[pull] master from materialsproject:master #8
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Pull Request Test Coverage Report for Build 1122097048
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* Add AseTrajAdaptor * add docstr * precommit / docstr * remove molecules logic from trajectory that was already migrated to the ASE traj interface * ensure Trajectory raises import error if ase not installed but ase functinoality requested * remove ciruclar import, make AseTrajAdaptor static methods on Trajectory; add tests * docstr cleanup / ruff * remove lingering import statments from io.ase * ensure frame_properties are checked for none in ase conversion * is_mol --> is_pbc * turn off delete in temp file for windows support * simplify names per review comments * simplify names per review comments * remove to_ase_trajectory staticmethod
* Add failing test for mixed-valence compositions * Update `items()` method for `Composition`, test now passing * pre-commit auto-fixes * Add docstring * Typing * Fix previous false test outputs --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
automatically add the override warning when using libxc
* Minor update to make `FermiDos` more robust * pre-commit auto-fixes * Update `get_cbm_vbm` methods * Add `test_get_vbm_cbm_doping` * pre-commit auto-fixes * Update test value (now closer to `eigenvalue_band_properties` result) * Cap min/max band edge indices for robustness * pre-commit auto-fixes * Update electronic structure tests --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <[email protected]>
See https://github.blog/changelog/2025-01-16-linux-arm64-hosted-runners-now-available-for-free-in-public-repositories-public-preview/ Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>
* improve docstring * relocate private parser method and as_dict * tweak class docstring * NEED CONFIRM: deprecate read_pattern, rename to _parse_pattern * update available readers * micro_pyawk doc clean up * schedule debug arg for removal * remove umask that is doing nothing * the docstring must be incorrect, tuple is not mutable * unpack tuple for readability * fix return type * use is to check None * Revert "NEED CONFIRM: deprecate read_pattern, rename to _parse_pattern" This reverts commit 6b80819. * relocate read_pattern * add type, use is to check None * enhance type * getattr default as False instead of None when using as condition * DEBUG: to be reverted, comment out isotope check * Revert "DEBUG: to be reverted, comment out isotope check" This reverts commit 4363d1b. * add test for make_symmetric_matrix_from_upper_tri * add shape require * simplify implementation * add tabledata type alias * revert unrelated changes * type and comment clean up * avoid np.array as type in docstring * clean up read_electrostatic_potential and read_freq_dielectric * fix a lot of NMR CS parser * more types * more type * fix the rest * finish read_igpar * fix mypy error
* Test that entries with run_type 'r2SCAN' would not be ignored; 'r2SCAN' as an input run_type is not case-sensitive. * Fix to ensure r2SCAN entries would not be ignored in mixing scheme correction --------- Co-authored-by: Shyue Ping Ong <[email protected]>
* JDFTx IO module - input submodules * JDFTx IO module - input submodules testing * Moving "flatten_list" utility function to "generic_tags" submodule and deleting "_input_utils.py" as it contained only one method that was used once in "generic_tags.py" * privatizing utility method "flatten_list" * Update from master * empty file for tmp * Update from master * explicit testing of "initial-magnetic-moments" * Correction for ruff - PLC0206 (Extracting value from dictionary without calling `.items()`) - This does not appear in my local pre-commit (which I believe is running correctly) but started causing the "lint" action to fail starting around 11/22 (along with other failures from unrelated pre-existing parts of pymatgen) * changing the previous "as_dict" method to be private, making a public "as_dict" method that passes through the __setitem__ method so that the values within the dictionary fed to "as_dict" can be as flexible as the values set explicitly by the user (also made minor updates to __setitem__ to handle setting multiple values for repeatable tags better) * Partial cleanup of tests * Partial cleanup of tests * Partial cleanup of tests * Cleanup of inputs - homogenized wording in error messages, added value validation methods to AbstractTag for validations that are called multiple times, cleaned up cluttered tests and added comments to make it more clear what is being tested * pre-commit auto-fixes * Length units consistency in inputs module * Changing all "zopen" to just "open" due to an error raised when monty.io tries to raise an "EncondingWarning", changing the dump files dir to be a fixture that creates itself, yields the path, and then removes itself (parts after a "yield" only run once the test using the fixture has finished) --------- Co-authored-by: Matthew Horton <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* sourcing output code from master to this branch * sourcing output code from master to this branch * Update from master * source from master * update from master * changing enumeration of valence electrons (the `valences` method does not exactly what I thought it did. I still think its a helpful function to have but not what I need here) * added "to_dict" method to JDFTXOutfile * adding `JDFTXOutfileSlice` to "test_dict_repr" in "test_repr_out.py" * removing fatal error from retrieving t_s from a JOutStructure that is None * Correction for ruff - PLC0206 (Extracting value from dictionary without calling `.items()`) - This does not appear in my local pre-commit (which I believe is running correctly) but started causing the "lint" action to fail starting around 11/22 (along with other failures from unrelated pre-existing parts of pymatgen) * We found some weird behavior when trying to export the JDFTXOutfile object to a mongo-db. A lot of the mystery in this output module was in how properties were being forced into memory through getattr, so here all properties are now attributes set up in post_init , get getatr is no longer explicitly defined (this also takes up a lot less lines to make reviewing easier). The only exception is charges and magnetic_moments for JOutStructure * adding **kwargs for JOutStructure for flexibility * Partial cleanup of tests * Partial cleanup of tests * Partial cleanup of tests * Adding "structure" attribute to JOutStructure for convenient way to avoid any issues with using a JOutStructure in place of a Structure, adding eigenvals and bandProjections to JDFTXOutputs * fixes for trajectory * fix "structure" attribute being initialized as a JOutStructure * old updates * Changing all "zopen" to just "open" due to an error raised when monty.io tries to raise an "EncondingWarning", changing the dump files dir to be a fixture that creates itself, yields the path, and then removes itself (parts after a "yield" only run once the test using the fixture has finished) * missing updated from master * Oversight that causes ionic positions from previous strucure to be passed incorrectly --------- Co-authored-by: Matthew Horton <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>
…y_equal` compare float array (#4159) * replace some float equality check * explicit encoding * charge is also float * enhance types * access gcd via math namespace as math is already imported * put dunder method to top * fix typo * tweak _proj implementation * support array like * add arg and return type * tweak type * avoid more == for float comparison * replace some == in test, more left to do * replace more in core test * replace more in test * replace even more * replace last batch * clean up assert approx * replace pytest.approx with approx * also fix membership check * replace some equality check of list * replace some sequences * fix test * replace float comparison as dict * fix test * replace more float compare, mostly for VASP * fix test * fix approx in condition block * replace sci notation * suppress buggy ruff sim300 * number_of_permutations to int * revert change for formula_double_format, in favor of another PR * c_indices seems to be int * use sci notation for crazily large int * simplify numpy.testing usage * set tol as pos arg * avoid array equal for list of str * assert_array_equal should not be used on float array * fix module level var name * more assert_array_equal on complex number * simplify approx on dict value * avoid module level var when it's used only 3 times * pytext.approx to approx * fix approx on nested dict * avoid unnecessary convert to np.array * array_equal to all close for float array * assert all close for float array * capital class attrib is treated as constant
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