[pull] master from materialsproject:master #8

This reverts commit ea8c3c5.

Most of the show() functions are broken.

* prettify periodic_table.json for readability * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Added MD input set and generator for aims * Added MD input set and generator for aims * Conditionally add velocities to site properties * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

comment comment

updates: - [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](pre-commit/mirrors-mypy@v1.10.0...v1.10.1) - [github.com/adamchainz/blacken-docs: 1.16.0 → 1.18.0](adamchainz/blacken-docs@1.16.0...1.18.0) - [github.com/RobertCraigie/pyright-python: v1.1.366 → v1.1.369](RobertCraigie/pyright-python@v1.1.366...v1.1.369) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Replaced SpaceGroup symbol attribute with its Hermann-Mauguin symbol, corrected Schoenflies point group attribute, changed handling of rhombohedral space group type settings by adding a SpaceGroup hexagonal bool attribute, modified and added tests. * Removed crystal class key from symm_ops.json. * Test for correct setting of hexagonal attribute when instantiating from int number. * Noted change and replacement option for SpaceGroup symbol in compatibility.md * Added from_space_group class method to PointGroup, added tests * Added mapping to standard setting in PointGroup.from_space_group(), modified symm_ops.json and symm_data.json (documented in dev_scripts/update_space_group_data.py) to have same notation, added point group and short Hermann Mauguin symbol to symm_ops, fixed some typos, fixed rhombohedral space group type orbit issue. * Updated core/test_surface.py to assign lattice as in SpaceGroup is_compatible(). * Modified databases and SpaceGroup init to ensure compatibility with non-underscore space group notations. * Added tests for issue #3862, modified full_symbol and point_group attribute setting. * Modified PointGroup.from_space_group() to also handle symbols with identity blickrichtungen and missed underscores, added warning to SpaceGroup init if full symbol is not available (for non-standard settings), added tests. * Added test for warning if SpaceGroup.full_symbol is not available. * Removed warning test. * tweak incompat warning * add test_full_symbol_warning * add author + date to dev_scripts/update_spacegroup_data.py * typos * warning occurs only once, move test_full_symbol_warning up as workaround to annoying test pollution from side effects to std lib warnings registry * Updated compatibility.md to also handle old symbol replacement of P2_12_12_1 and I2_12_12_1. * pre-commit auto-fixes * Updated dev script path to new src layout. --------- Signed-off-by: Katharina Ueltzen <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: J. George <[email protected]>

Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.6.2 to 2024.7.4. - [Commits](certifi/python-certifi@2024.06.02...2024.07.04) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <[email protected]>

…re-commit (#3920) * format aflow_prototypes.json * ignore aflow json in pre-commit

and mac in CI.

) * increment spglig min version * re-enable part of the test * use dot notation and tweak code format * add types for SpacegroupAnalyzer, mypy error to fix * final round of format tweaks * re-enable unit test for invalid spg number * fix mypy errors * migrate one more in unit test * add types for PointGroupAnalyzer * add types for remaining of analyzer

* prettify periodic_table.json * fix energy ordering of electronic structures for elements * fix typo * Species: implement electron configuration methods * prettify periodic_table.json * fix energy ordering of electronic structures for elements * fix typo * Species: implement electron configuration methods * fix get_crystal_field_spin * fix _get_number_of_d_electrons * fix PotcarSingle test * fix json typo * prettify periodic_table.json for readability * prettify periodic_table.json for readability * pre-commit auto-fixes * convert Electronic Structure in per table data to dict Dict is keyed by oxidation state of the element. This work is to prepare for implementation of Species.electronic_structure * add ion el str to Group I and II cations * implement Species.electronic_structure methods * update docstrings for electronic struct methods * pre-commit auto-fixes * linting * revert changes to degree symbol * revert reordered energy levels * complete ion electron configs * revert reordered energy levels * add comprehensive species test; correct json * pre-commit auto-fixes * add add'l oxi states relevant to aqueous media --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* fix: old algorithm to deduplicate spaces didn't find the minimum subset * test: direct test for remove_redundant_spaces static method * doc: clean up old comments, add details explaining why patchedphasediagram as_dict doesn't save computations due to shared memory id issue. * pre-commit auto-fixes * lint: spelling --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…orhombic cells (#3938)

* update BoltzTraP link * correct BoltzTraP case in docstring * remove unused gitignore items

…class (#3945) * correct Procar docs * more specific get_projection_on_elements return type --------- Co-authored-by: Janosh Riebesell <[email protected]>

…#3949)

…out having `mp-api` installed. (#3950)

* Fix chemical system when the same element appears in multiple oxidation states --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Matthew Horton <[email protected]>

…3936) * Added magmoms reading from nc files with Abinit. * Added tests. * Adding GSR files to tests setup. * Fixing test for collinear magmom. * Fixing test for noncollinear magmom. * Revert backward incompatible change introduced in #2a3608f and #565a8b4. * Added a test for PAW pseudopotentials with abinit. * Fix pseudo test. * Compressed large netCDF files for abinit. * Compressed pseudo file for abinit.

