[pull] master from materialsproject:master #8
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Pull Request Test Coverage Report for Build 1122097048
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* Update inequality in `get_linear_interpolated_value` * Add test for updated edge case behaviour * Rename `firs` to `fict_ionic_radii` for clarity and to avoid `codespell` errors in linting * Add `if not below_fermi or not above_fermi:` catch to `DOS.get_interpolated_gap()` (to be consistent with `Dos.get_interpolated_gap()`) * Return zero gap for case of VBM index = CBM index -1 (i.e. no gap found)
…gument (#4304) This was previously obscured by a hard-coded `num_orderings` class attribute.
Notifying @oashour @matthewkuner - let me know if alternative wording is preferred. Wanting to make sure these packages were linked out from docs to improve visibility/discoverability for others. Signed-off-by: Matthew Horton <[email protected]>
* deepcopy atoms.info/structure.properties during ase/pymatgen conversion this fixes bug where atoms/structure objects were themselves modified when converted * added tests to check spacegroup conversions * pre-commit auto-fixes * selective import for copy.deepcopy in keeping with style of ase.py * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Andrew S. Rosen <[email protected]>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.4 → v0.9.9](astral-sh/ruff-pre-commit@v0.9.4...v0.9.9) - [github.com/pre-commit/mirrors-mypy: v1.14.1 → v1.15.0](pre-commit/mirrors-mypy@v1.14.1...v1.15.0) - [github.com/RobertCraigie/pyright-python: v1.1.393 → v1.1.396](RobertCraigie/pyright-python@v1.1.393...v1.1.396) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* default to json * clarify docstring * minor test tweak
* pass kwargs to IStructure.to * fix codespell complain
Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.16.5 to 1.18.3. - [Release notes](https://github.com/sparklemotion/nokogiri/releases) - [Changelog](https://github.com/sparklemotion/nokogiri/blob/v1.18.3/CHANGELOG.md) - [Commits](sparklemotion/nokogiri@v1.16.5...v1.18.3) --- updated-dependencies: - dependency-name: nokogiri dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* fea: add method to get the pearson symbol * test: test the pearson symbols * clean: clean and comment sga tests * fix: LiPo4 actually FePO4 * fix linting and supress warning. --------- Signed-off-by: Matthew Horton <[email protected]> Co-authored-by: Matthew Horton <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>
* First pass add functional Vaspout parser * Add POTCAR spec attrs to standardize spec, add from_spec method to Potcar class, standardize potcar checking * pre-commit auto-fixes * fix failing lobster tests * pre-commit auto-fixes * pre-commit auto-fixes * Add Vaspout tests, fix method * pre-commit and fix test names * fix remaining linting and mypy errors * pre-commit auto-fixes * Fix python 3.9 support, add charge and magnetization site_properties in Vaspout.ionic_steps * pre-commit auto-fixes * Fix projected DOS parsing * linting / typing * remove dunder methods from potcar spec * linting * increase support for auto k point generation * linting * precommit * add h5py to ci extra install for testing * make vaspout tests optional * explicit reason pass to pytest skipif * remove os system call * precommit * tweak dos parsing * precommit --------- Signed-off-by: Aaron Kaplan <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
… features to Xdatcar (#4323)
* remove some legacy only tests * replace general Exception catch * query seems also legacy only * get_data is also legacy only * NEED CONFIRM: remove failing parts from test_get_entries * get_stability is also legacy only
* Update type-hinting for `pymatgen.io.qchem.outputs` Signed-off-by: Andrew S. Rosen <[email protected]> * pre-commit auto-fixes --------- Signed-off-by: Andrew S. Rosen <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* ruff autofix TC006: runtime cast value * autofix PLC1802: len(var) used as condition without comparison * ignore SIM905 for now * fix LOG015: log directly on root logger * NEED CONFIRM: avoid configuring the root logger * fix RUF040 Non-string literal used as assert message, likely many tests are not working correctly * remove todo tag in favor of a separate PR
* rearrange dunder methods to the top * add tests * add more tests * fix tests for 0D array
…` returns the corresponding type (#4321) * separate from_ase_atoms from abstraction class * fix typo * NEED CAREFUL CHECK: remove from_ase_atoms from ABC * fix return types * WIP: add extra tests for to_from ase atoms * use typevar to mark return type for ase adaptor * revert to original behaviour (only Molecule/Structure) * NEED DISCUSSION: also revert test to previous behaviour * add test for kwarg passing * tiny collection tweak * more complete type for cls * refactor to return correct type * fall back to get_structure for molecule.from_ase_atoms * fall back to get_structure and put from_ase_atoms back to SiteCollection * Update compatibility doc * remove manual line wrap * add version to previous breaking change * replace os.remove for check file existence * remove unused ase * fix typo in docstring * update compatibility details * put previous breaking change into version section * test exception * Linux shell could not be bash --------- Co-authored-by: Shyue Ping Ong <[email protected]>
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