twas output data update and twas pipeline workflow update #142
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| name: Build containers from conda environments | |
| on: | |
| pull_request: | |
| paths: | |
| - 'container/*/*.yml' | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| outputs: | |
| matrix: ${{ steps.export-directories.outputs.matrix }} | |
| all_changed_files_count: ${{ steps.changed-directories.outputs.all_changed_files_count }} | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get branch name | |
| id: branch-name | |
| uses: tj-actions/branch-names@v7 | |
| - name: Get SHA of last commit to main branch | |
| uses: nrwl/nx-set-shas@v3 | |
| id: last_successful_commit_pull_request | |
| with: | |
| main-branch-name: ${{ steps.branch-name.outputs.base_ref_branch }} | |
| - name: Get changed directories | |
| id: changed-directories | |
| uses: tj-actions/changed-files@v36 | |
| with: | |
| base_sha: ${{ steps.last_successful_commit_pull_request.outputs.base }} | |
| dir_names: true | |
| dir_names_exclude_current_dir: true | |
| json: true | |
| files: container/*/*.yml | |
| - name: Export changed directories | |
| if: steps.changed-directories.outputs.all_changed_files_count > 0 | |
| id: export-directories | |
| run: | | |
| echo "matrix={\"context\":${{ steps.changed-directories.outputs.all_changed_files }}}" > /tmp/changed_directories.json | |
| echo "matrix={\"context\":${{ steps.changed-directories.outputs.all_changed_files }}}" >> "$GITHUB_OUTPUT" | |
| - name: Upload changed directories | |
| if: steps.changed-directories.outputs.all_changed_files_count > 0 | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: changed_directories_${{ github.event.pull_request.head.sha }} | |
| path: /tmp/changed_directories.json | |
| docker_container: | |
| needs: setup | |
| if: needs.setup.outputs.all_changed_files_count > 0 | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.setup.outputs.matrix) }} | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup up docker buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Get basename | |
| id: context_basename | |
| run: echo "basename=$(basename ${{ matrix.context }})" >> "$GITHUB_OUTPUT" | |
| - name: Build and export docker containers | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: ${{ matrix.context }} | |
| file: .github/docker.df | |
| tags: ${{ steps.context_basename.outputs.basename }}_docker:latest | |
| outputs: type=docker,dest=/tmp/${{ steps.context_basename.outputs.basename }}_docker.tar | |
| apptainer_container: | |
| needs: setup | |
| if: needs.setup.outputs.all_changed_files_count > 0 | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJSON(needs.setup.outputs.matrix) }} | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: containers | |
| create-args: apptainer | |
| generate-run-shell: true | |
| - name: Get basename | |
| id: context_basename | |
| run: echo "basename=$(basename ${{ matrix.context }})" >> "$GITHUB_OUTPUT" | |
| - name: Build apptainer containers | |
| shell: micromamba-shell {0} | |
| run: | | |
| pushd ${{ matrix.context}}; \ | |
| apptainer build /tmp/${{ steps.context_basename.outputs.basename }}_apptainer.sif ${{ github.workspace }}/.github/apptainer.def; \ | |
| popd |