v2023.11.12

🐛 Bug Fixes

• Hot fix: pymatgen package missing potcar-summary-stats.json.bz2 by @janosh in #3468

🛠 Enhancements

• Add Composition.charge and charge_balanced properties by @janosh in #3471

v2023.11.10

🐛 Bug Fixes

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

🛠 Enhancements

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

🧹 House-Keeping

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

🤷‍♂️ Other Changes

• Create jekyll-gh-pages.yml by @shyuep in #3410
• Make from_(str|file) (static->class)methods by @janosh in #3429

New Contributors

• @RedStar-Iron made their first contribution in #3430
• @tawe141 made their first contribution in #3452
• @tpurcell90 made their first contribution in #3435

v2023.10.11

🐛 Bug Fixes

• Fix outdated setup.py find_namespace_packages and add test_egg_sources_txt_is_complete by @janosh in #3374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

🛠 Enhancements

• New class to handle NcICOBILIST.lobster files by @QuantumChemist in #2878
• Add inplace: bool=True arg to Structure.apply_strain() by @janosh in #3376
• Add Structure.to_(conventional|primitive|cell) methods by @janosh in #3384
• Add SiteCollection.to_ase_atoms() by @janosh in #3389
• Add mode: Literal["w", "a", "wt", "at"] = "w" keyword to CifWriter.write_file() by @janosh in #3399

📖 Documentation

• Add docs/fetch_pmg_contributors.py script by @janosh in #3387

🧹 House-Keeping

• Fix ruff FURB violations by @janosh in #3382
• Remove deprecated module pymatgen/util/convergence.py by @janosh in #3388
• Remove pylint: disable comments by @janosh in #3390
• Fix ruff N806 by @janosh in #3394

🧪 Tests

• Update incar_parameters.json to allow ISIF=8 by @matthewkuner in #3381
• Add test_potcar_summary_stats() by @janosh in #3395
• Mirror atomate2 fix and improve MPScanRelaxSet.test_kspacing edge case coverage by @janosh in #3396

💥 Breaking Changes

• Breaking: snake_case FiestaInput keywords and class attributes by @janosh in #3386
• Ion: default hydrates=False in reduced_formula by @rkingsbury in #3350

🏷️ Type Hints

• Add type annotations to io/lammps by @ab5424 in #3379
• Add type annotations to phonon by @ab5424 in #3393

Full Changelog: v2023.10.4...v2023.10.11

v2023.10.4

What's Changed

🐛 Bug Fixes

• Fix missing potcar_summary_stats.json.gz in setup.package_data by @janosh in #3372

Full Changelog: v2023.10.3...v2023.10.4

v2023.10.3

What's Changed

🐛 Bug Fixes

• Revert openbabel.OBAlign() in molecule_matcher.py to use positional args for includeH, symmetry by @janosh in #3353
• Fix MPMD set bug by @MichaelWolloch in #3355
• Fix TestMPResterNewBasic + AseAtomsAdaptor test errors and TransformedStructure.from_snl overwriting hist variable by @janosh in #3362
• Fix TypeError: can only join an iterable with AECCAR in VolumetricData.write_file by @chiang-yuan in #3343

🛠 Enhancements

• Don't rely on jsanitize in Atoms <--> Structure object interconversion by @Andrew-S-Rosen in #3359
• Breaking: New method of POTCAR validation by @esoteric-ephemera in #3351
• Add alias .to_file() for .to() method of structures and molecules by @QuantumChemist in #3356
• Update POTCAR summary stats to include 6.4 POTCARs and add dev_script utils for future updates by @esoteric-ephemera in #3370

🧹 House-Keeping

• Chargemol minor refactor by @janosh in #3357
• Breaking typo fix: Targe(tt->t)edPenaltiedAbundanceChemenvStrategy by @janosh in #3360
• Fix undiscovered tests by @janosh in #3369

🏥 Package Health

• Bump min numpy to v1.25.0 by @janosh in #3352

New Contributors

• @esoteric-ephemera made their first contribution in #3351
• @QuantumChemist made their first contribution in #3356

Full Changelog: v2023.9.25...v2023.10.3

v2023.9.25

What's Changed

🐛 Bug Fixes

• Fix MPSOCSet raising ValueError on structure=None by @janosh in #3310
• Fix AttributeError in BSPlotter.get_plot() by @janosh in #3327
• Use ax = fig.add_subplot(projection='3d') to create Axes3D by @janosh in #3330
• Fix breaking change to CoherentInterfaceBuilder.get_interfaces by @janosh in #3337
• Add properties @property/docstring to IStructure by @mkhorton in #3338
• Always return 0 for Composition.oxi_state_guesses() of diatomic molecules by @janosh in #3332
• Fix: TestMITMPRelaxSet.test_nelect claimed to but wasn't testing disordered structure by @janosh in #3344

🛠 Enhancements

• Allow usage of calculate_ng with a custom ENCUT and PREC values for VASP input sets by @matthewkuner in #3314
• Fix TestPotcar.test_write polluting git repo on failure by @janosh in #3347

📖 Documentation

• Update @arosen93 to @Andrew-S-Rosen by @Andrew-S-Rosen in #3311
• Google-style doc strings for class attributes by @janosh in #3320
• More Google-style class attribute doc strings by @janosh in #3323
• Readme notice regarding updated pymatgen publication by @janosh in #3325
• Breaking: rename get_ax3d_fig_plt->get_ax3d_fig and get_ax_fig_plt->get_ax_fig plus no longer return plt by @janosh in #3329

