Conda lock files #93
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: Wave | |
| # When environment.yml is changed | |
| on: | |
| pull_request: | |
| paths: | |
| - "**/environment.yml" | |
| env: | |
| WAVE_VER: "1.4.1" | |
| jobs: | |
| gen-matrix: | |
| name: generate-matrix | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Calculate file differences | |
| id: diff | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| json: true | |
| quotepath: false | |
| # TODO Add Dockerfiles | |
| files: | | |
| modules/**/environment.yml | |
| - name: Debug | |
| run: echo ${{ steps.diff.outputs.all_changed_files }} | |
| - id: set-matrix | |
| run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| build: | |
| if: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}" | |
| needs: gen-matrix | |
| name: build | |
| permissions: | |
| contents: write | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: "${{ fromJson(needs.gen-matrix.outputs.matrix) }}" | |
| steps: | |
| - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - uses: weiji14/conda-lock-refresh@main | |
| with: | |
| file: "${{ matrix.files }}" | |
| # TODO platform: ["linux-64", "osx-arm64"] | |
| # Action runs on the issue comment, so we don't get the PR by default | |
| # Use the gh cli to check out the PR | |
| - name: Checkout Pull Request | |
| run: gh pr checkout ${{ github.event.issue.number }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | |
| - name: Commit condalock files to PR | |
| run: | | |
| if [[ $(git ls-files --modified --others) ]]; then | |
| git config --global user.name 'actions-bot' | |
| git config --global user.email '[email protected]' | |
| git add --all | |
| git commit --message "[condalock-command] autogenerated conda-lock files" | |
| git push | |
| fi | |
| shell: bash -l {0} | |
| - name: Get the lock file path | |
| uses: actions/github-script@v7 | |
| id: lockfile-name | |
| with: | |
| result-encoding: string | |
| script: | | |
| return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml'); | |
| - name: Install wave-cli | |
| run: | | |
| wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64 | |
| sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave | |
| chmod +x /usr/local/bin/wave | |
| - name: Build container | |
| if: matrix.profile == 'docker' | |
| run: | | |
| wave --conda-package "${{steps.lockfile-name.outputs.result}}" \ | |
| --freeze \ | |
| --await \ | |
| --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \ | |
| --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} | |
| - name: Build Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| wave --conda-package "${{steps.lockfile-name.outputs.result}}" \ | |
| --freeze \ | |
| --await \ | |
| --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \ | |
| --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \ | |
| --singularity | |
| # TODO Build from Dockerfiles |