mirror of
https://github.com/openmm/openmmforcefields.git
synced 2026-06-06 18:39:48 +09:00
121 lines
3.5 KiB
YAML
121 lines
3.5 KiB
YAML
name: CI
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on:
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push:
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branches:
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- "main"
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pull_request:
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branches:
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- "main"
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schedule:
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- cron: "0 0 * * *"
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defaults:
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run:
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shell: bash -l {0}
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concurrency:
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group: "${{ github.workflow }}-${{ github.ref }}"
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cancel-in-progress: true
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jobs:
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test:
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name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, Latest openff-toolkit ${{ matrix.latest-openff-toolkit }}
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runs-on: ${{ matrix.os }}
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env:
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OE_LICENSE: ${{ github.workspace }}/oe_license.txt
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macOS-latest]
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python-version: ["3.8", "3.9", "3.10"]
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latest-openff-toolkit: [true, false]
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steps:
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- uses: actions/checkout@v2
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- name: Setup Conda Environment
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uses: mamba-org/provision-with-micromamba@main
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with:
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environment-file: devtools/conda-envs/test_env.yaml
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extra-specs: |
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python=${{ matrix.python-version }}
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- name: License OpenEye
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shell: bash -l {0}
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run: |
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echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
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python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
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env:
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SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
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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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- 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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- 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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- name: Test Installed Package
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run: |
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pytest -v -x --log-cli-level $LOGLEVEL --cov=openmmforcefields --durations=20 -nauto --cov-append --cov-report=xml \
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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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LOGLEVEL: "INFO"
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KMP_DUPLICATE_LIB_OK: "True"
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- name: Test AMBER conversion
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run: |
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python convert_amber.py --input gaff.yaml --log gaff-tests.csv --verbose
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working-directory: ./amber
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- name: Test CHARMM conversion
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run: |
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# TODO: Uncomment these tests when new ParmEd is released
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# TODO: Find a way to avoid timing out when running full charmm36.yaml conversion below
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# python convert_charmm.py --verbose --in files/waters.yaml && python convert_charmm.py --verbose --in files/charmm36.yaml
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# python convert_charmm.py --verbose --in files/waters.yaml
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# python convert_charmm.py --verbose
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# TODO: Uncomment this when tests are expected to work
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# python test_charmm.py --verbose
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working-directory: ./charmm
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- name: Upload coverage data
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uses: actions/upload-artifact@v3
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with:
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name: coverage-data
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path: ".coverage.*"
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if-no-files-found: ignore
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- name: Download coverage data.
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uses: actions/download-artifact@v2
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with:
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name: coverage-data
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- name: Combine coverage & fail if it's <100%.
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run: |
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python -m coverage combine
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python -m coverage html --skip-covered --skip-empty
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python -m coverage report --fail-under=100
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- name: Upload HTML report if check failed.
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uses: actions/upload-artifact@v2
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with:
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name: html-report
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path: htmlcov
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if: ${{ failure() }}
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