Maintenance #1985
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Maintenance #1985
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jaclark5
commented
Dec 13, 2024
jaclark5
commented
- Tag issue being addressed
- [NA] Add tests
- Update docstrings/documentation, if applicable
- [NA] Lint codebase
- [NA] Update changelog
updates: - [github.com/psf/black: 21.9b0 → 21.10b0](psf/black@21.9b0...21.10b0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 2.3.5 to 2.4.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2.3.5...v2.4.0) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Add 404 page * Use sphinx-notfound-page in RTD but skip building the 404 page if not installed * Improve language in 404 * Add link to stable version on 404 page
* Relocate the SMIRNOFF spec to standards * Update links to SMIRNOFF spec in standards * Update links in release history Co-authored-by: Matthew W. Thompson <[email protected]> Co-authored-by: Josh Mitchell <[email protected]> Co-authored-by: Jeff Wagner <[email protected]>
updates: - [github.com/PyCQA/isort: 5.9.3 → 5.10.0](PyCQA/isort@5.9.3...5.10.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Use pytest-rerunfailures on tests that rely on QCArchive * Update openff/toolkit/tests/test_molecule.py Co-authored-by: Jeff Wagner <[email protected]> Co-authored-by: Jeff Wagner <[email protected]>
updates: - [github.com/PyCQA/isort: 5.10.0 → 5.10.1](PyCQA/isort@5.10.0...5.10.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Make FrozenMolecule.to_hill_formula a class method * Skip Hill formula short-circuit in isomorphism check * Remove debug code * Support some amount of duck-typing in isomorphism check * Fix typo in test * Fix type annotation
* Add automated tests against OpenMM/OpenEye RCs * Rework to unconditionally test against all RC/beta builds * Run on push * Fix syntax * Make OE RC higher priority than OE beta * Remove dev code * Update beta_rc.yaml * Use strict channel priority * Switch back to debug * Remove dev trigger * Drop OpenEye beta channel
* Add Interchange + GROMACS to existing GROMACS example * Overhaul Amber + GROMACS example * Update conda env used by binder * Refactor protein-ligand examples to not use ParmEd * Add back ParmEd-based example * Fix other files * Rename notebooks * Add header notes to each notebook * add new example deps to example yaml * Skip Interchange example when AmberTools is not installed * Do not assume LAMMPS and GROMACS are installed * Fix how GROMACS/Amber notebook is detected * Debug files * Move debug so it might get printed * Split out Amber/GROMACS example into earlier step * Run examples with Python 3.9 * try not using mamba in case its causing trouble with ambertools * re enable mamba, force ambertools downgrade * Try running it as a test script * Unpin AmberTools * Revert some debugging in workflow * Remove script used for debugging * Pin to interchange v0.1.3+ * Update CHANGELOG Co-authored-by: Jeff Wagner <[email protected]>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2.2.2 to 2.3.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2.2.2...v2.3.0) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix tmp_path usage * Update release history
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 21.10b0 → 21.11b1](psf/black@21.10b0...21.11b1) - [github.com/nbQA-dev/nbQA: 1.1.1 → 1.2.1](nbQA-dev/nbQA@1.1.1...1.2.1) * Have pre-commit.ci run autoupdate monthly Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Matthew W. Thompson <[email protected]>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2.3.0 to 2.3.1. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2.3.0...v2.3.1) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* matrixify CI * fix list * Revert "fix list" This reverts commit 16cad1c. * redo packages * check uninstalled toolkits * tidy up and rm comment
* Update FAQ.md * Apply suggestions from code review Co-authored-by: Matt Thompson <[email protected]> * Apply suggestions from code review Co-authored-by: Josh A. Mitchell <[email protected]> * link to core concepts when talking about what an OFFMol needs to know * fix core concepts link Co-authored-by: Matt Thompson <[email protected]> Co-authored-by: Josh A. Mitchell <[email protected]>
updates: - [github.com/psf/black: 21.11b1 → 21.12b0](psf/black@21.11b1...21.12b0) - [github.com/nbQA-dev/nbQA: 1.2.1 → 1.2.2](nbQA-dev/nbQA@1.2.1...1.2.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ncing their reference molecules * Add test reproducing #1147 * Have TopologyMolecule reference their reference_molecule * Update release history * Use "is" in test for TopologyX.molecule == reference_molecule