@DanielYang59

* Initial commit; thank you, Santiago! * Refactoring to clean up parsing; add rings and cages * More progress * Almost done with first draft; just need to put all of the pieces together * Some cleaning up; some work still to be done here * First draft, done * First steps towards tests * Progress on tests; some small bugfixes * More tests * Finished! * Remove unnecessary files * Trying to fight linters and type checkers and all that nonsense * pre-commit auto-fixes * Please, ruff, be kind * Please no more linting, please no more linting * pre-commit auto-fixes * (hopefully) just one more mypy issue * Whoops * Opinionated linters hate Union and Optional * pre-commit auto-fixes * Someday, I will meet the creators of mypy, and they will feel my rage * Small type change suggested by @DanielYang59 * pre-commit auto-fixes * Added wavefunction output as a feature of Q-Chem sets * Add back in qtaim-based bond definition (rather than distance-based definition); seems to fail for metals, but might be better elsewhere * Somehow, the linter was mad at me for things that I never touched. Injustice! * Added a third way to define bonds * mypy, of course --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* fix Ion parsing bug introduced by commit b4a70ee * Ion: special handling of CH4, NH4, N3-, SCN-, formate, oxalate * pre-commit auto-fixes * Element / Species - add n_electrons * Revert "Element / Species - add n_electrons" This reverts commit 97ea180. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* set ruff.isort.known-first-party = ["pymatgen"] * pre-commit run --all-files

* add test case for Union type LREAL * remove debug msg * update type check mechanism * use eval for type checking * use isinstance syntax * try to increase dependency palettable version * bump monty to 2024.7.29 * pin torch version until matgl release * Revert "pin torch version until matgl release" This reverts commit 215c888. * skip failing matgl tests for now --------- Signed-off-by: Janosh Riebesell <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

Add joblib backend to process entries in parallel

@DanielYang59

* dedup numpy dep as pointed out by @DanielYang59's 71f5245#r144995852 * fix some ruff PERF401

* add types for bandstructure * relocate magic methods to top * add some types * fix type errors in bandstructure * temp save * first run of cohp, mypy errors to fix * fix collection generation * add type `SpinLike` and case tweaks * reduce repetition for `__str__` of `IcohpValue` * simplify condition * reduce indentation level * clarify `translation` * clarify `list_num` and other docstrings * clarify `label` as str * more type and docstring improvements * fix unit test * fix most mypy errors * fix remaining mypy errors * add DEBUG tag * reduce code repetition * Need Confirm: set `translation` as tuple * pre-commit auto-fixes * more type clarify * clarify `num` argument * clarify docstring of `bandstructure` * more minor tweaks * clarify type of labels_dict * replace unnecessary single-item list extend with append * fix typo * relocate magic method * clarify type of `list_icohp` * remove unused type alias * revert undesired rename * replace more single item extend with append * simplify dict generation * fix downstream lobsterpy error * tweak module docstring * need confirm: allow efermi to be None * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

see matplotlib/matplotlib#28551

found with regex \b\s{2,}\b[^\d]

… returning nothing fix brittle TestQuasiHarmonicDebyeApprox.test_gruneisen_parameter from tight assert_allclose abs tol

@DanielYang59

thanks @DanielYang59 caddde5#r145015623

The pdfs list should be constructed from filenames only without other path components, i.e. use last entry from split()

* Bugfix: `io.pwscf.PWInput.from_str()` Fixes wrong parsing of: - Namelist options ending with comma (`,`) - `ATOMIC_SPECIES` and `ATOMIC_POSITIONS` cards for structures with oxidation states * Additional fix in regexp - Must only have one of either + or - in oxidation states, not one of both --------- Co-authored-by: Janosh Riebesell <[email protected]>

* enable `boltztrap2` * Revert "enable `boltztrap2`" This reverts commit 3b1b077. * use explicit encoding * install graphviz * increment boltztrap version to 24.1.1 * fix bader patch * pre-commit auto-fixes * ruff fix * tweak bader test * need confirm: add `wheel` to dev dep * try install BoltzTraP2 with pip * add comment * try move bolt after numpy to fix win, remove wheel * try move boltrap2 to ubuntu only * more description more accurate * install BoltzTraP2 in CI * try to install BoltzTraP2 with uv * remove repeated numpy install in CI tests * update np.exceptions.RankWarning * Revert "update np.exceptions.RankWarning" This reverts commit 4128284. * install setuptool with uv * update BoltzTraP2 * install wheel for building boltztrap2 * try to install boltztrap2 with pip not uv * install cython before boltztrap2 * try to install boltztrap2 with optional * try to manually install bt2 in workflow * manually install bt2 with pip * remove bt2 ver * install bt2 only on ubuntu * skip bt2 for windows * try to fix failing bt2 test * more descriptive skip msg * finish typing of bzt2 * try to install pygraphviz * revert update to | replace for graphs * test.yml join install pymatgen and install dependencies steps * fix TestStructureGraph.test_draw unhashable type list error * skip BoltzTraP2 and matplotlib 3.9.1 --------- Co-authored-by: Janosh Riebesell <[email protected]>

* Fix d2k function Need to use the transpose of the inverse matrix for recipmatrix * breaking: snake_case method args kpt_density and recip_cell (better to do early while user base small) * d2k_recip_cell fix kpt_density type anno and doc str * Add test for aims density conversions * Fix mypy errors * Add print line to see what the actual errors look like All tests pass locally * for supercell round coords should fix error in tests * remove extra print line * refactor test_static_si_no_kgrid --------- Co-authored-by: Janosh Riebesell <[email protected]>

* Add OPTIMADE adapter --------- Co-authored-by: Janosh Riebesell <[email protected]>

* split pymatgen/io/vasp/sets.py into sub-modules * fix import auto-complete from wrong module

should have been deleted in #3865 but was missed due to the migration to src layout copying src/pymatgen/io/vasp/sets.py to a new location after #3865 was opened

