[ENH] Package #52
Workflow file for this run
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| --- | |
| name: docker build | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| USER_NAME: bids | |
| REPO_NAME: cat12 | |
| IMAGE: /home/runner/work/Remi-Gau/cat12-container/docker | |
| jobs: | |
| docker-build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # # cache tarred docker image to speed up build on follow up runs | |
| # - uses: actions/cache@v4 | |
| # id: cache | |
| # with: | |
| # path: ${{ env.IMAGE }}/image.tar | |
| # key: data | |
| # - if: ${{ steps.cache.outputs.cache-hit != 'true' }} | |
| # name: Load image | |
| # run: docker load -i ${{ env.IMAGE }}/image.tar | |
| - name: Build the Docker image | |
| run: | | |
| docker build . --tag ${{env.USER_NAME}}/${{env.REPO_NAME}} | |
| - name: Check image size and version | |
| run: | | |
| docker images | |
| docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --version | |
| - name: Run simple commands | |
| run: | | |
| docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --help | |
| docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant view segment --verbose 3 | |
| docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant copy segment --verbose 3 | |
| docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant segment --help | |
| - name: Save docker image | |
| run: | | |
| mkdir -p ${{ env.IMAGE }} | |
| docker save "${{env.USER_NAME}}/${{env.REPO_NAME}}" > "${{ env.IMAGE }}/image.tar" | |
| - name: Upload docker artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: docker | |
| path: ${{ env.IMAGE }} | |
| one-session: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| type: [default, simple, enigma] | |
| fail-fast: false | |
| needs: docker-build | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get -y -qq update | |
| sudo apt-get -y install tree | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Restore docker image | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: docker | |
| path: ${{ env.IMAGE }} | |
| - name: Load image | |
| run: docker load -i ${{ env.IMAGE }}/image.tar | |
| - name: Get data | |
| run: make tests/data/MoAEpilot | |
| - name: Segment | |
| run: | | |
| docker run --rm \ | |
| -v ${PWD}/tests/data/MoAEpilot:/data \ | |
| ${{env.USER_NAME}}/${{env.REPO_NAME}} \ | |
| /data /data/derivatives participant \ | |
| segment --verbose 3 --type ${{ matrix.type }} | |
| tree ${PWD}/tests/data/ | |
| - name: Upload output artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: output_${{ matrix.type }} | |
| path: /home/runner/work/cat12-container/cat12-container/tests/data/MoAEpilot/derivatives | |
| two-sessions: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| type: [long_0, long_2] | |
| fail-fast: false | |
| needs: docker-build | |
| steps: | |
| - name: Install python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get -y -qq update | |
| sudo apt-get -y install git-annex tree | |
| pip install datalad | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Restore docker image | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: docker | |
| path: ${{ env.IMAGE }} | |
| - name: Load image | |
| run: docker load -i ${{ env.IMAGE }}/image.tar | |
| - name: Get data | |
| run: make data_ds002799 | |
| - name: Segment | |
| run: | | |
| docker run --rm \ | |
| -v ${PWD}/tests/data/ds002799:/data \ | |
| ${{env.USER_NAME}}/${{env.REPO_NAME}} \ | |
| /data /data/derivatives participant \ | |
| segment --verbose 3 --type ${{ matrix.type }} \ | |
| --participant_label 292 294 \ | |
| --skip_validation | |
| tree ${PWD}/tests/data/ | |
| - name: Upload output artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: output_${{ matrix.type }} | |
| path: /home/runner/work/cat12-container/cat12-container/tests/data/ds002799/derivatives |