Add Docker improvements #530
Workflow file for this run
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
| name: tests | |
| on: | |
| push: | |
| pull_request: | |
| types: [opened, reopened] | |
| env: | |
| # Increase this value to reset cache if environment.yml has not changed. | |
| PY_CACHE_NUMBER: 2 | |
| PY_ENV: ccc_gene_expr | |
| jobs: | |
| ccc_pytest: | |
| name: Python tests for CCC | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 4 | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10"] | |
| os: [ubuntu-latest, macOS-latest, windows-latest] | |
| steps: | |
| - name: Checkout git repo | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest numpy scipy numba pandas==1.4.* scikit-learn==1.1.* | |
| - name: Test CCC with pytest | |
| env: | |
| PYTHONPATH: libs/ | |
| run: | | |
| pytest tests/test_coef.py tests/test_pytorch_core.py tests/test_scipy_stats.py tests/test_sklearn_metrics.py | |
| pytest: | |
| name: Python tests for analyses | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 4 | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9"] | |
| os: [ubuntu-latest, macOS-latest, windows-latest] | |
| steps: | |
| - name: Checkout git repo | |
| uses: actions/checkout@v3 | |
| - name: Cache conda | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: "${{ env.PY_ENV }}.tar.gz" | |
| key: ${{ runner.os }}-${{ env.PY_CACHE_NUMBER }}-${{ hashFiles('environment/environment.yml', 'environment/scripts/install_r_packages.r', 'environment/scripts/install_other_packages.sh') }} | |
| - name: Setup Miniconda | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| activate-environment: ${{ env.PY_ENV }} | |
| channel-priority: strict | |
| environment-file: environment/environment.yml | |
| auto-activate-base: false | |
| - name: Install other packages and Conda-Pack environment | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| # other packages (R packages mainly) | |
| bash environment/scripts/install_other_packages.sh | |
| # install conda-pack, and pack environment | |
| conda install --yes -c conda-forge conda-pack coverage | |
| conda pack -f -n ${{ env.PY_ENV }} -o "${{ env.PY_ENV }}.tar.gz" | |
| - name: Unpack environment | |
| shell: bash -l {0} | |
| run: | | |
| mkdir -p "${{ env.PY_ENV }}" | |
| tar -xzf "${{ env.PY_ENV }}.tar.gz" -C "${{ env.PY_ENV }}" | |
| - name: Setup data and run pytest (Windows systems) | |
| if: runner.os == 'Windows' | |
| env: | |
| PYTHONPATH: libs/ | |
| shell: cmd | |
| run: | | |
| echo on | |
| cd ${{ env.PY_ENV }} | |
| call .\Scripts\activate.bat | |
| .\Scripts\conda-unpack.exe | |
| cd .. | |
| set R_HOME=%CONDA_PREFIX%\Lib\R | |
| python environment\scripts\setup_data.py --mode testing | |
| pytest -v -rs tests | |
| - name: Setup data and run pytest (non-Windows systems) | |
| if: runner.os != 'Windows' | |
| shell: bash | |
| env: | |
| PYTHONPATH: libs/ | |
| run: | | |
| source ${{ env.PY_ENV }}/bin/activate | |
| conda-unpack | |
| python environment/scripts/setup_data.py --mode testing | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| # for linux/ubuntu, run the tests once: with numba jit activated | |
| # (which is the expected implementation) and with the jit | |
| # deactivated (otherwise coverage does not work). | |
| # numba jit activated | |
| pytest -v -rs tests | |
| # numba jit deactivated + code coverage | |
| export NUMBA_DISABLE_JIT=1 | |
| coverage run --source=libs/ -m pytest -v -rs tests | |
| coverage xml -o coverage.xml | |
| else | |
| pytest -v -rs tests | |
| fi | |
| - name: Codecov upload | |
| if: runner.os == 'Linux' | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| files: ./coverage.xml | |
| name: codecov-${{ matrix.os }}-python${{ matrix.python-version }} | |
| fail_ci_if_error: true | |
| verbose: true |