release build #164
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: 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_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 }} | |
| dest_paths: ${{ steps.cache.outputs.dest_paths }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: viash-io/viash-actions/project/sync-and-cache@v6 | |
| id: cache | |
| # phase 3 | |
| integration_test: | |
| runs-on: ubuntu-latest | |
| needs: [ build, sync_s3 ] | |
| if: "${{ 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: 'release' | |
| - uses: viash-io/viash-actions/setup@v6 | |
| - uses: nf-core/[email protected] | |
| # use cache | |
| - name: Cache resources data | |
| if: ${{ needs.sync_s3.outputs.cache_key != '' }} | |
| uses: actions/cache/restore@v4 | |
| timeout-minutes: 10 | |
| with: | |
| path: ${{ needs.sync_s3.outputs.dest_paths }} | |
| 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(.dependencies)' | jq -r -c '(.build_info.config | capture("^(?<dir>.*\/)").dir) as $dir | .test_resources | map(select(.type == "file")) | map($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: Build test dependencies | |
| run: | | |
| readarray -t test_dependencies < <(viash ns list --format json "${{ matrix.component.config }}" | jq -r -c '(.[].info.test_dependencies // []) | flatten | .[] | (.namespace + "/" + .name)') | |
| for dependency in "${test_dependencies[@]}"; do | |
| echo $dependency | |
| viash ns build -q "$dependency" -c ".version := 'integration_build'" -c ".engines[.type == 'docker'].target_tag := 'integration_build'" --setup alwayspullelsebuild | |
| done | |
| - name: Remove docker builder cache | |
| run: | | |
| docker builder prune -a -f | |
| - name: Run integration test | |
| timeout-minutes: 120 | |
| 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@v6 | |
| # use cache | |
| - name: Cache resources data | |
| if: ${{ needs.sync_s3.outputs.cache_key != '' }} | |
| uses: actions/cache/restore@v4 | |
| timeout-minutes: 10 | |
| with: | |
| path: ${{ needs.sync_s3.outputs.dest_paths }} | |
| 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(.dependencies)' | jq -r -c '(.build_info.config | capture("^(?<dir>.*\/)").dir) as $dir | .test_resources | map(select(.type == "file")) | map($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: 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: ${{ secrets.GTHB_PAT }} | |
| - name: Test component | |
| timeout-minutes: 40 | |
| run: | | |
| viash test \ | |
| "${{ matrix.component.config }}" \ | |
| --config_mod ".engines[.type == 'docker'].image := 'ghcr.io/openpipelines-bio/openpipeline/${{ matrix.component.namespace }}${{matrix.component.namespace_separator}}${{ matrix.component.name }}:${{ github.event.inputs.version_tag }}'" \ | |
| --config_mod ".engines[.type == 'docker'].setup := []" \ | |
| --cpus 4 \ | |
| --memory "14gb" \ | |
| --engine docker \ | |
| --runner executable |