v2023.5.10

• Fix mem leak in pbc_shortest_vector cython code. (@stichri)
• Set all cython code to language level 3.

v2023.5.8

❗ The Yb_2 deprecation release ❗

This release changes the Ytterbium (Yb) pseudo-potential (PSP) from Yb_2 to Yb_3 for all PBE_54 VASP input sets.

Background: The A-lab revealed that as a result of using Yb_2 the energy on Yb compounds is off by a lot, resulting in supposedly stable things being unsynthesizable. While an unfortunate mistake, it's also great to see how experiment can help surface simulation errors.

On pre-PBE_54 input sets, we now issue a warning that Yb_2 will give bad results for most systems since Yb is most often in oxidation state Yb3+.

Reason: The better fix Yb_3 only became available in the PBE_54 PSP set. Requiring it on pre-PBE_54 input sets would mean you can't run Yb compounds.

For more details see #2968 and #2969.

What's Changed

• Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to find_points_in_spheres() pbc kwarg by @janosh in #2907
• Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD by @janosh in #2908
• Fix VolumetricData.to_cube() not preserving structure dimensions by @janosh in #2909
• Update team.rst by @jmmshn in #2912
• Faff by @janosh in #2915
• Add formal_chempots option to ChemicalPotentialDiagram to plot the formal chemical potentials rather than the DFT energies by @kavanase in #2916
• Modified dosplotter by @kaueltzen in #2844
• auto version by @jmmshn in #2925
• bug fix for potcar parsing by @jmmshn in #2910
• Fix breaking changes from pandas v2 by @janosh in #2935
• add kwarg to MoleculeGraph method and fix PackmolSet bug by @orionarcher in #2927
• fix on reading multiple route in Gaussian input file by @Ameyanagi in #2939
• Fix CI errors by @janosh in #2940
• Add ResParser support for reading files with spin values by @ScottNotFound in #2941
• Ignore bad unicode characters in Structure.from_file() by @janosh in #2948
• Minor modification for symmetrically distinct Miller index generation by @fyalcin in #2949
• Fixed Wulff shape for new versions of matplotlib by @CifLord in #2950
• Test figure returned by WulffShape.get_plot() contains single Axes3D by @janosh in #2953
• Fix Cp2kOutput.spin_polarized() likely not doing what author intended by @janosh in #2954
• For MPcules: Molecule Trajectory and graph hashes by @espottesmith in #2945
• self.assertArrayEqual->assert by @janosh in #2955
• fix GaussianOutput bug with multiple route lines by @xjf729 in #2937
• Fix ValueError when passing selective_dynamics to Poscar by @chiang-yuan in #2951
• Bump beautifulsoup4 from 4.11.1 to 4.12.2 by @dependabot in #2962
• Bump pypa/cibuildwheel from 2.11.4 to 2.12.3 by @dependabot in #2959
• Bump uncertainties from 3.1.6 to 3.1.7 by @dependabot in #2960
• Bump numpy from 1.23.2 to 1.24.3 by @dependabot in #2963
• Bump tabulate from 0.8.10 to 0.9.0 by @dependabot in #2961
• Bump pandas from 1.4.4 to 2.0.1 by @dependabot in #2964
• Link /addons from new subsection on /contributing page by @janosh in #2967
• Breaking: change Yb pseudo-potential on all VASP input sets from Yb_2 to Yb_3 by @janosh in #2969
• fix recursion error by adding copy and deepcopy dunder methods by @orionarcher in #2973
• Revert to Yb_2 on pre-PBE_54 input sets by @janosh in #2972
• Enable flake8-pytest-style via ruff by @janosh in #2975
• Enable all ruff pylint rules (excl. PLR) by @janosh in #2977
• only return unique point group operations by @mueslo in #2942

New Contributors

• @kaueltzen made their first contribution in #2844
• @chiang-yuan made their first contribution in #2951
• @mueslo made their first contribution in #2942

Full Changelog: v2023.3.23...v2023.5.8

v2023.3.23

• Misc bug fixes.
• Enable Structure relaxations with TrajectoryObserver (@janosh)

v2023.3.10

Update docs

v2023.2.28

First release (in a while) with pre-built Linux wheels thanks to @njzjz! 🎉

What's Changed

• use cibuildwheel to build linux wheels by @njzjz in #2800
• Merge setup.cfg into pyproject.toml by @janosh in #2858
• del class AtomicFile, _maketemp(), ask_yesno() by @janosh in #2860
• fix reduced formula in Ion by @yang-ruoxi in #2864
• Prepare release 2023.2.28 by @janosh in #2867

Full Changelog: v2023.2.22...v2023.2.28

What's Changed

• use cibuildwheel to build linux wheels by @njzjz in #2800
• Merge setup.cfg into pyproject.toml by @janosh in #2858
• del class AtomicFile, _maketemp(), ask_yesno() by @janosh in #2860
• fix reduced formula in Ion by @yang-ruoxi in #2864
• Prepare release 2023.2.28 by @janosh in #2867

