[pull] master from materialsproject:master #8
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Pull Request Test Coverage Report for Build 1122097048
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not specific to VASP.
Bumps [rexml](https://github.com/ruby/rexml) from 3.3.6 to 3.3.9. - [Release notes](https://github.com/ruby/rexml/releases) - [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md) - [Commits](ruby/rexml@v3.3.6...v3.3.9) --- updated-dependencies: - dependency-name: rexml dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* src/pymatgen/io/vasp/help.py (VaspDoc.get_incar_tags): Use Mediawiki API instead of parsing the HTML source directly. The old approach is not stable against changes in the tag list because of the way URLs are constructed. pagefrom= parameters start from certain tag, which is not guaranteed to provide the complete tag list as the new tags are added before that tag given in pagefrom=. At the moment of writing this commit, PRECFOCK tag is already missed using the old approach. Following up: #4119 (comment)
* use agg backend * I don't think we need PMG_VASP_PSP_DIR env var
…nt` to round to nearest int (#4163) * add types * tweak formula_double_format implementation * test edge case * tweak docstring * fix round bug * use structure for now * tweak type and docstring * I believe the new formula is correct * avoid overwriting func name * clean up test * annotate matrix * use math.isclose * explicit rel_tol 0
…when core file missing (#4154) * fix valuerror raising * add unit test * fix condition * add extra space * add type * add more type * fix other value error, add type * fix glob string * add types for BorgQueen
updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.12.0 → v1.13.0](pre-commit/mirrors-mypy@v1.12.0...v1.13.0) - [github.com/adamchainz/blacken-docs: 1.19.0 → 1.19.1](adamchainz/blacken-docs@1.19.0...1.19.1) - [github.com/kynan/nbstripout: 0.7.1 → 0.8.0](kynan/nbstripout@0.7.1...0.8.0) - [github.com/RobertCraigie/pyright-python: v1.1.384 → v1.1.387](RobertCraigie/pyright-python@v1.1.384...v1.1.387) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* show FutureWarning and DeprecationWarning * TODO: mark FutureWarning and DeprecationWarning for this PR * from pymatgen.core.interface import GrainBoundaryGenerator * Suppress DeprecationWarnings on pkg_resources from pybtex * suppress all warning from pybtex * use single quote * ignore Userwarning * bump plotly to avoid SyntaxWarning * DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead. * suppress spglib.get_symmetry * fix get_vasp_input * add comment * replace piezo sensitivity * suppress warning * suppress known bader warning * add comment for something Im unable to fix * fix lammps input * n_elems * simplify warning filter in test * fix get_vasp_input * avoid warning leakage * fix lobster * replace phonopy * revert filter warn for that we might want to fix * fix pandas na filter * enhance filter msg * NEED CONFIRM: replace plotly colorbar * suppress intended test for MaterialsProjectCompatibility * fix pd.read_json * replace matrix with array * suppress too many figure warning * fix openff * clean up warning filter * add comment * filter intended usage * clean up warn filter * revert plotly bump * enhance comment * fix extractall * remove TODO tag as issue opened * copy central_diff_weights from scipy * copy derivative for quasiharmonic * fix extractall
The `AflowPrototypeMatcher` matches a structure against predefined AFLOW prototype structures using `StructureMatcher`. `StructureMatcher` requires preprocessing via lattice reduction and primitive-cell conversion. This commit optimizes performance by preprocessing AFLOW prototype structures during the initialization of `AflowPrototypeMatcher`. This change eliminates redundant processing when `AflowPrototypeMatcher.get_prototypes` is called multiple times. Co-authored-by: Shyue Ping Ong <[email protected]>
new flag for AutoOxi
* remove unnecessary processing * stupid manual update of GGA recording * stupid manually add ZAB_VDW tag * avoid casing SYSTEM value * fix SYSTEM case and add test * tweak comment * use a non capitalized string for test * fix test string * revert str compare, startswith is slower * add test for Incar pop method * check_params consider lower str exception * reuse proc_val in check_params, thanks @yantar92
* cp2k DftSet.get_basis_and_potential add keyword cp2k_data_dir which takes precedence over PMG_CP2K_DATA_DIR in pmgrc.yaml
* get_basis_and_potential don't raise on potentials specified as string instead Potential instance
* get_basis_and_potential if potential_filename or basis_filenames not already set, use the global ones
* fix KeyError in calculation_type if self.data.get("dft") returns None
* migrate setup_cp2k_data from ruamel.yaml pyyaml to fix AttributeError: "dump()" has been removed
* change Keyword + Section verbose default to False to stop printing explanatory comments for sections and flags into every CP2K input file
* fix trailing white space in Section._get_str
* fix typo
