get_sbml_model, enable to load file from history #110
Workflow file for this run
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| name: PullRequest | |
| 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: tools/** | |
| 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("tools"))) | 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_tools_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: ${{ fromJson(needs.list.outputs.matrix) }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: "Setup python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: | | |
| env/requirements.txt | |
| - name: 'Install packages' | |
| run: | | |
| pip install -r env/requirements.txt | |
| - name: 'Wrapper Lint' | |
| run: | | |
| planemo lint "tools/${{ matrix.repo }}" | |
| # no DOI checked due to restricted access | |
| - name: 'Shed lint' | |
| run: | | |
| planemo shed_lint --urls --xsd --ensure_metadata "tools/${{ matrix.repo }}" | |
| ./scripts/shed_lint.py -i "tools/${{ matrix.repo }}" | |
| - name: 'Test tool' | |
| if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }} | |
| timeout-minutes: 120 | |
| continue-on-error: true | |
| run: | | |
| planemo test \ | |
| --biocontainers \ | |
| --no_dependency_resolution \ | |
| --no_conda_auto_init \ | |
| --galaxy_source https://github.com/galaxyproject/galaxy \ | |
| --galaxy_branch release_22.05 \ | |
| --galaxy_python_version 3.7 \ | |
| "tools/${{ matrix.repo }}" | |
| - name: 'Prepare artefact' | |
| run: | | |
| touch tool_test_output.html tool_test_output.json | |
| zip -9 ${{ matrix.repo }}.zip tool_test_output.html tool_test_output.json | |
| - name: 'Upload Artifact Version' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.repo }}-artifact | |
| path: ${{ matrix.repo }}.zip | |
| - name: 'Aggregate results' | |
| if: ${{ ! contains(fromJson(needs.skip.outputs.matrix), matrix.repo) }} | |
| run: | | |
| ./scripts/aggregate_test.py -i . | |
| 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: ${{ fromJson(needs.list.outputs.matrix) }} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - name: "Setup python" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| cache: 'pip' # caching pip dependencies | |
| cache-dependency-path: | | |
| env/requirements.txt | |
| - name: 'Install packages' | |
| run: | | |
| pip install -r env/requirements.txt | |
| - name: 'Test ToolShed' | |
| run: | | |
| planemo shed_update --force_repository_creation --shed_target testtoolshed --shed_key "${{ secrets.TESTTOOLSHED }}" "tools/${{ matrix.repo }}" || planemo shed_update --force_repository_creation --shed_target testtoolshed --shed_key "${{ secrets.TESTTOOLSHED }}" "tools/${{ matrix.repo }}" | |
| - name: 'Main ToolShed' | |
| run: | | |
| planemo shed_update --force_repository_creation --shed_target toolshed --shed_key "${{ secrets.TOOLSHED }}" "tools/${{ matrix.repo }}" || planemo shed_update --force_repository_creation --shed_target toolshed --shed_key "${{ secrets.TOOLSHED }}" "tools/${{ matrix.repo }}" | |
| - name: 'Create release' | |
| uses: ./.github/workflows/release.yml |