get_sbml_model, enable to load file from history #30
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 }}" |