Pymatgen

🐛 Bug Fixes

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

🛠 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

📖 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

🧪 Tests

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

🏥 Package Health

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

🤷‍♂️ 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

🐛 Bug Fixes

* Fix label propagation in `Symmetry.from_spacegroup` by stefsmeets in https://github.com/materialsproject/pymatgen/pull/3527
* Bug fix: SpectrumPlotter.add_spectra by minhsueh in https://github.com/materialsproject/pymatgen/pull/3529
* Fix bug in SQSTransformation by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3541
* Fix failing CI due to broken BoltzTraP2 install by janosh in https://github.com/materialsproject/pymatgen/pull/3543
* Enforce `zval` to be an integer to avoid improper syntax in `.cri` file by wladerer in https://github.com/materialsproject/pymatgen/pull/3502
* Fix MaterialsProjectCompatibility run type handling for GGA+U by rkingsbury in https://github.com/materialsproject/pymatgen/pull/3540
* Accept `Path` objects as `filename` in `IStructure.to()` by janosh in https://github.com/materialsproject/pymatgen/pull/3553
* Retain `Structure.properties` in `structure_from_abivars()`/`structure_to_abivars()` round trip by janosh in https://github.com/materialsproject/pymatgen/pull/3552
* Support `magmoms` in `get_phonopy_structure()` by tomdemeyere in https://github.com/materialsproject/pymatgen/pull/3555
* Fix `ValueError: Invalid fmt` with `Structure.to(fmt='yml')` by janosh in https://github.com/materialsproject/pymatgen/pull/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 https://github.com/materialsproject/pymatgen/pull/3542
* Deprecate `Structure.ntypesp` replaced by `Structure.n_elems` by janosh in https://github.com/materialsproject/pymatgen/pull/3562
* Ruff fixes by janosh in https://github.com/materialsproject/pymatgen/pull/3564
* Fix highly-nested parens when formula parsing in `Composition` by janosh in https://github.com/materialsproject/pymatgen/pull/3569
* Fix floating point imprecision error in ordering property of CollinearMagneticStructureAnalyzer by kaueltzen in https://github.com/materialsproject/pymatgen/pull/3574
* Support parsing of "final_energy" in Q-Chem 6.1.1 by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3580

🛠 Enhancements

* Add GitHub Issue Templates by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3528
* Improve `PhononBandStructure.has_imaginary_gamma_freq()` by checking for negative freqs at all q-points close to Gamma by janosh in https://github.com/materialsproject/pymatgen/pull/3530
* Add default issue template labels by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3531
* Add functionality to read ASE *.traj file in Trajectory class method from_file() by exenGT in https://github.com/materialsproject/pymatgen/pull/3422
* Add `PhononDos.r2_score` method by janosh in https://github.com/materialsproject/pymatgen/pull/3535
* Add codespace container for reproducing issues by DanielYang59 in https://github.com/materialsproject/pymatgen/pull/3537
* Phonon convenience imports by janosh in https://github.com/materialsproject/pymatgen/pull/3544
* Add diffusive thermal conductivity model proposed by Agne et al. by naik-aakash in https://github.com/materialsproject/pymatgen/pull/3546
* Add flag `write_site_properties = False` in `CifWriter` for writing `Structure.site_properties` as `_atom_site_{prop}` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3550
* Add `pymatgen.io.pwmat` module by lhycms in https://github.com/materialsproject/pymatgen/pull/3512
* Lazy import `pandas` in `Structure.as_dataframe()` to improve startup speed by janosh in https://github.com/materialsproject/pymatgen/pull/3568
* Return `self` in `SiteCollection` spin/oxi state add/remove methods by janosh in https://github.com/materialsproject/pymatgen/pull/3573
* Added threshold_ordering parameter to CollinearMagneticStructureAnalyzer in addition to PR 3574 by kaueltzen in https://github.com/materialsproject/pymatgen/pull/3577

🧹 House-Keeping

* Pass file IO modes as kwarg by janosh in https://github.com/materialsproject/pymatgen/pull/3560
* Remove deprecated `(to|from|as|get)_string` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3561

🧪 Tests

* Improve handling of Vasprun POTCAR search, expanded fake POTCAR library for VASP I/O tests by esoteric-ephemera in https://github.com/materialsproject/pymatgen/pull/3491
* Add test for `NEBAnalysis.get_plot()` by janosh in https://github.com/materialsproject/pymatgen/pull/3570
* `tests/io/aims` use `numpy.testing.assert_allclose` and `pytest.MonkeyPatch` by janosh in https://github.com/materialsproject/pymatgen/pull/3575

💥 Breaking Changes

* Breaking: remove single-use `PolarizationLattice` which inherited from `Structure` (antipattern) by janosh in https://github.com/materialsproject/pymatgen/pull/3585

🤷‍♂️ Other Changes

* Standardise and update VASP input sets by utf in https://github.com/materialsproject/pymatgen/pull/3484

