Fix tmp_path usage #1130
Merged
Fix tmp_path usage #1130
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
j-wags
approved these changes
Nov 17, 2021
There was a problem hiding this comment.
Awesome. Thanks @mattwthompson. Feel free to update the releasenotes, or just merge it since it's so simple.
mattwthompson
added a commit
that referenced
this pull request
Dec 3, 2021
…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>
# for free
to join this conversation on GitHub.
Already have an account?
# to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #1129, see https://docs.pytest.org/en/6.2.x/tmpdir.html