* enable ruff rule family N * fix NPY002 in code (tests to be fixed) * fix NPY002 in tests * replace random with np where np is imported * fix miller index type * [Need Confirm] remove rnd seed and reduce distortion * fix random seed * correct replacement of randn with standard_normal * enable rule family S and format tweaks * suppress S501 error * suppress S105 errors * suppress S602 * replace weak `sha1` hash with `sha256` * ignore S311 as pymatgen is not for cryptography * suppress S605 for trusted source * NEED CONFIRM: fix S607 for the starting of a process with a partial executable path * suppress S310 for trusted source * suppress S608 for trusted source * NEED CONFIRMATION: rewrite subprocess without shell * suppress S301, but still enable it because pickle is known to have potential security issues * replace xml with defusedxml to fix S314 * Revert "replace xml with defusedxml to fix S314" This reverts commit 4947ff5. * ignore S314 * suppress S607 in tasks.py * Revert "NEED CONFIRM: fix S607 for the starting of a process with a partial executable path" This reverts commit 26ccb85. * Fix DTZ003 deprecated datetime API * pre-commit auto-fixes * update monty to fix datetime serialization * replace np.exceptions.RankWarning * update monty in pyproject * revert to np.RankWarning for now * revert accidental np.trapz change during merge * pre-commit auto-fixes * pre-commit auto-fixes * suppress S202 for trusted source * ignore NPY201 for now * Revert "pre-commit auto-fixes" This reverts commit f6a7275. * pre-commit auto-fixes * fix indentation * Revert "pre-commit auto-fixes" This reverts commit 134a11c. * regenerate requirement.txt * fix indentation * rename single-letter p = subprocess.run * replace stdlib random with numpy * avoid assign single use rng * fix unit test * keep non-imperative * replace os.system with subprocess * docstring and type tweaks for io.packmol * io.packmol format tweaks * fix subprocess run usage for stdin file * add return type in docstring * (feel free to revert) use list join over str concat * use f-str --------- Co-authored-by: Janosh Riebesell <[email protected]>

* fea: check that the coords have the right shape * clean up test test_incorrect_dims * drop backticks from doc str + err msg * pre-commit auto-fixes * lint

* build against NPY2 See https://numpy.org/devdocs/dev/depending_on_numpy.html * replace np.int_t with np.int64_t * replace `np.float_` with `np.float64` * replace simps with simpson * replace long with np.int64_t * fix copy=False * fix simpson * asarray Signed-off-by: Jinzhe Zeng <[email protected]> * RankWarning Signed-off-by: Jinzhe Zeng <[email protected]> * pre-commit auto-fixes * ImportError Signed-off-by: Jinzhe Zeng <[email protected]> * replace np.lib.pad with np.pad Signed-off-by: Jinzhe Zeng <[email protected]> * enable NPY201 Signed-off-by: Jinzhe Zeng <[email protected]> * skip several tests related to scipy, chgnet, and phonopy * pre-commit auto-fixes * skip more tests * make warning assertion more robust Signed-off-by: Jinzhe Zeng <[email protected]> * pre-commit auto-fixes * fix test_properties Signed-off-by: Jinzhe Zeng <[email protected]> * pre-commit auto-fixes * Revert "enable NPY201" This reverts commit dc1d719. * rename vars for readability * fix test_get_parchg with comment to explain assert inversion * don't depend on numpy RC in build-system.requires * disable assert altogether * bump optional dep pin abinit = ["netcdf4>=1.7.1"] temp install delvewheel>=1.7.4 in CI * merge * remove delvewheel --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

replace raise AssertionError in tests with equiv assert statement

#3979) * fea: assign frame properties to molecule/structure when indexing trajectory. * test: test that the frame properties are carried over when indexing a single frame

* improve type and simplify iterative_symmetrize * fix type error and tweak types for compatibility * fix packmol type * fix type for site_transformation * ignore type override * fix type for species * docstring tweak * since it says preprocess in comment above, prob not meant to return here --------- Co-authored-by: Janosh Riebesell <[email protected]>

…more coarse (#3986)

…rmation …" (#3987) This reverts commit 123abac.

* ignore mypy override error globally * standardize CP2K names * pre-commit auto-fixes * standarize more CP2K names * old trick: relocate magic methods to the top * format tweaks * fix type errors in cp2k inputs * remove reimport Sequence * use list[Kpoint] as getter return type * remove unnecessary cast --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Bumps [rexml](https://github.com/ruby/rexml) from 3.2.8 to 3.3.3. - [Release notes](https://github.com/ruby/rexml/releases) - [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md) - [Commits](ruby/rexml@v3.2.8...v3.3.3) --- 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>

* Update phase_diagram.py Adds marker labels to 3D ternary plots Adds additional spacing to 2D and 3D hovertext so it is easier to read. Signed-off-by: JoshuaNgXY <[email protected]> * Update phase_diagram.py Signed-off-by: JoshuaNgXY <[email protected]> * pre-commit auto-fixes * Update phase_diagram.py Variable name update Signed-off-by: JoshuaNgXY <[email protected]> * Quaternary Plot functionality Added Updated hovertext to specify "Formation energy" and "Energy above hull". Updated Quaternary plot to have labels for atomic concentration of elements. Added a label to quaternary plot which allows users to toggle the hull surfaces so that the inner points can be accessed. Signed-off-by: JoshuaNgXY <[email protected]> * pre-commit auto-fixes * Update phase_diagram.py Small variable name change to fix pre-commit Signed-off-by: JoshuaNgXY <[email protected]> * Update Voltage Graph Added labels for the x value to points on the voltage graph so they are easier to read. Signed-off-by: JoshuaNgXY <[email protected]> * Update plotter.py Trying to fix tests Signed-off-by: JoshuaNgXY <[email protected]> * pre-commit auto-fixes * Update plotter.py Barebones fix to pass tests Signed-off-by: JoshuaNgXY <[email protected]> * pre-commit auto-fixes --------- Signed-off-by: JoshuaNgXY <[email protected]> Signed-off-by: JoshuaNgXY <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

This reverts commit aab9092.

This reverts commit 81b802e.

…r parts (#3996) * docstring tweaks * fix typo * reduce indentation level * fix vasp case to VASP * use walrus operator * revert overlapping functional changes from #3994 * my bad, I get confused hopping between two PRs * remove debug code from vasp.help * fix `use-named-expression` with sourcery * clean up Vasprun.as_dict * simplify dict generation * re-raise and update -> |= * simplify logic conditions * remove unused logger * remove a lot of unused logger, wondering if they exist for a reason? * remove some unused module_dir, they must have gone stranded * CAPS LOCK ENGAGED: Go up! module level variables!

