Pull from materialsproject [WIP]#10
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* Boundary checking * Remove commented out code * Remove commented out code * typo * mypy fix?
Signed-off-by: Daniel Zügner <daniel.zuegner@gmail.com>
…ture` if successfully stores 'eigenvals' and 'kpts'. Initializes projections in `BandStructure` if successfully stores 'bandprojections'. (#4413)
* Organizing `JDFTXInfile` contents * `is_equal_to` method for AbstractTag for equality checking, default parameters for JDFTx, unwritten `is_comparable_to` method for `JDFTXInfile` * `get_tag_object_on_val` alternative to `get_tag_object` that auto-sets format option for `MultiformatTag`s * Fixing value types in default inputs, repeatable multiformattags to be set as a list with elements of different format options, changing `JDFTXStructure.get_str` to build a dictionary representation of each ion instead of a list (not sure how it was even working before) * changing `is_equal_to` to be defined in `AbstractTag` as a repeatability handler, and now `_is_equal_to` to the abstractmethod to be implemented which compares two non-list values * Series of methods for gathering differing tags between two JDFTXInfile objects, along convenience arguments to filter which tags to pay attention to. Not sure if `is_comparable_to` is implementable in a way generalizable enough to be useful. * typing check * Adding back for now, seems bloaty but could be helpful for readability in implementations * Removing commented out code * Changing my mind about ion-species inclusion as a default ensure_include_tag * reordering * TODOs * TODOs * Partial fix for setting selective_dynamics through site_properties in `JDFTXInfile.from_structure` * mypy fix
* Protecting the final JOutStructure with try/except so in-progress out files can be parsed * Enabling partial eigstats filling * Variety of small changes to improve durability of parsing partially finished out files - can return a usable `JDFTXOutfileSlice` as long as electronic minimize has started * Removing commented out code * Removing commented out code * Removing walk-through-helping lines from test
* adding radd dunder method to Volumetric data + test_outputs * more robust with warnings * swapped dos and volumetric, my bad * fixing indentation
…om encoder/decoder is not needed (#4411) * clean up pyproject * try to remove pybtex warning * sort optional dependencies * allow pyproject change to trigger test * also include workflow and setup in test workflow trigger * add orjson as dependency * replace json.dumps * replace json.loads * fix phonondos numpy handling * remove indent and see how many test will break * replace json.load * fix JSON str whitespace sensitivity * replace json.dump * fix os.path.exists * replace str | PathLike * use pmg typealias pathlike * clean up import * minor clean up of module docstring
…ibutes of IcohpCollection (#4391) * add custom from_dict method for proper initialization of attributes * pre-commit auto-fixes * add custom as_dict method for proper serialization * adapt existing test to check for serialization --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…tructure.as_dict` (#4421) * verbosity narrow down to 0 or 1 * cache frequently used lattice property * lint fix * use cached lengths over abc * numpy api is much faster * tweak docstring * add test for cached property invalidation * remove matrix setter
* cast uncertainty_per_atom to float * cast uncertainty to float * avoid == for possible float compare * more tests * add test and tweak docstring type
Signed-off-by: Matt Horton <mkhorton@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.8 → v0.11.12](astral-sh/ruff-pre-commit@v0.11.8...v0.11.12) - [github.com/pre-commit/mirrors-mypy: v1.15.0 → v1.16.0](pre-commit/mirrors-mypy@v1.15.0...v1.16.0) - [github.com/igorshubovych/markdownlint-cli: v0.44.0 → v0.45.0](igorshubovych/markdownlint-cli@v0.44.0...v0.45.0) - [github.com/RobertCraigie/pyright-python: v1.1.400 → v1.1.401](RobertCraigie/pyright-python@v1.1.400...v1.1.401) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…all_stability_map`. (#4428) * test for plotting functionality for NanoscaleStability * Fix labeling --------- Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
* Added possibility to set individual constraints in packmol. Added some sanity checks. Added unit tests. * Added atoms_constraints. * Update packmol.py Added missing argument in docstring.
