Merge pull request #130 from mskcc-omics-workflows/release/0.1.1 #261
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| name: Meta Yaml to MD | |
| # Controls when the workflow will run | |
| on: | |
| push: | |
| branches: [main] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [main] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| pytest-changes: | |
| name: pytest-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytest_modules.yml" | |
| token: "" | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - name: Combine all tags.yml files | |
| id: get_tags | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| token: "" | |
| new_feature: | |
| name: new feature | |
| runs-on: ubuntu-latest | |
| if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} | |
| needs: [pytest-changes, nf-test-changes] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: | |
| [ | |
| "${{ fromJson(needs.pytest-changes.outputs.modules) }}", | |
| "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | |
| ] | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event." | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - name: setup python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" # install the python version needed | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: docs | |
| - name: Update name of ${{ matrix.tags }} | |
| run: | | |
| MATRIX_FRAGMENT="${{ matrix.tags }}" | |
| TEMP_NAME=$(echo $MATRIX_FRAGMENT | sed 's/subworkflows\///g') | |
| SW_NAME=$(echo $TEMP_NAME | sed 's/modules\///g') | |
| echo "SW_NAME=$SW_NAME" >> $GITHUB_ENV | |
| - name: Rename md file | |
| id: replace_slash | |
| run: | | |
| FRAGMENT="${{ env.SW_NAME }}" | |
| MD_NAME=$(echo $FRAGMENT | sed 's/\//_/g') | |
| echo "MD_NAME=$MD_NAME" >> $GITHUB_ENV | |
| echo "${MD_NAME}" | |
| - name: Download convertor from yml to md | |
| run: | | |
| curl -o ${{ github.workspace }}/yaml_to_md.py https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/yaml_to_md.py | |
| curl -o ${{ github.workspace }}/requirements.txt https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/requirements.txt | |
| - name: Give convertor permissions | |
| run: chmod +x yaml_to_md.py | |
| - name: Install python packages | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r ${{ github.workspace }}/requirements.txt | |
| - uses: jaywcjlove/github-action-read-file@main | |
| id: cat_file_module | |
| with: | |
| branch: ${{ github.ref }} | |
| path: modules/msk/${{ env.SW_NAME }}/meta.yml | |
| - name: Write Module yaml to temp | |
| if: ${{ steps.cat_file_module.outputs.size }} | |
| id: write_yml_module | |
| run: | | |
| echo "${{ steps.cat_file_module.outputs.size }}" | |
| echo '${{ steps.cat_file_module.outputs.content }}' > ${{ github.workspace }}/temp.yml | |
| FEATURE_TYPE="modules" | |
| SUMMARY_TYPE="module" | |
| SUBWORKFLOW="" | |
| echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV | |
| echo "SUMMARY_TYPE=$SUMMARY_TYPE" >> $GITHUB_ENV | |
| echo "SUBWORKFLOW=$SUBWORKFLOW" >> $GITHUB_ENV | |
| - uses: jaywcjlove/github-action-read-file@main | |
| if: ${{ steps.cat_file_module.outputs.size == '' }} | |
| id: cat_file_subworkflow | |
| with: | |
| branch: ${{ github.ref }} | |
| path: subworkflows/msk/${{ env.SW_NAME }}/meta.yml | |
| - name: Write Subworkflow yaml to temp | |
| if: ${{ steps.cat_file_subworkflow.outputs.size }} | |
| id: write_yml_subworkflow | |
| run: | | |
| echo "${{ steps.cat_file_subworkflow.outputs.size }}" | |
| echo '${{ steps.cat_file_subworkflow.outputs.content }}' > ${{ github.workspace }}/temp.yml | |
| FEATURE_TYPE="subworkflows" | |
| SUMMARY_TYPE="subworkflow" | |
| SUBWORKFLOW="--subworkflows" | |
| echo "FEATURE_TYPE=$FEATURE_TYPE" >> $GITHUB_ENV | |
| echo "SUMMARY_TYPE=$SUMMARY_TYPE" >> $GITHUB_ENV | |
| echo "SUBWORKFLOW=$SUBWORKFLOW" >> $GITHUB_ENV | |
| - name: Run convertor to generate md file for new module | |
| run: | | |
| echo ${{ matrix.tags }} | |
| python ${{ github.workspace }}/yaml_to_md.py all --yaml-file ${{ github.workspace }}/temp.yml --output-file ./modules/${{ env.MD_NAME }}.md --schema-url https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/0.0.1/nextflow_schema/${{ env.FEATURE_TYPE }}/meta-schema.json ${{ env.SUBWORKFLOW }} | |
| - name: Check file existence for modules | |
| id: check_files | |
| uses: andstor/file-existence-action@v1 | |
| with: | |
| branch: docs | |
| files: ${{ env.FEATURE_TYPE}}/${{ env.MD_NAME }}.md | |
| - name: Add to SUMMARY for new features | |
| if: ${{ (steps.check_files.outputs.files_exists == 'false') }} | |
| run: | | |
| curl -o ${{ github.workspace }}/update_summary.py https://raw.githubusercontent.com/mskcc-omics-workflows/modules/develop/.github/workflows/update_summary.py | |
| python ${{ github.workspace }}/update_summary.py SUMMARY.md "* [${{ env.MD_NAME }}](${{ env.FEATURE_TYPE }}/${{ env.MD_NAME }}.md)" ${{ env.SUMMARY_TYPE }} > tmp_summary.md | |
| mv tmp_summary.md SUMMARY.md | |
| - uses: EndBug/add-and-commit@v9 | |
| with: | |
| default_author: github_actions | |
| message: "add doc for ${{ matrix.tags }}" | |
| add: '["*/*.md --force", "SUMMARY.md --force"]' | |
| cwd: "./" |