adding a PR template #170
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: "CI" | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| on: | |
| push: | |
| branches: [ "*" ] | |
| pull_request: | |
| types: [opened, ready_for_review] | |
| concurrency: | |
| group: ${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build-and-ci: | |
| name: miniconda build | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.6, 3.7, 3.8] | |
| env: | |
| SETUPTOOLS_USE_DISTUTILS: stdlib | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: test-environment | |
| python-version: ${{ matrix.python-version }} | |
| channels: bioconda,default,anaconda,r,conda-forge | |
| allow-softlinks: true | |
| channel-priority: 'flexible' | |
| show-channel-urls: true | |
| use-only-tar-bz2: true | |
| auto-update-conda: true | |
| - name: setup conda | |
| run: | | |
| conda config --set always_yes yes --set changeps1 no | |
| conda info -a | |
| conda list | |
| conda config --show-sources | |
| conda config --show | |
| - name: Install dependencies | |
| run: | | |
| conda install mamba | |
| mamba install pandas tzlocal rpy2 biopython ReportLab pytest-cov codecov bioconductor-deseq2 gfortran_linux-64 bioconductor-apeglm | |
| - name: hack for missing sysconfigdata (py3.7 and py3.8, doing nothing really) | |
| if: matrix.python-version != '3.6' | |
| run: | | |
| ls $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda*.py | |
| - name: hack for missing sysconfigdata (py3.6) | |
| if: matrix.python-version == '3.6' | |
| run: | | |
| ls $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64*.py | |
| cp $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda_cos6_linux_gnu.py $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda_linux_gnu.py | |
| - name: install package | |
| run: | | |
| conda activate test-environment | |
| pip install . | |
| - name: install R packages | |
| run: | | |
| Rscript setup.R | |
| - name: Test with pytest | |
| run: | | |
| coverage run -m pytest -vvv | |
| - name: codecov | |
| run: | | |
| bash <(curl -s https://codecov.io/bash) | |
| build-and-push-image: | |
| runs-on: ubuntu-latest | |
| needs: build-and-ci | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Build and push Docker image | |
| if: github.ref_name == 'master' | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| push: true | |
| target: diffexpr | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| tags: | | |
| ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr:${{ github.ref_name }} | |
| ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr:${{ github.sha }} | |
| - name: Build and push Dev Docker image | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| push: true | |
| target: diffexpr_dev | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| tags: | | |
| ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr-dev:${{ github.ref_name }} | |
| ${{ env.REGISTRY }}/${{ github.repository }}/diffexpr-dev:${{ github.sha }} |