release build #141
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| name: release build | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| version_tag: | |
| description: Version tag | |
| required: true | |
| jobs: | |
| # Build and create containers | |
| build: | |
| uses: ./.github/workflows/main-build.yml | |
| with: | |
| push_containers: true | |
| version: ${{ inputs.version_tag }} | |
| target_tag: ${{ inputs.version_tag }} | |
| deploy_to_viash_hub: true | |
| deploy_branch: release | |
| secrets: inherit | |
| # Synchronize S3 Bucket and create cache for per-component runs | |
| sync_s3: | |
| env: | |
| s3_bucket: s3://openpipelines-data/ | |
| runs-on: ubuntu-latest | |
| outputs: | |
| cache_key: ${{ steps.cache.outputs.cache_key }} | |
| steps: | |
| - uses: viash-io/viash-actions/project/sync-and-cache-s3@v5 | |
| id: cache | |
| with: | |
| s3_bucket: $s3_bucket | |
| dest_path: resources_test | |
| cache_key_prefix: resources_test__ | |
| # phase 3 | |
| integration_test: | |
| runs-on: ubuntu-latest | |
| needs: [ build, sync_s3 ] | |
| if: "${{ needs.build.outputs.workflow_matrix != '[]' }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| component: ${{ fromJson(needs.build.outputs.workflow_matrix) }} | |
| steps: | |
| # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
| - uses: data-intuitive/reclaim-the-bytes@v2 | |
| - name: Keep symlinks as-is | |
| run: | | |
| git config --global core.symlinks true | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: 'integration_build' | |
| - uses: viash-io/viash-actions/setup@v5 | |
| - uses: nf-core/[email protected] | |
| # use cache | |
| - name: Cache resources data | |
| uses: actions/cache@v4 | |
| timeout-minutes: 5 | |
| with: | |
| path: resources_test | |
| key: ${{ needs.sync_s3.outputs.cache_key }} | |
| fail-on-cache-miss: true | |
| - name: Remove unused test resources to save space | |
| shell: bash | |
| run: | | |
| readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" -c 'del(.functionality.dependencies)' | jq -r -c '(.info.config | capture("^(?<dir>.*\/)").dir) as $dir | .functionality.test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') | |
| to_not_remove=() | |
| for resource in "${resources[@]}"; do | |
| if [[ $resource == *"resources_test"* ]]; then | |
| relative_path=${resource#*resources_test/} | |
| relative_path_trailing_slash_removed=${relative_path%/} | |
| to_not_remove+=("-path" "./resources_test/$relative_path_trailing_slash_removed" "-prune" "-o") | |
| fi | |
| done | |
| # Remove last prune and -o | |
| if (( ${#errors[@]} )); then | |
| unset 'to_not_remove[${#to_not_remove[@]}-1]' | |
| unset 'to_not_remove[${#to_not_remove[@]}-1]' | |
| to_not_remove+=( "(" "${to_not_remove[@]}" ")" "-prune" "-o") | |
| fi | |
| echo "Not removing ${to_not_remove[@]}" | |
| find ./resources_test/ "${to_not_remove[@]}" -type f -exec rm {} + | |
| tree ./resources_test/ | |
| - name: Run integration test | |
| timeout-minutes: 60 | |
| run: | | |
| # todo: replace with viash test command | |
| export NXF_VER=22.04.5 | |
| nextflow run . \ | |
| -main-script "${{ matrix.component.main_script }}" \ | |
| -entry "${{ matrix.component.entry }}" \ | |
| -profile docker,mount_temp,no_publish \ | |
| -c src/workflows/utils/labels_ci.config \ | |
| -c src/workflows/utils/integration_tests.config | |
| ###################################3 | |
| # phase 4 | |
| component_test: | |
| needs: [ build, sync_s3 ] | |
| if: ${{ needs.build.outputs.component_matrix != '[]' && needs.build.outputs.component_matrix != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| component: ${{ fromJson(needs.build.outputs.component_matrix) }} | |
| steps: | |
| # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
| - uses: data-intuitive/reclaim-the-bytes@v2 | |
| - uses: actions/checkout@v4 | |
| - uses: viash-io/viash-actions/setup@v5 | |
| # use cache | |
| - name: Cache resources data | |
| id: restore_cache | |
| uses: actions/cache/restore@v4 | |
| env: | |
| SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 | |
| with: | |
| path: resources_test | |
| key: ${{ needs.sync_s3.outputs.cache_key }} | |
| - name: Login to the nvidia container registry | |
| uses: docker/login-action@v3 | |
| env: | |
| NVIDIA_PASSWORD: ${{ secrets.NVIDIA_PASSWORD }} | |
| if: ${{ env.NVIDIA_PASSWORD != '' }} | |
| with: | |
| registry: nvcr.io | |
| username: $oauthtoken | |
| password: ${{ env.NVIDIA_PASSWORD }} | |
| - name: Login to container registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ secrets.GTHB_USER }} | |
| password: ${{ secrets.GTHB_PAT }} | |
| - name: Test component | |
| timeout-minutes: 30 | |
| run: | | |
| viash test \ | |
| "${{ matrix.component.config }}" \ | |
| --config_mod ".platforms[.type == 'docker'].image := 'ghcr.io/openpipelines-bio/${{ matrix.component.namespace }}${{matrix.component.namespace_separator}}${{ matrix.component.name }}:${{ github.event.inputs.version_tag }}'" \ | |
| --config_mod ".platforms[.type == 'docker'].setup := []" \ | |
| --cpus 4 \ | |
| --memory "12gb" |