Run unit tests, integration tests, and publish package if tagged #286
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| name: Run tests | |
| on: | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| branches: [main, dev] | |
| release: | |
| schedule: | |
| - cron: '0 2 * * 3,6' | |
| jobs: | |
| run-tests: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", | |
| "macos-13", | |
| # "windows-latest" # rrcovNA cannot be build from source on windows-server | |
| ] | |
| python-version: ["3.8"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Set up Miniconda | |
| # ! change action https://github.com/mamba-org/setup-micromamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| # miniforge-version: latest | |
| use-mamba: true | |
| channel-priority: disabled | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| activate-environment: vaep | |
| auto-activate-base: true | |
| # auto-update-conda: true | |
| - name: inspect-conda-environment | |
| run: | | |
| conda info | |
| conda list | |
| conda info -e | |
| - name: test-r-kernel-imports | |
| run: | | |
| Rscript -e "library(stringi)" | |
| Rscript -e "library(stringr)" | |
| Rscript -e "library(reshape2)" | |
| # # currently part of environment | |
| # - name: Install package and install library | |
| # run: | | |
| # pip install pytest pytest-cov | |
| - name: Run Unit tests on installed package | |
| run: | | |
| pytest . | |
| - name: View papermill help message for notebooks (as scripts) | |
| run: | | |
| cd project | |
| papermill 01_0_split_data.ipynb --help-notebook | |
| papermill 01_1_train_VAE.ipynb --help-notebook | |
| papermill 01_1_train_DAE.ipynb --help-notebook | |
| papermill 01_1_train_CF.ipynb --help-notebook | |
| - name: Run demo workflow (integration test) | |
| run: | | |
| cd project | |
| snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml -n | |
| snakemake -p -c1 -k --configfile config/single_dev_dataset/example/config.yaml | |
| - name: Archive results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: example-workflow-results-${{ matrix.os }} | |
| path: project/runs/example/01_2_performance_plots.html | |
| test_pip_pkg_install: | |
| runs-on: ${{ matrix.os }} | |
| name: test-pip-installation | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| python-version: ["3.8"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: install pimms | |
| run: python -m pip install . | |
| - name: Install pytest | |
| run: python -m pip install pytest pytest-cov | |
| - name: Run pytest | |
| run: pytest . | |
| publish: | |
| name: Publish package | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| needs: | |
| - run-tests | |
| - test_pip_pkg_install | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/[email protected] | |
| with: | |
| python-version: "3.8" | |
| - name: Install twine and build | |
| run: python -m pip install --upgrade twine build | |
| - name: Build | |
| run: python -m build | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |