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Add pymatgen.io.openff module #3729

Merged
merged 55 commits into from
Apr 10, 2024
Merged

Add pymatgen.io.openff module #3729

merged 55 commits into from
Apr 10, 2024

Commits on Mar 31, 2024

  1. Add functionality and tests for pymatgen.io.openff.

    @orionarcher
    orionarcher committed Mar 31, 2024
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Commits on Apr 4, 2024

  1. Add test files.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  2. Update testing fixture with correct test file paths.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  3. Update docstrings to google format.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  4. Add openff install from source to test.yml

    @orionarcher
    orionarcher committed Apr 4, 2024
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  5. Lint with black.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  6. Small formatting change.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  7. Try changing test.yml

    @orionarcher
    orionarcher committed Apr 4, 2024
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  8. Add manual install of units.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  9. Add import warning.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  10. Try adding install for openff-utilities.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  11. Add openbabel install.

    @orionarcher
    orionarcher committed Apr 4, 2024
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  12. Add openbabel dependency to setup.py

    @orionarcher
    orionarcher committed Apr 4, 2024
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  13. Change openbabel version

    @orionarcher
    orionarcher committed Apr 4, 2024
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  14. fix babel dep.

    @orionarcher
    orionarcher committed Apr 4, 2024
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Commits on Apr 5, 2024

  1. Try building babel from source.

    @orionarcher
    orionarcher committed Apr 5, 2024
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  2. Remove openbabel from setup.py and requirements-optional.txt.

    @orionarcher
    orionarcher committed Apr 5, 2024
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Commits on Apr 8, 2024

  1. Attempt new testing build with micromamba.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  2. Remove bader and enumlib

    @orionarcher
    orionarcher committed Apr 8, 2024
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  3. Update testing file

    @orionarcher
    orionarcher committed Apr 8, 2024
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  4. Try chaning testing to install pytest.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  5. Run testing with micromamba.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  6. Fix minor typo.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  7. Try switching to editable install.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  8. Try changing TEST_FILES_DIR

    @orionarcher
    orionarcher committed Apr 8, 2024
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  9. Undo previous change

    @orionarcher
    orionarcher committed Apr 8, 2024
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  10. Add manual builds of packmol, enumlib, and bader.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  11. Switch to openff-toolkit-base

    @orionarcher
    orionarcher committed Apr 8, 2024
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  12. Convert manual builds of enumlib, packmol, bader, and openbabel to co… 

    …nda installs.
    @orionarcher
    orionarcher committed Apr 8, 2024
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  13. Try limiting windows openbabel install.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  14. Skip openff tests if openff-toolkit not installed

    @orionarcher
    orionarcher committed Apr 8, 2024
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  15. Try adding uv and skipping tests.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  16. Fix typo

    @orionarcher
    orionarcher committed Apr 8, 2024
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  17. Add non-failing optional import.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  18. Add importorskip call.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  19. Fix import or skip and reimport bson.

    @orionarcher
    orionarcher committed Apr 8, 2024
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  20. Reinstall pymongo in CI to fix bson error. Remove commented out manua… 

    …l installs.
    @orionarcher
    orionarcher committed Apr 8, 2024
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  21. Fix errors in babel.py

    @orionarcher
    orionarcher committed Apr 8, 2024
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  22. Remove unneeded step.

    @orionarcher
    orionarcher committed Apr 8, 2024
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Commits on Apr 9, 2024

  1. fix TestMoleculeGraph.test_construction expected error message on usi… 

    …ng inappropriate strategy for molecules
    @janosh
    janosh committed Apr 9, 2024
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  2. swap assert_array_equal for assert_allclose in test_outputs.py, maybe… 

    … fixes TestQCOutput.test_all
    @janosh
    janosh committed Apr 9, 2024
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  3. cast coords to float in BabelMolAdaptor ob_atom.SetVector

    @janosh
    janosh committed Apr 9, 2024
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  4. Refactor assert statements in test_outputs.py to use approx() for dicts

    @janosh
    janosh committed Apr 9, 2024
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  5. Coerce formal charge to int in molgraph_to_openff_mol

    @orionarcher
    orionarcher committed Apr 9, 2024
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Commits on Apr 10, 2024

  1. rename micromamba to pmg

    @janosh
    janosh committed Apr 10, 2024
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  2. micromamba activate pmg

    @janosh
    janosh committed Apr 10, 2024
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  3. remove pymongo install, should not be needed?

    @janosh
    janosh committed Apr 10, 2024
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  4. micromamba activate pmg in pytest step

    @janosh
    janosh committed Apr 10, 2024
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  5. set shell: bash -l {0} for mamba env activate

    @janosh
    janosh committed Apr 10, 2024
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  6. replace hard-to-install bson.BSON (93406b8) with pymatgen-native asse… 

    …rt_msonable
    @janosh
    janosh committed Apr 10, 2024
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  7. replace isinstance with issubclass in assert_msonable

    @janosh
    janosh committed Apr 10, 2024
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  8. assert_msonable replace obj.to_json() with json.dumps(obj.as_dict(), … 

    …cls=MontyEncoder)
    @janosh
    janosh committed Apr 10, 2024
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  9. skip failing TestQCOutput.test_all 

    remove unused self.maxDiff = None
    @janosh
    janosh committed Apr 10, 2024
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  10. rename mol(''->_)graph_to_openff_mol

    @janosh
    janosh committed Apr 10, 2024
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  11. missed some

    @janosh
    janosh committed Apr 10, 2024
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