/pymatgen/pull/3272>
* Add `PotcarSingle.__repr__` by janosh in <https://github.com/materialsproject/pymatgen/pull/3273>
* `__str__` to `__repr__` by janosh in <https://github.com/materialsproject/pymatgen/pull/3274>
* Ion: handle dissolved gas formulas by rkingsbury in <https://github.com/materialsproject/pymatgen/pull/3275>
* Add VASP input set `MatPESStaticSet` by SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3254>
* Fix `test_valid_magmom_struct()` error message regex by janosh in <https://github.com/materialsproject/pymatgen/pull/3276>
* fix tests of MatPESStaticSet by SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3281>
* Breaking: bump minimum Python version to 3.9 by janosh in <https://github.com/materialsproject/pymatgen/pull/3283>
* Breaking: Update `AseAtomsAdaptor` to handle `Structure.properties`/`Molecule.properties` by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3270>
* Slightly relax the constraint satisfy condition of get_primitive_structure() by fyalcin in <https://github.com/materialsproject/pymatgen/pull/3285>
* [WIP] add custodian modified incar settings to incar and modify tests by SophiaRuan in <https://github.com/materialsproject/pymatgen/pull/3284>
* Add keyword `bandgap_tol: float = 1e-4` to `MPScanRelaxSet` by janosh in <https://github.com/materialsproject/pymatgen/pull/3287>
* `np.(arange->linspace)` in `io/vasp/optics.py` `get_delta`, `get_setp` and `epsilon_imag` by LucasGVerga in <https://github.com/materialsproject/pymatgen/pull/3286>
* MatPESStaticSet restore GGA tag removal if xc_functional.upper() == "R2SCAN" by janosh in <https://github.com/materialsproject/pymatgen/pull/3288>
* Bump pypa/cibuildwheel from 2.14.1 to 2.15.0 by dependabot in <https://github.com/materialsproject/pymatgen/pull/3294>
* Bump cython from 3.0.0 to 3.0.2 by dependabot in <https://github.com/materialsproject/pymatgen/pull/3292>
* Bump scipy from 1.11.1 to 1.11.2 by dependabot in <https://github.com/materialsproject/pymatgen/pull/3291>
* Bump plotly from 5.11.0 to 5.16.1 by dependabot in <https://github.com/materialsproject/pymatgen/pull/3289>
* Bump joblib from 1.3.1 to 1.3.2 by dependabot in <https://github.com/materialsproject/pymatgen/pull/3290>
* Bump mp-api from 0.33.3 to 0.35.1 by dependabot in <https://github.com/materialsproject/pymatgen/pull/3293>
* xyz.**iter**() -> iter(xyz) by janosh in <https://github.com/materialsproject/pymatgen/pull/3228>
* Deprecate overlooked `from/as_..._string` methods by janosh in <https://github.com/materialsproject/pymatgen/pull/3295>

