Merge pull request #351 from bcgsc/release/v3.1.1 #430
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| name: python-${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: install machine dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install -e .[test] # need editable to make sure the coverage reports correctly | |
| - name: install bwa | |
| run: | | |
| git clone https://github.com/lh3/bwa.git | |
| cd bwa | |
| git checkout v0.7.17 | |
| make | |
| cd .. | |
| - name: install blat | |
| run: | | |
| wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat | |
| chmod a+x blat | |
| - name: set up .pth file | |
| run: | | |
| python tests/setup_subprocess_cov.py | |
| - name: run full tests with pytest | |
| run: | | |
| export PATH=$PATH:$(pwd):$(pwd)/bwa | |
| export COVERAGE_PROCESS_START=$(pwd)/.coveragerc | |
| pytest tests -v \ | |
| --junitxml=junit/test-results-${{ matrix.python-version }}.xml \ | |
| --cov mavis \ | |
| --cov tools.convert_annotations_format \ | |
| --cov-report term-missing \ | |
| --cov-report xml \ | |
| --durations=10 \ | |
| --cov-branch | |
| env: | |
| RUN_FULL: 1 | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: junit/test-results-${{ matrix.python-version }}.xml | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: always() | |
| - name: Update code coverage report to CodeCov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| env_vars: OS,PYTHON | |
| name: codecov-umbrella | |
| fail_ci_if_error: true | |
| if: matrix.python-version == 3.8 | |
| docker: | |
| runs-on: ubuntu-latest | |
| name: docker build | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: build the docker container | |
| run: | | |
| docker build --file Dockerfile --tag bcgsc/mavis:latest . | |
| - name: test the help menu | |
| run: | | |
| docker run bcgsc/mavis -h | |
| - name: Set up Python 3.7 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Install workflow dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install mavis_config pandas | |
| - uses: eWaterCycle/setup-singularity@v6 | |
| with: | |
| singularity-version: 3.6.4 | |
| - name: docker2singularity | |
| run: | |
| docker run --mount type=bind,source=/var/run/docker.sock,target=/var/run/docker.sock --mount type=bind,source="$(pwd)",target=/output --privileged -t --rm singularityware/docker2singularity bcgsc/mavis:latest | |
| - name: Run analysis with snakemake & singularity | |
| run: | | |
| # get the SIMG filename | |
| export SNAKEMAKE_CONTAINER=$(ls *mavis*.simg) | |
| snakemake -j 2 --configfile tests/mini-tutorial.config.json --use-singularity | |
| if: always() |