[pull] master from materialsproject:master #8
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Pull Request Test Coverage Report for Build 1122097048
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…on` and siblings, minor type clean up for `core.Composition` (#4265) * add some types * more types * fix factor type * fix IUPAC writing * fix another factor type * fix factor * fix type * add test for composition error * add test for reduce formula
* use P1 symmop str * minor type improve * use NDArray over np.ndarray * patch a cif with no symmop info available * assert warning msg
* Composition support formula strings with curly brackets
this PR extends the existing bracket normalization for square brackets to curly brackets
important e.g. for bulk metallic glass compositions
* link source paper for formulas in test doc str
* link test from new lines
* fix mypy error
src/pymatgen/io/vasp/outputs.py:4724: error: Unsupported operand types for < ("int" and "None") [operator]
src/pymatgen/io/vasp/outputs.py:4724: note: Right operand is of type "int | None"
Found 1 error in 1 file (checked 295 source files)
updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.2 → v0.9.4](astral-sh/ruff-pre-commit@v0.9.2...v0.9.4) - [github.com/codespell-project/codespell: v2.3.0 → v2.4.1](codespell-project/codespell@v2.3.0...v2.4.1) - [github.com/igorshubovych/markdownlint-cli: v0.43.0 → v0.44.0](igorshubovych/markdownlint-cli@v0.43.0...v0.44.0) - [github.com/RobertCraigie/pyright-python: v1.1.391 → v1.1.393](RobertCraigie/pyright-python@v1.1.391...v1.1.393) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* add types * use timeout in communicate * enable timeout test * reduce timeout * fix types * increase timeout to reveal the issue * fix test command * avoid passing default args * avoid single letter var also avoid shadowing outside * send SIGKILL after timeout * update timeout test * compress test file * err msg with more details
…4274) * move occ_tol to initialization parameters * add tests * fix: ruff formatting issues * pre-commit auto-fixes --------- Co-authored-by: Hui Zheng <v-huizhe@microsoft.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…gneticStructureEnumerator` (#4275) * minor type and comment cleanup * fix default kwargs dict * add unit test * skip if no enumlib * refactor to one liner
…le.electron_configuration` (#4278) * add types * make module level private variables all cap * clarify valence elec config * use symbol over sym as sym could be mistaken for symmetry? * Revert "use symbol over sym as sym could be mistaken for symmetry?" This reverts commit 66da01c. * remove unnecessary type ignore * enhance unit test and add scrambled POTCARs * use explicit None check instead of truthy * fix fake POTCAR position * rewrite electron config parser * avoid Ambiguous variable name l * less explicit tuple as i'm unable to cast type * replace K_sv with Ca_sv as it seems to interfer with LOBSTER test * drop unnecessary temp config recording * add occu_cutoff * add test for POT_PAW_PBE_64 * also change species full_electronic_structure property * implement tolerance
* Update `get_cbm_vbm` functions to use interpolation * Refactor `start`/`end` to `vbm`/`cbm` for consistency & clarity * Update tests * Update `test_outputs.py` * Consolidate functions and remove redundant code * pre-commit auto-fixes * Catch incomplete DOSs (e.g. CP2K non-SCF calc) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
* 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 <mkhorton@users.noreply.github.com>
* 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 <asrosen93@gmail.com>
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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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