* Enable formatting customization of PWInput files - Default values set to preserve backwards compatibility * Fix: Preserve format upon write-then-read - Preserve indent and max decimal precision

* VaspInputSet.write_input: Improve error message * src/pymatgen/io/vasp/inputs.py (PotcarSingle.from_symbol_and_functional): Raise custom PMG_VASP_PSP_DIR_Error when PMG_VASP_PSP_DIR is not configured. (PMG_VASP_PSP_DIR_Error): New error inheriting from ValueError. * src/pymatgen/io/vasp/sets.py (VaspInputSet.write_input): When PMG_VASP_PSP_DIR_Error provide a more helpful message advicing that potcar_spec argument can be used. The idea is to provide instructions for users with no VASP license who are also not aware about potcar_spec argument. * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* crude phonon dos comparison * add wasserstein metric, add dosfingerprint class * update dos fingerprint test * add exceptions, add PhononDosFingerprint class * fix type hints and doc-strings * fix type hints and doc-strings for phonon fingerprints * adapt tests with recent changes to src code * add simple phonon dos comparison test * move methods and tests to PhononDos class * fix dos fp exceptions test * address review comments and adapt tests accordingly * fix pending doc-strings --------- Co-authored-by: J. George <[email protected]>

* bump ruff version in pre-commit * fix PT001

… modes (#3994) * kpoints as int in auto Gamma and Monkhorst * add deprecation warning and docstring tweak * add unit test * filter Kpoints warning * docstring tweaks * also test deprecation warning * merge tests into test_static_constructors * assert int type in automatic_density methods * clarify typing for Kpoint * relocate setter and getter to avoid mypy redefine errors * type annotate some class vars * remove boilerplate code * revert changes in io.vasp.inputs * revert change in POTCAR_spec * reapply deprecation warning * My bad, reapply float -> int change * use Tuple3Ints for more specific typing * use Tuple3Floats when type is known

* drop python 3.9 and add python 3.13 * remove yanked matplotlib pin * remove clarified TODO tag * bump python version in CI * try to explicitly declare python 313 in mamba * use 3.13 pre-release rc1 * remove Python 3.13 * remove TODO for Python 2 * remove docstring TODO for unit test * enable this seemingly passing test * tweak and fix typo in get_dos_fp_similarity ValueError msg * ruff auto-fixes * manual fix: type unions use pipe op * replace union with | operator * add TypeAlias to honor type-alias-without-annotation (PYI026) * replace pariwise iteration using zip with itertools * fix error message * not sure why it failed, try to separate available index * sure I forgot about double quote and single quote * use | in INCAR tag check from #3958 * fix RUF017 * Revert "fix RUF017" as I haven't got time to verify This reverts commit b6dbf20. * fix DeprecationWarning: dict interface (SpglibDataset['international']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead --------- Co-authored-by: Janosh Riebesell <[email protected]>

…et. (#3955) * Add HSE-specific vdW parameters for dftd3 and dftd3-bj to MPHSERelaxSet. * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* global replacement of strict=True, very prone to error and need careful check * revert changes on non-zip functions * revert to strict=F for failing tests * revert a missing one * remove a call-overload ignore tag * fix another unit test * fix typos --------- Co-authored-by: Janosh Riebesell <[email protected]>

* simplify: prefer sum over len + if astral-sh/ruff#13050 * fix ruff PD901 pandas-df-variable-name * fix cast df_energies as float in cp2k parse_energy_file

Bumps [rexml](https://github.com/ruby/rexml) from 3.3.3 to 3.3.6. - [Release notes](https://github.com/ruby/rexml/releases) - [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md) - [Commits](ruby/rexml@v3.3.3...v3.3.6) --- 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>

…rt. (#3967) * Add VASP setting for the dftd4 vdW functional and extend PBE_64 support - Add IVDW: 13 for dftd4 in vdW_parameters.yaml - Support PBE_64 functional in MPScanRelaxSet, MVLRelax52Set, MVLScanRelaxSet, and LobsterSet - Update documentation and error messages to include PBE_64 - Add warning for LobsterSet when using PBE_64 POTCARs with PBE_54 basis functions - Update relevant test cases to accommodate PBE_64 support * Update the warning message of LobsterSet to include PBE_52 POTCARs as well. --------- Co-authored-by: Janosh Riebesell <[email protected]>

…#3992) * use explicit int64 to avoid OS inconsistency * pin np <1 to run tests * add missing replacement in cython code * more missing spglib api replacement * globally replace dtype=int with int64 * pre-commit auto-fixes * use int64 in coord_cython * fix assert dtype * NEED confirmation: skip chgnet tests * docstrring tweaks of linear assignment * enough docstring tweaks, go back to real business * last batch of docstring tweak and remove isort tag as it doesn't seem to be used * revert to NP2 in dependency * try to add a np1 test for windows * try another way to install np1 * fix opt dep name * add comment in NP1 install

