Bump actions/checkout from 2.3.5 to 2.4.0 #1121
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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] <support@github.com>
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…nal dependencies (#1142) * Add openff-units to test environments * Make OpenMM optional in most of topology and typing modules * More fixes in Molecule * Improve parsing of SMIRNOFF XML source * More fixes for force field tests * Test against openff-units/smirnoff-per-mol * Fix energy tests * Patch some unit interoperability in utils/utils.py * Fixes for charge assignment tests * Let some Molecule setters take in openmm.unit quantities * [pre-commit.ci] pre-commit autoupdate (#1119) 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> * Bump actions/checkout from 2.3.5 to 2.4.0 (#1121) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add 404 page to docs (#1115) * 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 (#949) * Relocate the SMIRNOFF spec to standards * Update links to SMIRNOFF spec in standards * Update links in release history Co-authored-by: Matthew W. Thompson <mattwthompson@protonmail.com> Co-authored-by: Josh Mitchell <yoshanuikabundi@gmail.com> Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com> * [pre-commit.ci] pre-commit autoupdate (#1124) 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 (#1116) * Use pytest-rerunfailures on tests that rely on QCArchive * Update openff/toolkit/tests/test_molecule.py Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com> Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com> * [pre-commit.ci] pre-commit autoupdate (#1127) 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 (#1120) * 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 (#1111) * 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 * Replace ParmEd with Interchange in Amber/GROMACS example (#1113) * 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 <jwagnerjpl@gmail.com> * Fix examples workflow (#1128) * Simplify virtual site serialization, fix some tests * Fix tmp_path usage * Bump actions/setup-python from 2.2.2 to 2.3.0 (#1131) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix tmp_path usage (#1130) * Fix tmp_path usage * Update release history * Fixes for topology unit tests * Fixes for test_molecule * Fixes for test_toolkits*py * Fixes for test_utils * Fix units of virtual site positions * [pre-commit.ci] pre-commit autoupdate (#1134) * [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 <mattwthompson@protonmail.com> * Fix fstrings for Python 3.7 compatibility * Fixes for GBSA tests * Fix test_tip5p_dimer_energy * Style fixes * Fixes for some parameter assignment tests * Install released version of openff-units * Fix GLOBAL_TOOLKIT_REGISTRY etc being expanded in sigs (#1135) * Bump actions/setup-python from 2.3.0 to 2.3.1 (#1138) 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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update examples to use openff-units * Streamline CI github actions (#1125) * matrixify CI * fix list * Revert "fix list" This reverts commit 16cad1c. * redo packages * check uninstalled toolkits * tidy up and rm comment * Fix Mypy * Remove unused imports * Update FAQ.md (#1139) * Update FAQ.md * Apply suggestions from code review Co-authored-by: Matt Thompson <mattwthompson@protonmail.com> * Apply suggestions from code review Co-authored-by: Josh A. Mitchell <yoshanuikabundi@gmail.com> * link to core concepts when talking about what an OFFMol needs to know * fix core concepts link Co-authored-by: Matt Thompson <mattwthompson@protonmail.com> Co-authored-by: Josh A. Mitchell <yoshanuikabundi@gmail.com> * Fix typing tests * Switch to mendeleev * Drop simtk support * Update dependencies * Mark failing tests as flaky * More forceful xfail * Make entire openmm module optional * Add mendeleev to test envs * Fix imports * Fix merge conflict * Fix imports * Fix mypy Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Josh A. Mitchell <yoshanuikabundi@gmail.com> Co-authored-by: SimonBoothroyd <simon.boothroyd@hotmail.com> Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com> Co-authored-by: Lily Wang <31115101+lilyminium@users.noreply.github.com>
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Bumps actions/checkout from 2.3.5 to 2.4.0.
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Commits
ec3a7ceset insteadOf url for org-id (#621)fd47087codeql should analyze lib not dist (#620)3d677acscript to generate license info (#614)826ba42npm audit fix (#612)eb8a193update dev dependencies and react to new linting rules (#611)c49af7cCreate codeql-analysis.yml (#602)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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