* fix `estimate_nbands` function by matthewkuner in <https://github.com/materialsproject/pymatgen/pull/3149>
* Add `CifParser.get_structures(on_error='warn')` by janosh in <https://github.com/materialsproject/pymatgen/pull/3175>
* `ruff . --fix` by janosh in <https://github.com/materialsproject/pymatgen/pull/3176>
* `AseAtomsAdaptor`: Retain `tags` property when interconverting `Atoms` and `Structure`/`Molecule` by Andrew-S-Rosen in <https://github.com/materialsproject/pymatgen/pull/3151>
* Fix a bug in pwscf.py. The proc_val function modifies string values. by pablogalaviz in <https://github.com/materialsproject/pymatgen/pull/3172>
* Delete commented out print statements by janosh in <https://github.com/materialsproject/pymatgen/pull/3178>
* lots of `from_string` should be `classmethod` by njzjz in <https://github.com/materialsproject/pymatgen/pull/3177>
* Extend lobsterenv for coop/cobi by naik-aakash in <https://github.com/materialsproject/pymatgen/pull/3050>
* BUG: fix setting zero magmoms by lbluque in <https://github.com/materialsproject/pymatgen/pull/3179>
* Prefer `pymatviz` interactive plotly version of periodic table heatmap if available by janosh in <https://github.com/materialsproject/pymatgen/pull/3180>
* Better Composition `repr` by janosh in <https://github.com/materialsproject/pymatgen/pull/3182>
* Breaking: Return True for `Element in Composition` if `Species.symbol` matches `Element` by janosh in <https://github.com/materialsproject/pymatgen/pull/3184>
* Revert `LMAXMIX` "fix" added in 3041 by janosh in <https://github.com/materialsproject/pymatgen/pull/3189>
* Add `bader_exe_path` keyword to `BaderAnalysis` and run `bader` tests in CI by janosh in <https://github.com/materialsproject/pymatgen/pull/3191>
* Unskip and fix `packmol` tests by janosh in <https://github.com/materialsproject/pymatgen/pull/3195>
* Propagate labels through various Structure operations by stefsmeets in <https://github.com/materialsproject/pymatgen/pull/3183>
* Delete variable self assignments by janosh in <https://github.com/materialsproject/pymatgen/pull/3196>
* Improve `Structure` tests by janosh in <https://github.com/materialsproject/pymatgen/pull/3197>
* Test `class XYZ` edge cases by janosh in <https://github.com/materialsproject/pymatgen/pull/3206>
* Fix `EnergyAdjustment.__repr__` by janosh in <https://github.com/materialsproject/pymatgen/pull/3207>
* Markdownlint by janosh in <https://github.com/materialsproject/pymatgen/pull/3209>
* Fix codecov by janosh in <https://github.com/materialsproject/pymatgen/pull/3210>
* Update `pytest-split` durations by janosh in <https://github.com/materialsproject/pymatgen/pull/3211>
* Fix GitHub language statistics after test files migration by janosh in <https://github.com/materialsproject/pymatgen/pull/3214>
* Fix `automatic_density_by_lengths` and add tests for it by janosh in <https://github.com/materialsproject/pymatgen/pull/3218>
* Prefer `len(structure)` over `structure.num_sites` by janosh in <https://github.com/materialsproject/pymatgen/pull/3219>
* Add `PhaseDiagram` method `get_reference_energy` by janosh in <https://github.com/materialsproject/pymatgen/pull/3222>
* Fix isomorphic for molecular graphs by rohithsrinivaas in <https://github.com/materialsproject/pymatgen/pull/3221>
* Add `Structure.elements` property by janosh in <https://github.com/materialsproject/pymatgen/pull/3223>
* Add keyword `in_place: bool = True` to `SiteCollection.replace_species` by janosh in <https://github.com/materialsproject/pymatgen/pull/3224>
* list offending elements in `BVAnalyzer.get_valences` error message by janosh in <https://github.com/materialsproject/pymatgen/pull/3225>
* Add `Entry.elements` property by janosh in <https://github.com/materialsproject/pymatgen/pull/3226>
* Move `PymatgenTest.TEST_FILES_DIR` attribute into module scope by janosh in <https://github.com/materialsproject/pymatgen/pull/3227>
* f-string path construction everywhere, no need for `os.path.join(...)` by janosh in <https://github.com/materialsproject/pymatgen/pull/3229>
* speed up `bader_caller` and `chargemol_caller` by chiang-yuan in <https://github.com/materialsproject/pymatgen/pull/3192>
* Fix `ruff` PYI041 and ignore PYI024 by janosh in <https://github.com/materialsproject/pymatgen/pull/3232>
* Deprecate `get_string()` methods in favor of `get_str()` by janosh in <https://github.com/materialsproject/pymatgen/pull/3231>
* `Structure/Molecule.to()` now always return same string written to file by janosh in <https://github.com/materialsproject/pymatgen/pull/3236>

New Contributors

* matthewkuner made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3149>
* pablogalaviz made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3172>
* rohithsrinivaas made their first contribution in <https://github.com/materialsproject/pymatgen/pull/3221>

**Full Changelog**: <https://github.com/materialsproject/pymatgen/compare/v2023.7.20...v2023.08.10>