Conda lock files #104
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| # TODO Change to Wave | |
| name: Generate conda-lock | |
| # 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 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: conda-lock-env | |
| create-args: >- | |
| python=3.11 | |
| conda-lock | |
| mamba | |
| - name: Get the lock file path | |
| uses: actions/github-script@v7 | |
| id: lockfile-name | |
| with: | |
| result-encoding: string | |
| script: | | |
| return '${{ matrix.files }}'.replace('/environment.yml', '/conda-lock.yml'); | |
| - name: Run conda-lock | |
| run: | | |
| rm --force "${{steps.lockfile-name.outputs.result}}" | |
| conda-lock lock $MAMBA --file "${{ matrix.files }}" --kind lock --platform linux-64 --conda-lock --lockfile "${{steps.lockfile-name.outputs.result}}" | |
| env: | |
| MAMBA: "--mamba" | |
| shell: bash -l {0} | |
| - name: Commit & push changes | |
| run: | | |
| git config user.email "[email protected]" | |
| git config user.name "nf-core-bot" | |
| git config push.default upstream | |
| git add . | |
| git status | |
| git commit -m "[automated] autogenerated conda-lock file" | |
| git push | |
| # TODO Build containers with Wave |