New Contributors

* DanielYang59 made their first contribution in https://github.com/materialsproject/pymatgen/pull/3528
* minhsueh made their first contribution in https://github.com/materialsproject/pymatgen/pull/3529
* exenGT made their first contribution in https://github.com/materialsproject/pymatgen/pull/3422
* wladerer made their first contribution in https://github.com/materialsproject/pymatgen/pull/3502
* tomdemeyere made their first contribution in https://github.com/materialsproject/pymatgen/pull/3555
* lhycms made their first contribution in https://github.com/materialsproject/pymatgen/pull/3512

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.12.18...v2024.1.26

🐛 Bug Fixes

* Improve doc strings substitution_probability.py by JaGeo in https://github.com/materialsproject/pymatgen/pull/3477
* Convert all FHI-aims stresses to be 3x3 instead of Voigt notation by tpurcell90 in https://github.com/materialsproject/pymatgen/pull/3476
* Revert `pymatgen/symmetry/groups.py` module-scoped `SymmOp` import causing circular import by janosh in https://github.com/materialsproject/pymatgen/pull/3486
* fix reciprocal_density in MPHSEBSSet and tests by fraricci in https://github.com/materialsproject/pymatgen/pull/3499
* fix TypeError when attr force_field not exists by xjf729 in https://github.com/materialsproject/pymatgen/pull/3495
* Fix pdplotter.show with matplotlib backend by lbluque in https://github.com/materialsproject/pymatgen/pull/3493
* Fix legend label order in `PhononBSPlotter.plot_compare()` by janosh in https://github.com/materialsproject/pymatgen/pull/3510

🛠 Enhancements

* Define `PBE64Base.yaml` for new VASP PBE_64 POTCARs by janosh in https://github.com/materialsproject/pymatgen/pull/3470
* `(Structure|Molecule).alphabetical_formula` by janosh in https://github.com/materialsproject/pymatgen/pull/3478
* Improvements to `PhononDosPlotter` and `PhononBSPlotter` by janosh in https://github.com/materialsproject/pymatgen/pull/3479
* `PhononDosPlotter.plot_dos()` add support for existing `plt.Axes` by janosh in https://github.com/materialsproject/pymatgen/pull/3487
* Allow Structure.interpolate to extrapolate by kyledmiller in https://github.com/materialsproject/pymatgen/pull/3467
* Updates for Vasprun with MD simulations by gpetretto in https://github.com/materialsproject/pymatgen/pull/3489
* Add gradient, Hessian, and orbital coeffs scratch file parsers to `pymatgen.io.qchem.outputs` by Andrew-S-Rosen in https://github.com/materialsproject/pymatgen/pull/3483
* Add multipole parsing for Q-Chem IO by espottesmith in https://github.com/materialsproject/pymatgen/pull/3490
* `CifParser` only warn about `primitive` default value change to `False` if not passed to `parse_structures` explicitly by janosh in https://github.com/materialsproject/pymatgen/pull/3505
* `PhononBSPlotter.plot_compare()` add legend labels by janosh in https://github.com/materialsproject/pymatgen/pull/3507
* Define arithmetic ops `__add__` `__sub__` `__mul__` `__neg__` `__eq__` for `PhononDos` with tests by janosh in https://github.com/materialsproject/pymatgen/pull/3511
* Equalize `Phonon(Dos|BS)Plotter` colors, allow custom plot settings per-DOS by janosh in https://github.com/materialsproject/pymatgen/pull/3514
* Add bold flag to `latexify` by janosh in https://github.com/materialsproject/pymatgen/pull/3516
* `Composition` raise `ValueError` if `formula` string is only numbers and spaces by janosh in https://github.com/materialsproject/pymatgen/pull/3517
* Raise `ValueError` for `float('NaN')` in `Composition` by janosh in https://github.com/materialsproject/pymatgen/pull/3519
* Add `PhononDos.mae()` and `PhononBandStructure.has_imaginary_gamma_freq()` methods by janosh in https://github.com/materialsproject/pymatgen/pull/3520
* `PhononDos.get_smeared_densities` return unchanged for `sigma=0` by janosh in https://github.com/materialsproject/pymatgen/pull/3524
* Add `PhononDos.get_last_peak()` by janosh in https://github.com/materialsproject/pymatgen/pull/3525

📖 Documentation

* QCInput: add docstrings for svp and pcm_nonels by rkingsbury in https://github.com/materialsproject/pymatgen/pull/3522

🚀 Performance

* Avoid redirects in `MPRester` requests by tschaume in https://github.com/materialsproject/pymatgen/pull/3496

🧪 Tests

* Fix weak `__str__` tests across pymatgen by janosh in https://github.com/materialsproject/pymatgen/pull/3472
* Test improvements by janosh in https://github.com/materialsproject/pymatgen/pull/3497

🏷️ Type Hints

* `ruff` automatic type annotations by janosh in https://github.com/materialsproject/pymatgen/pull/3498

New Contributors

* kyledmiller made their first contribution in https://github.com/materialsproject/pymatgen/pull/3467

**Full Changelog**: https://github.com/materialsproject/pymatgen/compare/v2023.11.12...v2023.12.18

🐛 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>