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mikemhenrymattwthompson
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Fix toolkit tests (#227)
* Ensure 0.11.0 RC version of toolkit is installed * Possible fix to finish #191 * Try to ensure bash args thing is passed through * Naive unit refactor * Work through tests * Update CI matrix * Use mamba for development * Debug, add boilerplate .gitignore * Fix syntax * make sure the package didn't get installed before we install it * Do not install Espaloma * Fix some unit registries in tests * install espaloma, but remove openmmforcefields * add back in espaloma * switch to micromamba * Explicitly move ffxml sources into entry point * Remove symlinking * Add boilerplate `.gitignore` * Update package installation in CI * Fix finding Amber files in test * Soft import whatever units module is used by the toolkit * Switch to micromamba for setting up conda environment Add boilerplate `.gitignore` file Do not pull from non-standard labels Install instead of update Try to figure out why if: {{ false }} still triggers Syntax? Tinker Bring in (full) mamba Bash thing everywhere Bring down old toolkit Do not present un-loadable ff14SB port as available More pins * Fix YAML syntax * Use pip * More fixes * No particles * Fix unit serialization * Fix Atom.element calls * Update some tests * Clean up un-used imports * Fix more tests * Fix more tests * Exclude Python 3.10 on macOS * Skip ff14SB being treated as a small molecule * Fix test * Track duration of longest 20 tests * Update action versions * Try to fix exclusions in CI matrix * Fix pathing in Amber conversion * Run `pyupgrade --py38-plus` * Try directly uploading coverage report * Fix syntax * Add back some tests * Debug * Drop `pytest-xdist` arg * Fiddle with path * Just try to get stuff passing * Try uploading again * Switch back to codecov * Simply coverage reporting * Allow 0 coverage * Simplify coverage arguments * Add `__init__.py` in `/tests/` submodule https://stackoverflow.com/a/60579142 * Add `__init__.py` in `/tests/` submodule https://stackoverflow.com/a/60579142 * Simplify coverage arguments * Add back durations argument * Apply suggestions from code review * only upload report if it is not scheduled Co-authored-by: Matthew W. Thompson <[email protected]>
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‎.github/workflows/ci.yaml‎

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@@ -27,12 +27,15 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macOS-latest]
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.8", "3.9", "3.10"]
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latest-openff-toolkit: [true, false]
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exclude:
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- python-version: "3.10"
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os: macos-latest
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steps:
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- uses: actions/checkout@v3.0.2
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- uses: actions/checkout@v3
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- name: Setup Conda Environment
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uses: mamba-org/provision-with-micromamba@main
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- name: "Install latest openff-toolkit"
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if: ${{ matrix.latest-openff-toolkit == true }}
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run: |
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# Until #225 is complete, we should not assume compatibility with new API
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micromamba install "openff-toolkit =0.10.6" -c conda-forge -y
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micromamba update -y -c conda-forge "openff-toolkit >=0.11.0"
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- name: Install Package
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run: |
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# Can't use 'develop' mode because we remove symlinks after install is complete
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python setup.py install
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pip list
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micromamba list
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micromamba remove --force openmmforcefields
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python -m pip install .
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- name: Conda Environment Information
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run: |
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conda info
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conda list
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micromamba info
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micromamba list
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python -c "from openmmforcefields import __version__, __file__; print(__version__, __file__)"
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- name: Test Installed Package
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run: |
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pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_amber_import.py
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pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_template_generators.py
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pytest -v -x -s --log-cli-level $LOGLEVEL --cov=openmmforcefields openmmforcefields/tests/test_system_generator.py
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pytest -v -x --log-cli-level $LOGLEVEL $COV_ARGS --durations=20 \
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openmmforcefields/tests/test_amber_import.py \
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openmmforcefields/tests/test_template_generators.py \
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openmmforcefields/tests/test_system_generator.py
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env:
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COV_ARGS: --cov=openmmforcefields --cov-config=setup.cfg --cov-append --cov-report=xml
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LOGLEVEL: "INFO"
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KMP_DUPLICATE_LIB_OK: "True"
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working-directory: ./charmm
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- name: CodeCov
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- name: Upload coverage report to CodeCov
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uses: codecov/[email protected]
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if: ${{ github.repository == 'openmm/openmmforcefields'
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&& github.event != 'schedule' }}
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uses: codecov/[email protected]
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml
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flags: unittests
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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fail_ci_if_error: true

‎.gitignore‎

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# Django stuff:
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*.log
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local_settings.py
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# Sphinx documentation
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docs/_build/
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docs/api/generated
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# Flask stuff:
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instance/
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# PyCharm
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*.idea/vcs.xml
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# Jupyter
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# Jupyter Notebook
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.ipynb_checkpoints
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# In-tree generated files
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*/_version.py
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# OS X extra files
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# macOS
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*.DS_Store
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# Caches
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openmmforcefields/data/perses_jacs_systems/*/cache.json
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# Test molecules
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testsystem-bace*

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