…m_vasp_multiple_branches` (#4061) * docstring tweak and support Path * isfile -> isdir fix * raise error if vasprun.xml missing in any branch dir * sort pymatgen core imports * add some unit test * raise error if no vasprun.xml file found at all * deprecation warning for fall back branch * remove unused ignore tag * add a temporary solution * update inherit_incar docstring * remove scratch dir * extend deprecation deadline * drop unsure test --------- Co-authored-by: Matt Horton <mkhorton@users.noreply.github.com>
* Update dos.py * Update dos.py * pre-commit auto-fixes * Apply suggestions from code review Signed-off-by: J. George <JaGeo@users.noreply.github.com> * Apply suggestions from code review Signed-off-by: J. George <JaGeo@users.noreply.github.com> --------- Signed-off-by: J. George <JaGeo@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…#4433) * Use more efficient algorithm for `is_periodic_image` * pre-commit auto-fixes * Fix unrelated test failure --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* single source of truth for potcar directory structure * revert unrelated composition change * ensure vasp website tests only run if the manual is up
Bumps [requests](https://github.com/psf/requests) from 2.32.3 to 2.32.4. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.32.3...v2.32.4) --- updated-dependencies: - dependency-name: requests dependency-version: 2.32.4 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Filling out `JOutStructure.properties` for feeding to `frame_properties` for `Trajectory` in `JDFTXOutfileSlice.trajectory` * unneccessary line * better comments on joutstructure initialization order * TODOs * Adding missing kinetic_functional option * Removing vestigial function --------- Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
Bumps [orjson](https://github.com/ijl/orjson) from 3.10.18 to 3.11.6. - [Release notes](https://github.com/ijl/orjson/releases) - [Changelog](https://github.com/ijl/orjson/blob/master/CHANGELOG.md) - [Commits](ijl/orjson@3.10.18...3.11.6) --- updated-dependencies: - dependency-name: orjson dependency-version: 3.11.6 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.5.4 to 6.5.5. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.5.4...v6.5.5) --- updated-dependencies: - dependency-name: tornado dependency-version: 6.5.5 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
api documentation generation.
Bumps [requests](https://github.com/psf/requests) from 2.32.4 to 2.33.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.32.4...v2.33.0) --- updated-dependencies: - dependency-name: requests dependency-version: 2.33.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…cts from the repo (#4626)
updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.15.9](astral-sh/ruff-pre-commit@v0.15.4...v0.15.9) - [github.com/pre-commit/mirrors-mypy: v1.19.1 → v1.20.0](pre-commit/mirrors-mypy@v1.19.1...v1.20.0) - [github.com/codespell-project/codespell: v2.4.1 → v2.4.2](codespell-project/codespell@v2.4.1...v2.4.2) - [github.com/igorshubovych/markdownlint-cli: v0.47.0 → v0.48.0](igorshubovych/markdownlint-cli@v0.47.0...v0.48.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fea: add update method to ppd * linty * formaty
Signed-off-by: Dorian Depriester <dorian@crans.org>
…d removals (#4615) - Replace mutation-during-iteration with direct list reset - Apply fix in both mixing_scheme modules - Add regression test for multiple adjustments
Bumps [activesupport](https://github.com/rails/rails) from 7.0.7.2 to 7.2.3.1. - [Release notes](https://github.com/rails/rails/releases) - [Changelog](https://github.com/rails/rails/blob/v8.1.2.1/activesupport/CHANGELOG.md) - [Commits](rails/rails@v7.0.7.2...v7.2.3.1) --- updated-dependencies: - dependency-name: activesupport dependency-version: 7.2.3.1 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…reduction (#4614) * fix: exclude same-composition entries from inner hull reduction * fix: add fallback to full competing set if reduced hull fails
…4629) * fix: use projected element space for GP equilibrium reaction energy Use projected composition elements when building the equilibrium-reaction sub-hull for GrandPotential entries, and add a regression test covering open-element original compositions. Made-with: Cursor * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
been moved to pymatgen-core.
Bumps [addressable](https://github.com/sporkmonger/addressable) from 2.8.4 to 2.9.0. - [Changelog](https://github.com/sporkmonger/addressable/blob/main/CHANGELOG.md) - [Commits](sporkmonger/addressable@addressable-2.8.4...addressable-2.9.0) --- updated-dependencies: - dependency-name: addressable dependency-version: 2.9.0 dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…4631) * Add preparation step for Jekyll deployment and include static files * Update Jekyll deployment workflow to use UV for documentation generation and remove docs from default groups in pyproject.toml * Moved the prepare step into the Generate Sphinx API docs step for consistency
Bumps [pytest](https://github.com/pytest-dev/pytest) from 9.0.2 to 9.0.3. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@9.0.2...9.0.3) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.0.3 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Shyue Ping Ong <shyuep@users.noreply.github.com>
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Summary
Pull updates from materialsproject master to make this branch compatible with python 3.9. Only take commits up until version 2022.1.20 (January 20, 2022).
TODO (if any)
Need to test this branch to ensure it functions and can be installed on python 3.9 (and possible 3.8 and 3.10)
Checklist
Before a pull request can be merged, the following items must be checked:
is to run the following in the correct sequence on your local machine. Start with running
black on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
pycodestyle, followed by
flake8.
Run pydocstyle on your code.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply
cp pre-commit .git/hooksand a check will be run prior to allowing commits.