* fix RUF017 * fix B018: useless expressions * NEED confirm: fix TRY004 type error * fix PGH003: bare # type: ignore * fix FBT003 boolean-positional-value-in-call * fix PYI024 collections-named-tuple * relocate io.aims test file and rename test dir * NEED CONFIRM: relocate io.aims test helper functions * add __init__.py * try to fix helper function path * pre-commit auto-fixes * clean up pyproject.toml * relocate type check import * use relative import, TODO how to use abs import in this case? * fix NPY201 * turn of paradox box of S101 * Revert "turn of paradox box of S101" This reverts commit 735cb62. * tweak type and docstring * fix PD011, got a lot false pos in cp2k keywords * ignore PD011 as too many false pos astral-sh/ruff#6432 * one missing pd011 * fix usage of pytest raise message PT011 * fix B009 get attribute * fix B018, attr test * use np array to avoid RUF005 error * fix RUF005 with np array * fix typo in hasattr use * NEED CONFIRM: turn on SSL certificate check * replace http with https, there're many other cases might need test and replace * Revert "replace http with https, there're many other cases might need test and replace" This reverts commit 8fdd1c5. * Move to another PR, Revert "NEED CONFIRM: turn on SSL certificate check" This reverts commit ae52433. * rename _SpinMode to SpinModeTuple * use list comprehension over function tool to flat list of lists --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* recover test_delta_func Signed-off-by: Jinzhe Zeng <[email protected]> * pre-commit auto-fixes * bump scipy for Windows * add comments to pyproject.toml * pre-commit auto-fixes --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

* temp save of cleaning lobsterenv * fix type errors in lobsterenv * temp save of lobster.outputs * revert chemenv additional_condition rename * first go of lobster.outputs * fix typo in get_doc * separate lobster inputs and outputs tests * fix unit test * more var name and comment cleanups * fix my errors (some unit tests fail) * fix some unit test * fix unit test * Need Confirm: change `np.float64` to float for spilling * clarify data form in docstring * use deprecated decorator * pre-commit auto-fixes * pre-commit auto-fixes * remove DEBUG tag and var name tweaks * add more specific types * use PeriodicSite over Site * standardize idx var name * limit matplotlib version * remove matplotlib pin * remove left out matplotlib pin * remove ignore override tag * pre-commit auto-fixes * Apply suggestions from code review Signed-off-by: J. George <[email protected]> * use specific type for get_nn_info return * add TODO for a very likely TODO comment * remove implemented TODO tag * replace Literal with | in docstring * use atom{idx}_list over atom{idx}s * revert bool description --------- Signed-off-by: J. George <[email protected]> Co-authored-by: J. George <[email protected]>

…4021) * replace http with https, all committed changes verified * replace more http with https * replace expired abinit urls * replace scipy expired url * update NIST url and w3.org * update netCDF4 doc url * replace some http with https in unit test * remove debug leftover * add missing build doc dependency * rebuild docs * add invoke to docs dependency * Revert "rebuild docs" as it makes it impossible to review This reverts commit 47e4d59. * revert replace on io.exciting * revert replacement for structureNL metadata * fix from pytest import raises or mark * directly access MonkeyPatch when pytest is already imported * regenerate documents

* Initial update, SOC PROCAR parsing now working * Allow parsing multiple files, handle combining etc * Tidy up, all current pmg tests passing * Add SOC PROCAR test * Add test for multiple PROCARs (SOC and with LORBIT = 14 phase factors) * Formatting * Remove completed TODO * Formatting * Formatting * Use `itertools.chain` for `dict_array` * pre-commit auto-fixes * pre-commit auto-fixes * add missing types to Procar._read --------- Signed-off-by: Seán Kavanagh <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

* Update `FermiDos.get_doping()` to be more robust. * Update `tol` defaults for DOS methods, and add small notes to `Vasprun` DOS parsing docstrings * pre-commit auto-fixes * Use `scipy.special.expit` function for Fermi-Dirac distribution, slightly faster, cleaner and no masking required to avoid overflow warnings * Update `FermiDos.get_doping()` to be more robust. * Update `tol` defaults for DOS methods, and add small notes to `Vasprun` DOS parsing docstrings * pre-commit auto-fixes * Use `scipy.special.expit` function for Fermi-Dirac distribution, slightly faster, cleaner and no masking required to avoid overflow warnings * Merge pymatgen master (pt 2) * pre-commit auto-fixes * pre-commit auto-fixes * Fix default `tol` update * Remove yaml files to force re-eval * Ensure LF line endings for yamls --------- Signed-off-by: Seán Kavanagh <[email protected]>

@janosh

* turn on S101 for non test code * replace some assert * fix S101 in phonon * fix bad replacement in util.coord * fix S101 in dev_scripts * fix alchemy apps.battery and command_line * fix analysis * fix entries * fix core * fix electronic_structure * fix io.abinit and io.aims * fix cif common and cp2k of io * fix io gaussian packmol exciting and feff * fix io.lammps * fix io.vasp * reapply ignore S101 in tests * print variable values in err messages * augment error message, thanks for the advice @janosh * replace use of assert * use type(x).__name__ in TypeError messages fix typo --------- Co-authored-by: Janosh Riebesell <[email protected]>

…instead (#4027) * recover some commented out test unit * replace legacy random generator * recover more commented out test * avoid code-like comment in case we want to enable ERA someday

* add `src` in link generator * rebuild docs

@QuantumChemist

* enable TLS cert verify * use https over http * explicitly declare bs4 * add bs4 as opt dep * reduce timeout in CI to 60 secs * add test for io.vasp.help * add test for get_incar_tags * declare html parser * reduce test timeout to 5 sec * use pytest importorskip * also except timeout and assert incar tags as list * bump python to 3.10+ in readme, thanks @QuantumChemist * update `test_get_incar_tags` to check incar_parameters.json * skip init for cls method test * add missing VASP wiki INCAR page * include length in error msg * fix typo * update doc py 3.9 to 3.10 * reduce requests timeout to 60 secs, 600 sec might be impractical * make comment docstring * revert to just assert incar_tags_wiki * assert some hard coded INCAR tags

* revert LNONCOLLINEAR match condition * avoid hard coding number of spaces * NEED CONFIRM: turn on terminate_on_match for boolean tags * put True/False in different branches * add unit test for ncl True * reuse existing test file * revert using `terminate_on_match` as True