Full Changelog: v2023.2.22...v2023.2.28

v2023.2.22

What's Changed

• Fix pre-commit.ci isort error by @janosh in #2825
• Changes to Q-Chem IO to allow CDFT and coupling calculations by @espottesmith in #2674
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #2834
• Add inplace flag to select whether to adjust entries in place by @peikai in #2841
• Default check_stable to False in PatchedPhaseDiagram.get_decomp_and_e_above_hull() for speed by @janosh in #2842
• Document difference between Composition.get_el_amt_dict() and Composition.as_dict() by @janosh in #2846
• Manually update OPTIMADE database aliases and add option to refresh on init by @ml-evs in #2848
• Add Ruff linter by @janosh in #2847
• Fix auto-fixable pydocstyle errors through ruff by @janosh in #2850
• Fix OPTIMADE client generated filters and URLs by @ml-evs in #2853
• Run pyupgrade and flake8-simplify through ruff by @janosh in #2851
• Fix typo in OPTIMADE client: remove quotes in response fields by @ml-evs in #2856
• Ruff c4+ruf rules by @janosh in #2854
• Add python-version 3.11 to GH action matrix strategy by @janosh in #2714
• 2023.2.22 release by @janosh in #2857

Full Changelog: v2023.1.30...v2023.2.22

v2023.1.30

Update docs

v2023.1.20

• Passthrough kwargs support for Structure.from_file and Structure.from_str
• Allow the frac_tolerance to be specified for rounding coordinates in CifParser.
• PR #2803 from @amkrajewski add_weightbasedfunctions

v2023.1.9

What's Changed

• Fix failing piezo tests by @janosh in #2729
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #2722
• Document rare structure dependence of MaterialsProjectCompatibility corrections by @janosh in #2731
• Markdown readme by @janosh in #2733
• Fix extremum_icohpvalue() for ICOBILIST.lobster files by @naik-aakash in #2734
• use build to build packages by @njzjz in #2735
• Sunset module pymatgen/util/serialization.py by @janosh in #2736
• Fix lobsterout.get_doc() typo by @naik-aakash in #2737
• {ADMIN,CONTRIBUTING,LICENSE}.{rst->md} by @janosh in #2738
• rm MANIFEST.in by @janosh in #2739
• Resurrect requirements{,optional}.txt by @janosh in #2741
• Enable dependabot for pip by @janosh in #2742
• Fix loose endpoints in NEBPathfinder.string_relax() by @janosh in #2740
• QChem: add CMIRS solvent model support by @rkingsbury in #2215
• Added missing keyword from LOBSTER 4.1 to lobsterin generation class by @naik-aakash in #2764
• Fix CI by @janosh in #2767
• Cython linting by @janosh in #2769
• Add setup.py project_urls by @janosh in #2771
• Move VolumetricData to io/common and merge cube support by @nwinner in #2667
• Fix typo in Poscar get_string by @dgaines2 in #2774
• Update to the hashing systems for PotcarSingle that fixes some small bugs and allows for verification with the sha256 hash written in new POTCARs by @MichaelWolloch in #2762
• Fix lobster out doc by @naik-aakash in #2775
• BUG FIX for merged pull request #2762 by @MichaelWolloch in #2776
• Colorbar label for PDPlotter by @ab5424 in #2773
• Added methods to compute and compare DOS fingerprints by @naik-aakash in #2772
• Fix coord_list_mapping_pbc() by @janosh in #2782
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #2789
• Cp2k 2.0 by @nwinner in #2672
• One attempt to fix ChemEnv error in tests by @JaGeo in #2792
• Prefer generator over list comprehension where equivalent by @janosh in #2793
• Added a missing multi element POTCAR file by @MichaelWolloch in #2796
• isort auto insert __future__ annotations import by @janosh in #2797
• Release v2023.1.9 by @janosh in #2798

New Contributors

• @njzjz made their first contribution in #2735

Full Changelog: v2022.11.7...v2023.1.9

v2022.11.7

What's Changed

• Fix release workflow by @janosh in #2717
• Parsing the Fock matrix and eigenvalues from the QChem output file by @sudarshanv01 in #2562
• Add copy() methods to ComputedEntry and ComputedStructureEntry by @janosh in #2719
• Fix tensor mapping by @utf in #2720
• Raise ValueError in SpacegroupAnalyzer.get_symmetrized_structure() if spglib returns no symmetries by @janosh in #2724
• Release v2022.11.7 by @janosh in #2726
• VaspInputSet couldn't write cif structures by @JiQi535 in #2721
• Fix release CI workflow by @janosh in #2728
• Do not introduce zero magmoms in SpacegroupAnalyzer by @lbluque in #2727

New Contributors

• @sudarshanv01 made their first contribution in #2562
• @JiQi535 made their first contribution in #2721

Full Changelog: v2022.11.1...v2022.11.7