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Add information about RO-Crate 1.2 validation, and F-UJI score #65
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| build: | |
| name: cwltool tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.13 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| cache: "pip" | |
| - name: Upgrade pip | |
| run: python -m pip install --upgrade pip | |
| - name: Find and install requirements files | |
| run: | | |
| set -e | |
| echo "Searching for requirements.txt files..." | |
| files=$(find . -name "requirements.txt") | |
| if [ -z "$files" ]; then | |
| echo "No requirements.txt files found." | |
| else | |
| for req in $files; do | |
| echo "Installing dependencies from $req" | |
| python -m pip install -r "$req" | |
| done | |
| fi | |
| - name: Install CWL Runners used in the thesis | |
| run: | | |
| python -m pip install \ | |
| cwltool==3.2.20260413085819 \ | |
| toil==9.4.1 \ | |
| streamflow==0.2.0rc2 | |
| - name: Run CWL workflows | |
| run: | | |
| set -e | |
| echo "== Appendix/Hello World ==" | |
| cwltool workflows/hello_world/hello_world.cwl | |
| cwltool workflows/hello_world/hello_world_containerized.cwl | |
| cwltool workflows/hello_world/hello_world_wf.cwl | |
| toil-cwl-runner workflows/hello_world/hello_world.cwl | |
| toil-cwl-runner workflows/hello_world/hello_world_containerized.cwl | |
| toil-cwl-runner workflows/hello_world/hello_world_wf.cwl | |
| echo "== Simple MPI Workflow ==" | |
| cwltool workflows/mpich-sr/mpicc.cwl | |
| cwltool workflows/mpich-sr/sr-workflow-base-command.cwl | |
| rocrate-validation: | |
| name: RO-Crate validation | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.13 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| cache: "pip" | |
| - name: Install rocrate-validator | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r ./ro-crate/requirements.txt | |
| - name: Validate RO-Crate | |
| run: | | |
| FILE="ro-crate-metadata.json" | |
| if [ ! -f "$FILE" ]; then | |
| echo "No RO-Crate file found!" | |
| exit 1 | |
| fi | |
| rocrate-validator validate --verbose --no-paging --output-format text ./ |