get_sbml_model, enable to load file from history #35
Workflow file for this run
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| name: PullRequestWorkflow | |
| on: | |
| pull_request: | |
| types: | |
| - edited | |
| - opened | |
| - reopened | |
| - synchronize | |
| pull_request_target: | |
| types: | |
| - closed | |
| jobs: | |
| list: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| nb: ${{ steps.set-matrix.outputs.nb }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: 'Select modified files' | |
| id: files | |
| #uses: Ana06/[email protected] | |
| uses: tj-actions/changed-files@v37 | |
| with: | |
| files: workflows/** | |
| separator: "," | |
| - name: 'List repos' | |
| id: set-matrix | |
| run: | | |
| echo "list file modified" | |
| echo ${{ steps.files.outputs.all_changed_and_modified_files }} | |
| matrix=$(echo ${{ steps.files.outputs.all_changed_and_modified_files }} | jq -R -s -c 'split(",") | map(select(contains("workflows"))) | map(split("/")[1]) | sort | unique') | |
| echo "list of repo: ${matrix}" | |
| echo "matrix=$matrix" >> "${GITHUB_OUTPUT}" | |
| nb=$(echo ${matrix} | jq -s -c '.[] | length') | |
| echo "Number of repos: ${nb}" | |
| echo "nb=$nb" >> "${GITHUB_OUTPUT}" | |
| skip: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: 'List repos' | |
| id: set-matrix | |
| run: | | |
| matrix=$(jq -R -s -c '[split("\n")[] | select(.|length>0)]' .github/workflows/test_workflows_skip.txt) | |
| echo "Number of repos: ${matrix}" | |
| echo "matrix=$matrix" >> "${GITHUB_OUTPUT}" | |
| test: | |
| needs: [list, skip] | |
| if: ${{ github.event.pull_request.merged == false && needs.list.outputs.nb > 0 }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| repo: ${{ fromJson(needs.list.outputs.matrix) }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: "Setup python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: | | |
| env/requirements.txt | |
| - name: 'Install packages' | |
| run: | | |
| pip install -r env/requirements.txt | |
| - name: 'Worfklow Lint' | |
| run: | | |
| planemo workflow_lint \ | |
| --fail_level error \ | |
| "workflows/${{ matrix.repo }}" | |
| - name: 'Test tool' | |
| if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }} | |
| timeout-minutes: 60 | |
| run: | | |
| planemo test \ | |
| --engine external_galaxy \ | |
| --galaxy_url https://galaxy-synbiocad.org \ | |
| --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}" \ | |
| "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga" | |
| shed: | |
| needs: list | |
| if: ${{ github.event.pull_request.merged == true && needs.list.outputs.nb > 0 }} | |
| runs-on: ubuntu-latest | |
| continue-on-error: true | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| repo: ${{ fromJson(needs.list.outputs.matrix) }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: "Setup python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: | | |
| env/requirements.txt | |
| - name: 'Install packages' | |
| run: | | |
| pip install -r env/requirements.txt | |
| - name: 'Deploy' | |
| run: | | |
| ./scripts/upload_workflow.py \ | |
| --workflow "workflows/${{ matrix.repo }}/${{ matrix.repo }}.ga" \ | |
| --galaxy_url https://galaxy-synbiocad.org \ | |
| --galaxy_user_key "${{ secrets.GG_SYNBIOCAD_TOKEN }}" |