Add Repeatmasking workflow #799
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
| # workflow level env vars cannot be used at the job level | |
| # https://github.community/t/how-to-set-and-access-a-workflow-variable/17335/15 | |
| name: Galaxy Workflow Tests for push and PR | |
| on: [push, pull_request] | |
| env: | |
| GITHUB_USER: iwc-workflows-bot | |
| jobs: | |
| setup: | |
| name: Setup cache and determine changed repositories | |
| uses: ./.github/workflows/setup.yml | |
| with: | |
| python-version-list: "[\"3.7\"]" | |
| galaxy-fork: galaxyproject | |
| galaxy-branch: release_22.05 | |
| max-chunks: 4 | |
| # Planemo lint the changed repositories | |
| lint: | |
| name: Lint workflows | |
| needs: setup | |
| if: needs.setup.outputs.repository-list != '' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install wheel | |
| run: pip install wheel | |
| - name: Planemo lint workflows | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: lint | |
| workflows: true | |
| repository-list: "${{ needs.setup.outputs.repository-list }}" | |
| test: | |
| name: Test workflows | |
| needs: setup | |
| if: needs.setup.outputs.repository-list != '' | |
| uses: ./.github/workflows/test_workflows.yml | |
| with: | |
| galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }} | |
| chunk-count: ${{ fromJSON(needs.setup.outputs.chunk-count) }} | |
| chunk-list: ${{ needs.setup.outputs.chunk-list }} | |
| python-version-list: "[\"3.7\"]" | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| galaxy-fork: galaxyproject | |
| galaxy-branch: master | |
| check-outputs: false | |
| combine_outputs: | |
| # same as tool step | |
| name: Combine chunked test results | |
| needs: [setup, test] | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| path: artifacts | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_{{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Combine outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: combine | |
| with: | |
| mode: combine | |
| html-report: true | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: 'All tool test results' | |
| path: upload | |
| - name: Check outputs | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| id: check | |
| with: | |
| mode: check | |
| # deploy workflows to organization | |
| deploy: | |
| name: Deploy | |
| needs: [setup,test,combine_outputs] | |
| strategy: | |
| matrix: | |
| python-version: ['3.7'] | |
| runs-on: ubuntu-latest | |
| if: github.ref == 'refs/heads/main' && github.repository_owner == 'galaxyproject' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache .cache/pip | |
| uses: actions/cache@v3 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: pip_cache_py_${{ matrix.python-version }}_gxy_{{ needs.setup.outputs.galaxy-head-sha }} | |
| - name: Install requirements for gen_crates.py | |
| run: pip install -r workflows/requirements.txt | |
| - name: Generate RO-Crate metadata for workflow repositories | |
| run: python workflows/gen_crates.py workflows | |
| - name: Set git user | |
| run: | | |
| git config --global user.email "$GITHUB_USER@galaxyproject.org" | |
| git config --global user.name "$GITHUB_USER" | |
| git config --global init.defaultBranch main | |
| - uses: fusion-engineering/setup-git-credentials@v2 | |
| with: | |
| credentials: 'https://${{ env.GITHUB_USER }}:${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }}@github.com/' | |
| - name: Update or create repositories in github namespace | |
| uses: galaxyproject/planemo-ci-action@v1 | |
| with: | |
| mode: deploy | |
| repository-list: ${{ needs.setup.outputs.repository-list }} | |
| workflows: true | |
| workflow-namespace: iwc-workflows | |
| github-token: ${{ secrets.IWC_WORKFLOWS_BOT_TOKEN }} |