* fix 1152 * update releasehistory * isort
* Add specific exception for Molecule.from_file with XYZ files * Update release history
#1155) * Add tests mocking serialization on big- and little-endian * Enfore big-endian in serialize_numpy/deserialize_numpy * Add missing import * Add specific exception for Molecule.from_file with XYZ files (#1148) * Add specific exception for Molecule.from_file with XYZ files * Update release history * Apply suggestions from code review Co-authored-by: Lily Wang <[email protected]> * Fix test, update docstrings, add type annotations * Fix hard-coding of bytes to list for JSON serialization * Fix typos * Update release history, docstrings Co-authored-by: Lily Wang <[email protected]>
* Test Molecule._ipython_display_ without nglview * Let MissingDependencyError also import from ImportError * Update release history
* fix #1159 and add test * update releasehistory * black * isort and relocate imports * isort * Apply suggestions from code review Co-authored-by: trevorgokey <[email protected]> * black Co-authored-by: trevorgokey <[email protected]>
* Turn off `--warn-unused-ignores` to avoid false failures * Fix history
* Remove deprecated exceptions * Update release history * Remove some unused imports * Fix broken import
* Migrate entry point discovery `pkg_resources` -> `importlib_metadata` * move plugins used for testing to a separate, internally-contained test package * update tests to install test plugin package * Turn off `--warn-unused-ignores` to avoid false failures * fix typo in CI yaml * update releasehistory Co-authored-by: j-wags <[email protected]>
Co-authored-by: Jeff Wagner <[email protected]>
* Expand on smirnoff spec in toolkit docs * Update changelog * Split SMIRNOFF page into two sections
* Add description of constraints to the FAQ * Update changelog * Apply changes from code review
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2.3.1 to 2.3.2. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2.3.1...v2.3.2) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Refactor Molecule._get_rings() to ToolkitWrapper.call() * Refactor .n_rings, .is_in_ring to methods that call toolkit wrappers * Add Molecule.n_rings and OpenEye implementations, tests * Add bond_is_in_ring methods in cheminformatics toolkit wrappers * Add back Molecule.rings with deprecation warning * Add test for biphenyl's central bond not being "in a ring" * Have Bond.is_in_ring route to wrapper methods * Update release history * Update pre-commit config, re-run black * Fix mypy and tests * Move is_in_ring tests to test_toolkits.py * Fix tests, add back Molecule.n_rings as deprecated * Update docs/releasehistory.md Co-authored-by: Jeff Wagner <[email protected]> * Remove Molecule.rings and Molecule.n_rings * Fix TestMolecule::test_is_in_ring * Update biphenyl ring tests with mapped smiles * Remove unused import * Apply suggestions from code review Co-authored-by: Jeff Wagner <[email protected]> * Rework ring checks to only take Atom or Bond * Add test for error when Atom/Bond not attached to molecule * Update docstring and changelog * Fix test for unattached bond case * Cleanup Co-authored-by: Jeff Wagner <[email protected]>
* Add clear error message to openeye apply_elf_conformer_selection in silent failures * Fix apply_elf_conformer_selection when specifying rdkit wrapper * Add test for Molecule.apply_elf_conformer_selection with toolkit wrapper * Add Molecule._make_carboxylic_acids_cis method + tests * Make COOH cis when generating conformers in assign_partial_charges with openeye toolkit * Make COOH cis when generating conformers in assign_fractional_bond_orders with openeye toolkit and an ELF10 method * Update changelog * Typo in release notes * Update docs/releasehistory.md Co-authored-by: Jeff Wagner <[email protected]> * Improve robustness of make_carboxylic_acids_cis tests * Remove two safety checks from molecule.py now that they're in test_molecule.py * Add make_carboxylic_acids_cis switch to rdkit and molecule generate_conformers() * Add toolkit_registry argument to Molecule._make_carboxylic_acids_cis() * Remove erroneous comment from _make_carboxylic_acids_cis * _make_carboxylic_acids_cis: Exit early if molecule has no COOH groups * Make OE assign methods consistent * Update openff/toolkit/topology/molecule.py Co-authored-by: SimonBoothroyd <[email protected]> * Switch make_carboxylic_acids_cis test to formic acid Clarifies test by using simpler molecule and using dummy values to lay out the molecule obviously Co-authored-by: SimonBoothroyd <[email protected]> * Lint and clean up * Simplify test_make_carboxylic_acids_cis * generate_conformers makes COOH cis by default Co-authored-by: Jeff Wagner <[email protected]> Co-authored-by: SimonBoothroyd <[email protected]>