* remove unused read_cube import * tweak test.yml comments * try to install BoltzTraP * fix decompress command * make installation script modular * try to modify PATH, test split 4 * fix boltztrap unit test * use rtol * properly skip unit test * fix fig.xticks to ax migration in #3237 * ax.gca -> plg.gca() * properly use ScalarFormatter * NEED CONFIRM: fix number of lines * NEED CONFIRM: fix unit test values * try to install open babel * NEED CONFIRM: include fdint * Revert "NEED CONFIRM: include fdint" This reverts commit 6b19836. * skip tests if no fdint * try to install Vampire * make vampire executable * relocate attribute to class docstring * try to use absolute path in PATH * use VAMPEXE * mark vampire test for fix and skip for now * restore conda openbabel install * use openbabel-wheel instead * make download and decompress less verbose * make module level var all capital * re-enable matgl tests * add TODO tag for skipped unit test * bump matgl version * bump matgl in optional * pin torch version in CI * add reference url * clarify comment * remove unused guarded matgl import * relocate import * update requirements.txt * bump openbabel version * bump openbabel-wheel to latest release 19 * remove matplotlib != 3.9.1 pin as it has been yanked * remove linux only pin for openbabel-wheel * add more comment about bolztrap2 * skip openbabel for windows for now * add TODO tag * make module var all cap * rename non test function to avoid test_xxx pattern * install tblite thru conda-forge * sort conda forge pack order alphabetically * fix io.qchem test dir path * add separate dir var for new qchem files * TO FIX: enable qchem test * I tried but failed, need someone smarter than me to fix this * remove non-win pin for openbabel-wheel * skip failing openbabel tests for Windows * skip left out tests for openbabel on win * uncomment hiphive * use numpy recommended 2.0.0rc1 * bumpy build sys numpy to 2.1.0 * fall back to numpy 2.0.1 as 2.1.0 don't support python39 * mark test_zsl as to be fixed in this PR * use float array as per fast_norm require * reverse numba version bump * drop upgrade arg for pip install torch * instead of hinting, just handle * re-raise from previous error * make ubuntu dep install inline * fix test skip and make module var all cap * add TODO tags * renames * Revert "properly use ScalarFormatter" This reverts commit e2ff5fa. * Revert "ax.gca -> plg.gca()" This reverts commit 1d104cb. * Revert "fix fig.xticks to ax migration in #3237" This reverts commit a8d04f9. * Revert "NEED CONFIRM: fix number of lines" This reverts commit eb7978d. * Revert "NEED CONFIRM: fix unit test values" This reverts commit f6a3fc7. * ruff fix * skip entire TestBoltztrapPlotter * use platform.system() == "Windows" over os.name == "nt" * use platform.system() == "Windows" over sys.platform == "win32" --------- Co-authored-by: Janosh Riebesell <[email protected]>

…4037) Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.1.7. - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@v3...v4.1.7) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

@kbuma

* add LRU cache to _get_reduced_structure computations * pre-commit auto-fixes * make structure hashable via as_dict * make structure hash recursive as_dict, change structure test to check hashability * precommit * moved computation using lru_cache out of class method to avoid memory leakage issue * pre-commit auto-fixes * fix structure matcher caching, fix a few tests (mcsqs wrong file destination and missing pytest approx in TestBSPlot) * precommit * add suggested SiteOrderedIStructure from @kbuma * pre-commit auto-fixes * add cast in eq for SiteOrderedIStructure to make mypy happy * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: esoteric-ephemera <[email protected]>

… dict (not `Incar` instance) (#4052) * in-place VaspInput.incar updates have no effect if incar is dict (not Incar instance) * TestVaspInput check incar attr can be updated in place

#3878) * Add modification to FHI-aims input to match atomate2 magnetic order script --------- Signed-off-by: Thomas Purcell <[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> Co-authored-by: Janosh Riebesell <[email protected]>

* Modify for proper dataclass remove commented code and __init__ function * refactor and use Self return type for from_... methods --------- Co-authored-by: Janosh Riebesell <[email protected]>

* avoid importing namespace package pymatgen directly * reapply tool.coverage clean up * avoid import pymatgen.core as pmg * rebuild docs

* fix ruff PLC0206 * fix/ignore ruff PLR6104 * simplify np.prod(arr.shape) -> arr.size * add missing args to get_partial_doses doc str * fix ruff N818 Exception name `SymmetryUndetermined` should be named with an Error suffix * fix TestGruneisenParameter.test_average_gruneisen def test_average_gruneisen(self): assert self.gruneisen_obj.average_gruneisen() == approx(1.164231026696211) > assert self.gruneisen_obj.average_gruneisen(squared=False) == approx(0.849759667411049) E assert 1.3554338835221134 == 0.849759667411049 ± 8.5e-07 E E comparison failed E Obtained: 1.3554338835221134 E Expected: 0.849759667411049 ± 8.5e-07 * auto-format .github/workflows/issue-metrics.yml * rename index variables

…->'']eld")` (#4055) * fix typo in Cp2kOutput.parse_hirshfeld add_site_property("hirshf[i->'']eld") * fix Polarization doc str format * fix pwmat type hints: np.array->np.ndarray * rename single-letter index vars * fix doc str return type np.(''->nd)array * define successive immutable same-value vars on one line found with regex \w+ = (\w+)\n\s+\w+ = \1 more left

* Fix `apply_operation(fractional=True)` * Add tests for `apply_operation` * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…config='cp39-*', skip_config='*musllinux*', requires_python=<SpecifierSet('>=3.10')>, prerelease_pythons=False)

* Use distinct names for artifacts * Bump `upload-artifact` * allow any v4 download-artifact --------- Co-authored-by: Janosh Riebesell <[email protected]>

