Remove workaround for utility functions on NXF Fusion #7567
Workflow file for this run
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| name: viash test | |
| on: | |
| pull_request: | |
| push: | |
| branches: [ main ] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: ${{ !contains(github.ref, 'main')}} | |
| jobs: | |
| # phase 1 | |
| list: | |
| env: | |
| s3_bucket: s3://openpipelines-data/ | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.detect_changed_components.outputs.output_matrix }} | |
| cache_key: ${{ steps.cache.outputs.cache_key }} | |
| dest_paths: ${{ steps.cache.outputs.dest_paths }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' | |
| - uses: data-intuitive/reclaim-the-bytes@v2 | |
| - uses: viash-io/viash-actions/setup@v6 | |
| - name: Check if all config can be parsed if there is no unicode support | |
| run: | | |
| LANG=C viash ns list > /dev/null | |
| JAVA_TOOL_OPTIONS=-Dfile.encoding=ascii viash ns build --parallel > /dev/null | |
| - uses: viash-io/viash-actions/project/sync-and-cache@v6 | |
| id: cache | |
| - id: ns_list | |
| uses: viash-io/viash-actions/ns-list@v6 | |
| with: | |
| engine: docker | |
| runner: executable | |
| format: json | |
| query_namespace: ^(?!workflows|test_workflows) | |
| - id: detect_changed_components | |
| uses: viash-io/viash-actions/project/detect-changed-components@v6 | |
| with: | |
| input_file: "${{ steps.ns_list.outputs.output_file }}" | |
| # phase 2 | |
| viash_test: | |
| needs: list | |
| if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| component: ${{ fromJson(needs.list.outputs.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 | |
| - uses: viash-io/viash-actions/project/update-docker-engine@v6 | |
| # use cache | |
| - name: Restore test resources cache | |
| if: ${{ needs.list.outputs.cache_key != '' }} | |
| uses: actions/cache/restore@v4 | |
| timeout-minutes: 10 | |
| with: | |
| path: ${{ needs.list.outputs.dest_paths }} | |
| key: ${{ needs.list.outputs.cache_key }} | |
| fail-on-cache-miss: true | |
| - name: Remove unused test resources to save space (only when restoring from cache) | |
| shell: bash | |
| run: | | |
| readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" | 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 | |
| find ./resources_test/ "${to_not_remove[@]}" -type f -exec rm {} + | |
| - 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: ${{ env.NVIDIA_PASSWORD }} | |
| - name: Run test | |
| timeout-minutes: 40 | |
| run: | | |
| viash test \ | |
| "${{ matrix.component.config }}" \ | |
| --cpus 4 \ | |
| --memory "14gb" \ | |
| --engine docker \ | |
| --runner executable |