* Add test for TIP3P charges with Sage * Do not uniquify SMARTS in LibraryChargeHandler * Also test standalone TIP3P file * Consolidate tip3p charge tests * black * Update release history Co-authored-by: j-wags <[email protected]>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2.3.2 to 3. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v2.3.2...v3) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 2.4.0 to 3. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v2.4.0...v3) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
updates: - [github.com/nbQA-dev/nbQA: 1.2.3 → 1.3.0](nbQA-dev/nbQA@1.2.3...1.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Port #1214 to 0.10.x line * Update release history Co-authored-by: Jeff Wagner <[email protected]>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.1.0 to 3. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md) - [Commits](codecov/codecov-action@v2.1.0...v3) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 2 to 3. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@v2...v3) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Reformulate RDKit stereo assignment as CSP problem * Fix exception on no stereogenic bonds * Drop RDKit mangled check as single mol no longer mangled * Remove duplicate numpy import * Fix mypy errors * Port second half of #1231 https://github.com/openforcefield/openff-toolkit/pull/1231/files/7a9955633e3ffcfd1659f99852988f561f31ef89..86df78d062269a6ab8bf4658ba5072e2a51fc85e Co-authored-by: Jeff Wagner <[email protected]> * Update release history Co-authored-by: Matthew W. Thompson <[email protected]> Co-authored-by: Jeff Wagner <[email protected]>
* Refactor virtual site handler
* Attempts to make virtual site handler more resilient through code simplification.
* Virtual sites are now associated with a particular 'parent' atom, rather than
with a set of atoms. In particular, when checking if a v-site has been assigned
we now only check the main 'parent' atom associated with the v-site, rather than
all additional orientation atoms. As an example, if a force field contained a
bond-charge v-site that matches [O:1]=[C:2] and a monovalent lone pair that matches
[O:1]=[C:2]-[*:3] in that order, then only the monovalent lone pair will be assigned
to formaldehyde as the oxygen is the main atom that would be associated with both v-sites,
and the monovalent lone pair appears later in the hierarchy. This constitutes a behaviour
change over previous versions.
* all v-site exclusion policies have been removed except for 'parents' which has been updated
to match OFF-EP 0006.
* checks have been added to enforce that the 'match' keyword complies with the SMIRNOFF
spec.
* Molecule virtual site classes no longer store FF data such as epsilon and sigma.
* Sanity checks have been added when matching chemical environments for v-sites that ensure
the environment looks like one of our expected test cases.
* Fixes di(try)talent lone pairs mixing the :1 and :2 indices.
* Fixes trivalent v-site positioning.
* Correctly splits `TopologyVirtualSite` and `TopologyVirtualParticle` so that virtual particles
no longer have attributes such as `particles`, and ensure that indexing methods now work
correctly.
* Update docs pages
* Fix mypy and example
* police charge increment list length and add tests
* move vsite connectivity checking so it gets run in create_force, make error text even wordier
* add test comments
* add a complex test for vsite assignment and overwriting with varied parameters
* add simple test that connectivity checking error is raised in create_force
* black
* remove {val=} from fstrings because something in example tests doesn't like them
* Update vsite partial charges test for connectivity checking
* update for picky tests
* update releasehistory
* isort
* make mypy happy
Co-authored-by: j-wags <[email protected]>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 4. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v3...v4) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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