* Update surface and interface generating functions 1. fixing problem for the lll_reduce process when making slabs, doing mapping before updating the structure 2. allow to set ftol of the termination distances for hierarchical cluster so that some non-identical terminations close to each other can be identified 3. allow to add index for terminations so that terminations with the same space group can be distinguished Interfaces made by identical slabs can be non-identical because the relative transformation of the misorientation and the termination variation do not ensure symmetry, especially when the film and substrate have different point groups. Therefore, the termination finding function should allow to generate all the possible terminations. This can help others to develop more robust algorithm to group the equivalent interfaces made by different terminations. --------- Signed-off-by: Jason Xie <[email protected]> Signed-off-by: Jason Xie <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>

* push a random commit to get a baseline * install native micromamba + native uv * trigger uv to run a second time, hopefully cached * get a benchmark of pip install uv * remove manual install of build dependencies * more verbose uv * remove debug output

* fix all ruff DOC202 https://docs.astral.sh/ruff/rules/docstring-extraneous-returns/ * doc str format: "list[...]: List of ..." -> "list[...]: ..."

…nd_functional

* fixed electronic step check with algo = exact and nelm = 1 * pre-commit auto-fixes * fixed the cases in which ALGO does not appear in incar * pre-commit auto-fixes --------- Co-authored-by: yanghan-microsoft <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Added DebyeCalculator as an external tool Signed-off-by: Andy S. Anker <[email protected]>

* Update `slme` function so it doesn't overwrite the input data * Basic plotting updates; remove hard-coded x-limit, add some labels

* Fix bug with species defaults NEed to specify the default value properly * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* revert to strict=False for some zip * add some return types * Revert "add some return types" This reverts commit 0663667. * make test names follow naming convention * avoid module level variable * separate tests for basis and potential

* use np.testing to check dict equality * add unit tests * perhaps use a helper function instead? * add test for misc, thanks gpt * fix typo * add check if return type

* pip install BoltzTraP2 * remove windows exclusion pin and see what happens * bump bt2 ver * skip bt2 for windows * bump bt2 ver again * still skip win for now as cannot build * give VS build tools a try * revert to skip windows * remove unnecessary venv activate

* Added support to aims format from Structure instance * More tests added

…ctures (#4104) * fix parsing of monatomic xdatcars / clean up parsing code * precommit * make mypy happy * fix volumetric bug with newer POTCAR hashing * ruffn * fix ubuntu-latest test to run on 3.12 as gh workflow indicates, stop trying to run 3.13 * bump down ubuntu-latest to 3.11, mypy too aggressive * change lint version to 3.11 explicitly * pin mypy < 1.12 for linting wf

* added new LOBSTER 5.0/5.1 keywords * update grosspop parser * remove redundant condition check * add POLARIZATION.lobster parser * update icohplist parser * update lobsterout parser * update lobsterout test * add parser to read BWDF.lobster files * minor doc-string improvement * adapt icohplist, cohpcar parsers to work with *.LCFO.lobster files * make doscar partially work with doscar.lcfo.lobster files (LobsterCompleteDos methods needs to be updated) * add todo comment * add todo comment * minor improvment in doscar parser * bypass LobsterCompleteDos error when reading DOSCAR.LCFO.lobster files * add test files * update grosspop tests * update charge, doscar & gropsspop parser * add BWDF and polarization test * minor improvments * replace special character from Polarization parser * rename test files, update icohplist & polarization parser * try adding encoding to parser * add test files, update icohplist parser tests * add tests for doscar.lcfo reading * gzipped test files and added pending tests * use path for filename * use path for filename * address review comments * fix typo in exception * add exeception test * address review comments > add new arg is_lcfo to the parsers --------- Co-authored-by: J. George <[email protected]>

- get_atoms() and get_structure() methods now preserve PBC

Co-authored-by: Shyue Ping Ong <[email protected]>

a directory. Especially useful for working with finished calculations.

…ocessing for str/float/int (#4122) * move ENCUT from int to float list * remove str case sensitivity in check_params * fix return type annotation * fix unit test failure * use original key for warning msg * add duplicate check in check_params * add test first, issue not fixed yet * init from dict also use setter method and fix val filter logic * relocate test_from_file_and_from_dict * Revert "init from dict also use setter method and fix val filter logic" This reverts commit adcdba7. * remove seemingly unused monkeypatch * tweak type * make module level var all cap * casting to list doesn't seem necessary, remain iterator for lazy eval * add docstring to clarify parse list * remove duplicate check * reduce indentation level * remove docstring of warn that doesn't exist * fix typo in incar tag ECUT -> ENCUT * inherit from UserDict, and make more ops case insensitive * also override del and in methdos * issue warning for duplicate keys * enhance warning check * tweak docstring * fix type of float/int casting * enhance test for from_dict consistency check * relocate duplicate check to setter so that both from str and dict would be checked * fix index error for vasprun * move duplicate warning to init otherwise get false pos when update * enhance unit test from type cast from dict * remove unnecessary get default * remove unnecessary type cast in check_params * tweak Incar docstring --------- Co-authored-by: Shyue Ping Ong <[email protected]>

Make sure site properties are properly transferred from the original cell to the primitive or refined one. Co-authored-by: Shyue Ping Ong <[email protected]>

…stall failed: `ImportError: cannot import name 'Mapping' from 'collections'` (#4116) * try to bump networkx to 3.0 * lower to 2.3 * 2.7 seem to pass locally, have a more thorough test * recover pin

* fix plot save fig and enhance type * tweak decorator usage * plt -> fig to avoid shadowing matplotlib.pyplot as plt * fix type error for electronic_structure plotter * pin 3.12 in ci * fix sources path for src layout * split tests for cli * Revert "split tests for cli" This reverts commit f159d5e. * Revert "fix sources path for src layout" This reverts commit 3dfe21c. * recover no type check decorator, intend for another PR * Revert "recover no type check decorator, intend for another PR" This reverts commit f4dabf9. * Reapply "split tests for cli" This reverts commit b01deab. * Reapply "fix sources path for src layout" This reverts commit a7b7e25. * pin mypy for now * improve comment * add unit test for plot * also check incorrect usage