…lex expression) (#4164) * replace hard-coded math.isclose * add todo tag * replace more isclose in code * remove TODO tag * replace more in code * fix seemingly wrong quote position * avoid import when it's used only once or very few * replace last batch * revert change to isotropic check * replace some numpy isclose allclose * remove debug tag * remove some hard coded np allclose * revert some change on very simple evals * avoid unnecessary compare with zero * revert simple comparison * avoid minus zero * revert some simple expressions * simplify sci notation * revert simple comparisons * avoid 1.0e-x as it's already float * revert simple compare * use sci not * revert simple * use abs as we don't need always float * fix round usage * all close * revert as i'm not sure about the shape broadcasting * avoid import from numpy * clean up math import, reduce namespace cluster * simplify all close * sci notation * simplify import of math * simplify assert all close * simplify int(len(a) / b) to len(a) // b
…tr` (#4143) * insert warning for element mismatch * try value error and see if there's any breakage * fix typo in comment * revise message to cover cases where default_name is given as arg * NEED DISCUSSION: re-raise ValueError * add todo tag * clean up POTCAR element check * recover code logic * add comment * fix mismatch in unit test * improve glob logic * add some test, pmg test cannot be parametrized * fix warning and exception logic * remove dummy POSCAR * fix test_from_str_default_names * fix test_from_file_potcar_overwrite_elements * suppress many expected warnings * fix condition * clean up comment * add superset * also test elements * clean up overwrite logic for readability * recover vasp5or6_symbols tag * WIP: halfed done logic cleanup * clean up comment * fix test across OS owing to rounding * finish VASP 4 overwrite test * reduce code repetition * enhance test a tiny bit --------- Signed-off-by: Shyue Ping Ong <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>
…which leads to infinite loop (#4133) * add min_vol check * increase min_vol to 1 * round volume to 4 digits * add test * use min thickness for robustness * compress test file * lower the threshold even further * update comment
… time regression test, lazy load some rarely used but costly modules (#4128) * copy pyproject from 4073 * bump monty * recover networkx pin, and bump sympy * pin monty to lower ver to see what is causing the failure * revert all changes to pyproject but monty * bump sympy * sort and group optional deps * loose networkx pin for compatibility * lazy import sympy * lazy load scipy * Revert "lazy load scipy" This reverts commit 9688244. * try netcdf4 install with delvewheel, 1dfc9e4 * Revert "try netcdf4 install with delvewheel, 1dfc9e4" This reverts commit 75e23b1. * test netcdf4 1.7.1.post2, notice new release is out today * netcdf4 1.7.1.post2 doesn't work, try latest 1.7.2 * reset netcdf4 pin * why <= doesn't work? * add comment * exclude 1.7.2 as well (perhaps conditionally skip that test?) * add place holder * enhance comment * add TODO tag * tweak placeholder * replace assert_allclose for scalar compare * replace assert_allclose with isclose * fix is close * use np.allclose over np.all(np.isclose()) * lazy import AseAtomsAdaptor * guard type check import * lazy import matplotlib * toggle reference generation * update import time records * skip in not CI env * include current time in err msg * loose hard threshold to 100%, as it appear macos runner is prone to fluctuation * update type * skip test for macos * add PR tag for easy tracing * use perf_counter_ns for precision * bump torch timeout all the way to 5 min * Revert "bump torch timeout all the way to 5 min" This reverts commit 9c3d186. * migrate missing allclose relative tolerance --------- Co-authored-by: Shyue Ping Ong <[email protected]>
…4073) * comment tweaks * pin python 3.12 in CI * try to install from sdist * try to add test files dir * uncomment resolution * set lower pin for bs4 from year 2017 * remove duplicate in dep declare * drop quotes * remove duplicated comment * sort optional dependencies * TEST: test exclude a required file from sdist would lead to CI failure * Revert "TEST: test exclude a required file from sdist would lead to CI failure" This reverts commit 0dba028. * perhaps install from wheels? * skip failing test as dgl doesn't support torch 2.4.1 * revert pyproject in favor in separate PR * fix missing @
* Modified SpaceGroup.is_subgroup() following issue #3937, added tests. * Added crystal_system attribute to PointGroup, modified is_subgroup warning of SymmetryGroup. * Modified is_subgroup of PointGroup to raise NotImplementedError if group subgroup relationship would be possible (fr. crystal system), but cannot be checked currently due to crystallographic direction issue. * Enabled PointGroup init from different settings, added test for that, added missing setting differences (trigonal groups), re-enabled SpaceGroup.is_subgroup shortcut with constraint of non-klassengleiche group subgroup relationship * Removed bug in short Hermann Mauguin symbol of some trigonal groups introduced by myself in #3859 --------- Signed-off-by: Katharina Ueltzen <[email protected]>
…` rename (#4151) * reverse breaking rename * add unit test * reduce indentation level * simplify square calculation and avoid reimport * reduce indentation level * simplify return statement * fix lazy import of MoleculeGraph
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