🧹 House-Keeping

• Fix internal SymmOp.from_xyz_string and MagSymmOp.from_xyzt_string deprecation warnings by @janosh in #3315
• Fix ruff A001 violations: Variable is shadowing a Python builtin by @janosh in #3331
• Delete unused or numpy-provided routines from pymatgen.util.num by @janosh in #3333
• fix ruff FBT003: Boolean positional value in function call by @janosh in #3335
• Snake case test method names by @janosh in #3339

🤷‍♂️ Other Changes

• Fix atomic mass for Og by @mkhorton in #3317

Full Changelog: v2023.9.10...v2023.9.25

v2023.9.10

What's Changed

🐛 Bug Fixes

• Fix code comment in ASE adapter by @Andrew-S-Rosen in #3298
• Fix IndexError when parsing Hessian from Gaussian frequency job by @janosh in #3308

🛠 Enhancements

• Add an input arg check for Kpoints.automatic_density_by_lengths by @Andrew-S-Rosen in #3299

🏥 Package Health

• Remove pydantic < 2 from setup.py and bump monty in requirements.txt by @Andrew-S-Rosen in #3303
• Move py.typed to package root by @Andrew-S-Rosen in #3307
• Consistent casing setup->setUp across test classes by @janosh in #3305

🤷‍♂️ Other Changes

• v2023.9.10 by @janosh in #3309

Full Changelog: v2023.9.2...v2023.9.10

v2023.9.2

What's Changed

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

New Contributors

• @mbercx made their first contribution in #3260
• @jonathanjdenney made their first contribution in #2836
• @kaifengZheng made their first contribution in #3256
• @Na-Kawa made their first contribution in #3261
• @SophiaRuan made their first contribution in #3254
• @LucasGVerga made their first contribution in #3286

Full Changelog: v2023.8.10...v2023.9.2

v2023.8.10

What's Changed

• fix estimate_nbands function by @matthewkuner in #3149
• Add CifParser.get_structures(on_error='warn') by @janosh in #3175
• ruff . --fix by @janosh in #3176
• AseAtomsAdaptor: Retain tags property when interconverting Atoms and Structure/Molecule by @arosen93 in #3151
• Fix a bug in pwscf.py. The proc_val function modifies string values. by @pablogalaviz in #3172
• Delete commented out print statements by @janosh in #3178
• lots of from_string should be classmethod by @njzjz in #3177
• Extend lobsterenv for coop/cobi by @naik-aakash in #3050
• BUG: fix setting zero magmoms by @lbluque in #3179
• Prefer pymatviz interactive plotly version of periodic table heatmap if available by @janosh in #3180
• Better Composition repr by @janosh in #3182
• Breaking: Return True for Element in Composition if Species.symbol matches Element by @janosh in #3184
• Revert LMAXMIX "fix" added in #3041 by @janosh in #3189
• Add bader_exe_path keyword to BaderAnalysis and run bader tests in CI by @janosh in #3191
• Unskip and fix packmol tests by @janosh in #3195
• Propagate labels through various Structure operations by @stefsmeets in #3183
• Delete variable self assignments by @janosh in #3196
• Improve Structure tests by @janosh in #3197
• Bump pypa/cibuildwheel from 2.12.3 to 2.14.1 by @dependabot in #3202
• Bump numpy from 1.24.3 to 1.25.2 by @dependabot in #3201
• Bump matplotlib from 3.5.2 to 3.7.2 by @dependabot in #3200
• Bump scipy from 1.9.0 to 1.11.1 by @dependabot in #3199
• Test class XYZ edge cases by @janosh in #3206
• Fix EnergyAdjustment.__repr__ by @janosh in #3207
• Markdownlint by @janosh in #3209
• Fix codecov by @janosh in #3210
• Update pytest-split durations by @janosh in #3211
• Fix GitHub language statistics after test files migration by @janosh in #3214
• Fix automatic_density_by_lengths and add tests for it by @janosh in #3218
• Prefer len(structure) over structure.num_sites by @janosh in #3219
• Add PhaseDiagram method get_reference_energy by @janosh in #3222
• Fix isomorphic for molecular graphs by @rohithsrinivaas in #3221
• Add Structure.elements property by @janosh in #3223
• Add keyword in_place: bool = True to SiteCollection.replace_species by @janosh in #3224
• list offending elements in BVAnalyzer.get_valences error message by @janosh in #3225
• Add Entry.elements property by @janosh in #3226
• Move PymatgenTest.TEST_FILES_DIR attribute into module scope by @janosh in #3227
• f-string path construction everywhere, no need for os.path.join(...) by @janosh in #3229
• speed up bader_caller and chargemol_caller by @chiang-yuan in #3192
• Fix ruff PYI041 and ignore PYI024 by @janosh in #3232
• Deprecate get_string() methods in favor of get_str() by @janosh in #3231
• Structure/Molecule.to() now always return same string written to file by @janosh in #3236

New Contributors

• @matthewkuner made their first contribution in #3149
• @pablogalaviz made their first contribution in #3172
• @rohithsrinivaas made their first contribution in #3221

Full Changelog: v2023.7.20...v2023.8.10

v2023.7.20

What's Changed

• Unreadable string concat ops to f-string by @janosh in #3162
• Revert mp-api<0.34.0 pin by @janosh in #3165
• Fix CI error "pdentries_test.csv" not found by @janosh in #3168
• Fix issues with labels by @stefsmeets in #3169
• v2023.7.20 by @janosh in #3171

Full Changelog: v2023.7.17...v2023.7.20