Added notebook for beluga figure generation #30
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| name: Test Sea and publish dockerfiles | |
| on: | |
| push: | |
| pull_request: | |
| branches: [ master ] | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
| required: false | |
| default: "false" | |
| env: | |
| REGISTRY: ghcr.io | |
| jobs: | |
| run-tests: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os-name: [xenial, bionic, focal, centos7, fedora32, fedora33, fedora34] | |
| name: Test in ${{ matrix.os-name }} | |
| steps: | |
| - run: docker --version | |
| - name: Git checkout | |
| uses: actions/checkout@v2 | |
| - run: cd ${{ github.workspace }} | |
| - run: docker build . -f containers/base/Dockerfile.${{ matrix.os-name }} -t imagetest:${{ matrix.os-name }} | |
| - run: docker run --rm -v $PWD:$PWD -w $PWD imagetest:${{ matrix.os-name }} make test debug_opts="-g -ggdb --coverage -fprofile-arcs -ftest-coverage" | |
| - run: docker run --rm -v $PWD:$PWD -w $PWD imagetest:${{ matrix.os-name }} bats tests/tests.bats tests/test_flusher.bats tests/test_prefetch.bats | |
| - run: docker run --rm -v $PWD:$PWD -w $PWD imagetest:${{ matrix.os-name }} bash -c "MOUNT=$PWD/mount SOURCE=$PWD/source SOURCE_1=$PWD/source_1 levels=1 bash tests/setup.bash" | |
| - run: docker run --rm -v $PWD:$PWD -w $PWD -e SEA_HOME=$PWD -e LD_PRELOAD=$PWD/build/sea.so imagetest:${{ matrix.os-name }} tests/test_custom | |
| - uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| gcov_executable: docker run --rm -v $PWD:$PWD -w $PWD imagetest:${{ matrix.os-name }} gcov -abcfu build | |
| - name: setup tmate session | |
| if: ${{ failure() && github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled == 'true' }} | |
| uses: mxschmitt/action-tmate@v3 | |
| build-and-push-base-image: | |
| if: github.event_name != 'pull_request' | |
| needs: run-tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| os-name: [ xenial, bionic, focal, centos7, fedora32, fedora33, fedora34 ] | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker - Base images | |
| id: meta | |
| uses: docker/metadata-action@v3 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ github.repository_owner }}/sea-${{ matrix.os-name }} | |
| - name: Build and push Docker image - Base images | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| file: containers/base/Dockerfile.${{ matrix.os-name }} | |
| pull: true | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| build-and-push-application-image: | |
| if: github.event_name != 'pull_request' | |
| needs: [ run-tests, build-and-push-base-image ] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| application: [ fmriprep, AFNI, fsl, HCP, SPM ] | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Log in to the Container registry | |
| uses: docker/login-action@v1 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker - Application images | |
| id: meta | |
| uses: docker/metadata-action@v3 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ github.repository_owner }}/sea-${{ matrix.application }} | |
| - name: Build and push Docker image | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| file: containers/applications/Dockerfile.${{ matrix.application }} | |
| pull: true | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |