Merge pull request #512 from Lnaden/statsfix #753
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| - 'pymbar4' | |
| - 'gha' | |
| pull_request: | |
| branches: | |
| - 'master' | |
| - 'pymbar4' | |
| - 'gha' | |
| schedule: | |
| # Nightly Tests | |
| - cron: '0 0 * * *' | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macOS-latest, ubuntu-latest, windows-latest] | |
| python-version: [3.8, 3.11] # Check against oldest and newest versions | |
| jax: ["", "_jax"] | |
| exclude: # Skip win + jax | |
| - jax: "_jax" | |
| os: windows-latest | |
| env: | |
| PYVER: ${{ matrix.python-version }} | |
| CI_OS: ${{ matrix.os }} | |
| PACKAGE: "pymbar" | |
| steps: | |
| - name: Checkout the code | |
| uses: actions/checkout@v3 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Setup Conda via Mamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: devtools/conda-envs/test_env${{ matrix.jax }}.yaml | |
| environment-name: test | |
| channels: conda-forge,defaults | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install . --no-deps | |
| micromamba list | |
| - name: Run tests (pytest) | |
| shell: bash -l {0} | |
| run: | | |
| pytest -v --cov=$PACKAGE --cov-report=xml --color=yes --doctest-modules $PACKAGE/ | |
| - name: Run examples | |
| shell: bash -l {0} | |
| run: | | |
| ### constant-force-optical-trap | |
| cd examples/constant-force-optical-trap | |
| python extract-data.py | |
| python force-bias-optical-trap.py | |
| ### harmonic-oscillators | |
| cd ../harmonic-oscillators | |
| python harmonic-oscillators.py | |
| python harmonic-oscillators-distributions.py | |
| cd ../heat-capacity | |
| python heat-capacity.py -b 2 | |
| ### parallel-tempering-2dfes | |
| cd ../parallel-tempering-2dfes | |
| python parallel-tempering-2dfes.py | |
| ### umbrella-sampling-fes | |
| cd ../umbrella-sampling-fes | |
| python umbrella-sampling.py | |
| python umbrella-sampling-advanced-fes.py | |
| - name: CodeCov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| yml: ./.codecov.yml | |
| lint-format: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8] | |
| env: | |
| PACKAGE: "pymbar" | |
| steps: | |
| - name: Checkout the code | |
| uses: actions/checkout@v1 | |
| - name: Setup Conda via Mamba | |
| uses: mamba-org/provision-with-micromamba@main | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| environment-name: test | |
| channels: conda-forge,defaults | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: Install linter and formatter | |
| shell: bash -l {0} | |
| run: | | |
| micromamba install pylint black | |
| - name: Run pylint | |
| shell: bash -l {0} | |
| run: | | |
| pylint $PACKAGE/ | |
| # Black has a default --exclude which reads .gitignore. | |
| # Black's --exclude and --extend-exclude are single specified RegEx patterns and overwrite if multi-marked. | |
| - name: Run black check | |
| shell: bash -l {0} | |
| if: always() | |
| run: | | |
| black --check -l 99 $PACKAGE/ examples/ --extend-exclude "$PACKAGE/_version.py" |