* tweak comments * reduce default timeout as 10 minutes is unrealistic * remove mysql test in test * finish rewrite * use tighter timeout in test * capture timeout errors in ci * make the timeout skip a wrapper * use a conditional timeout * better deprecation handle without breaking * use a formula with only one match

* Bugfix: Correct float parsing in io.pwscf.PWInput * Test: Add test case related to previous commit * Bugfix: K_POINTS card parsing in io.pwscf.PWInput - In "automatic" mode - Add test case to prevent regression

* fix arg passing * add more unit test * perhaps overwrite? not sure which is better * what about making a copy? * make sure copy is correctly done * use np.asarray to avoid copying * remove unnecessary id check now that we're deep copy * try to bump networkx to 3.0+ * Revert "try to bump networkx to 3.0+" This reverts commit b27adba.

…rator (#4111)

…odule level test skip (#4107) * use a single skip mark * use a single skip mark * properly test no ase installed * use specific import error * check None instead of truthy * use single skip mark * separate two skip conditions * use module level skip mark * more descriptive var name * try to remove ignore code * simplify conditional skip for package * use is not None to instead of Falsy * enable unit test * importorskip might be even cleaner * NEED CONFIRM: redirect emmet graph_hashing import * correctly test module not available * fix mock --------- Signed-off-by: Shyue Ping Ong <[email protected]> Co-authored-by: Shyue Ping Ong <[email protected]>

) * remove no_type_check mark * remove no_type_check from plotter as it seems this have to go first * remove mypy version pin * take it slow and pin mypy for now * fix io.lmto * fix electronic structure plotter * fix phase diagram * fix pourbaix diagram * migrate config * bump pyright version * fix pyright in io.lmto * fix pyright in phase diagram * remove mypy pin * fix vis.structure_vtk * fix core ptable * pre-commit auto-fixes * fix lobtser outputd * fix typo in vasprun test * handle converged_electronic for vasp ALGO=CHI * fix another vasp.output error * tweak code style a bit * suppress overload error for now * fix electronic structure plotter * tweak code style a bit * fix type * fix incorrect type of cn * use overload type * bump pre-commit, mainly to get mypy 1.12 * fix incorrect return type of get_parameters * fix most errors in local_env * all done * use set to check membership * a bit more specific type for DEFAULT_OP_PARAMS --------- Signed-off-by: Shyue Ping Ong <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <[email protected]>

* pin python 3.12 in CI * pin `requires-python` * looks like still need to pin 3.12 explicitly --------- Co-authored-by: Shyue Ping Ong <[email protected]>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.4 → v0.6.9](astral-sh/ruff-pre-commit@v0.6.4...v0.6.9) - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/igorshubovych/markdownlint-cli: v0.41.0 → v0.42.0](igorshubovych/markdownlint-cli@v0.41.0...v0.42.0) - [github.com/RobertCraigie/pyright-python: v1.1.379 → v1.1.383](RobertCraigie/pyright-python@v1.1.379...v1.1.383) Signed-off-by: Shyue Ping Ong <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <[email protected]>

Bumps [webrick](https://github.com/ruby/webrick) from 1.8.1 to 1.8.2. - [Release notes](https://github.com/ruby/webrick/releases) - [Commits](ruby/webrick@v1.8.1...v1.8.2) --- updated-dependencies: - dependency-name: webrick dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* add unit test for more data types * Add experimental is_np_dict_equal_try_except function * remove experimental implementation for now

* Allow more than 20 terminal groups in CompoundPhaseDiagram * Allow more than 20 terminal groups in CompoundPhaseDiagram * pre-commit auto-fixes --------- Co-authored-by: Sasha Fonari <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Support pymatgen Species in FHI-aims control.in * Simplify building geometry.in file * A bug fixed

* Correctly compute rotational symmetry number for D*h point group Correct value is 2 * pre-commit auto-fixes * Add docs * pre-commit auto-fixes --------- Co-authored-by: Sasha Fonari <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* `pre-commit migrate-config` * `pre-commit autoupdate` * Replace deprecated `ExpCellFilter` with `FrechetCellFilter` * Fix test for new `FrechetCellFilter` * `dos2unix` --------- Co-authored-by: Shyue Ping Ong <[email protected]>

VaspDir.

Co-authored-by: Shyue Ping Ong <[email protected]>

a particular type of file, e.g., OUTCAR, vasprun, etc. Also fixes handling of GW Vaspruns in VASP6.

* sort var a bit * rename some internal var for readability * wrap func def for readability * max_r to max_rep to avoid confusion * use unsigned int when we're sure it would never be negative

* pass comment * add test for gamma centered and other comment * take comment as arg * tweak comment and type

* rename setup method * use temp dir for TestBztTransportProperties * revert to setup method * revert previous changes, but split tests by sp/non-sp * use temp dir * Revert "use temp dir" This reverts commit f403974. * Revert "revert previous changes, but split tests by sp/non-sp" This reverts commit 950ac97. * properly capture bt2 import exception * properly setup * try to revert to HEAD * also revert testcase * typo, that's the reason * add back TestCase inherit * extract tests from setup method * use temp dir * use a global skip mark * use temp dir for TestBztInterpolator as well * NEED CONFIRM: replace BoltztrapError with more semantic exception * pre-commit auto-fixes --------- Signed-off-by: Shyue Ping Ong <[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>

reason why the parsing should fail.

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

@yantar92

* 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

Commits on Sep 24, 2024

Return bool instead of np.bool_ (#4074 )

jmmshn authored Sep 24, 2024

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Commits on Oct 30, 2024

Simplify implementation of PMGDir.

shyuep committed Oct 30, 2024

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