Additional environment vars corresponding to CLI options that didn't have them #39
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| name: CI/CD | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| release: | |
| types: [published] | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| test: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] # , macos-latest, windows-latest] | |
| python-version: ["3.10", "3.11"] | |
| fail-fast: false | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Disable etelemetry | |
| run: echo "NO_ET=TRUE" >> $GITHUB_ENV | |
| - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # - name: Install other dependencies | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install -y libxml2-dev libxslt-dev git dcmtk | |
| - name: Install Minconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| activate-environment: "" | |
| - name: Install MRtrix via Conda | |
| run: | | |
| conda install -c mrtrix3 mrtrix3 | |
| mrconvert --version | |
| - name: Update build tools | |
| run: python${{ matrix.python-version }} -m pip install --upgrade pip | |
| - name: Install Xnat-Ingest | |
| run: python${{ matrix.python-version }} -m pip install .[test] | |
| - name: Save XNAT username/password in ~/.netrc | |
| run: | | |
| echo "machine localhost:8080" > $HOME/.netrc | |
| echo "user admin" >> $HOME/.netrc | |
| echo "password admin" >> $HOME/.netrc | |
| - name: Pytest | |
| run: pytest -vvs --cov xnat_ingest --cov-config .coveragerc --cov-report xml . | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| deploy: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Unset header | |
| # checkout@v2 adds a header that makes branch protection report errors | |
| # because the Github action bot is not a collaborator on the repo | |
| run: git config --local --unset http.https://github.com/.extraheader | |
| - name: Fetch tags | |
| run: git fetch --prune --unshallow | |
| - name: Set up Docker buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Get version from latest git tag and construct image tags | |
| id: versions | |
| run: | | |
| VERSION=$(git describe --tags --abbrev=0) | |
| IMAGE=${{ env.REGISTRY }}/$(echo "${{ env.IMAGE_NAME }}" | awk '{print tolower($0)}') | |
| echo "IMAGE=$IMAGE" >> $GITHUB_OUTPUT | |
| echo "TAG=$IMAGE:$VERSION" >> $GITHUB_OUTPUT | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v3 | |
| with: | |
| cache-from: type=registry,ref=${{ steps.versions.outputs.IMAGE }}:buildcache | |
| cache-to: type=registry,ref=${{ steps.versions.outputs.IMAGE }}:buildcache,mode=max | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| push: ${{ github.event_name == 'release' }} | |
| tags: | | |
| ${{ steps.versions.outputs.TAG }} | |
| ${{ steps.versions.outputs.IMAGE }}:latest |