Add passthrough test for prot_singlesample again #3985
Workflow file for this run
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| name: viash test | |
| on: | |
| pull_request: | |
| push: | |
| branches: [ '**' ] | |
| jobs: | |
| run_ci_check_job: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| run_ci: ${{ steps.github_cli.outputs.check }} | |
| steps: | |
| - name: 'Check if branch has an existing pull request and the trigger was a push' | |
| id: github_cli | |
| run: | | |
| pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') | |
| # If the branch has a PR and this run was triggered by a push event, do not run | |
| if [[ "$pull_request" != "null" && "$GITHUB_REF_NAME" != "main" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then | |
| echo "check=false" >> $GITHUB_OUTPUT | |
| else | |
| echo "check=true" >> $GITHUB_OUTPUT | |
| fi | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GTHB_PAT }} | |
| # phase 1 | |
| list: | |
| needs: run_ci_check_job | |
| env: | |
| s3_bucket: s3://openpipelines-data/ | |
| runs-on: ubuntu-latest | |
| if: "needs.run_ci_check_job.outputs.run_ci == 'true'" | |
| outputs: | |
| matrix: ${{ steps.set_matrix.outputs.matrix }} | |
| cache_key: ${{ steps.cache.outputs.cache_key }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: viash-io/viash-actions/setup@v4 | |
| - name: Check if all config can be parsed if there is no unicode support | |
| run: | | |
| LANG=C viash ns list > /dev/null | |
| - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 | |
| id: cache | |
| with: | |
| s3_bucket: $s3_bucket | |
| dest_path: resources_test | |
| cache_key_prefix: resources_test__ | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v39 | |
| with: | |
| separator: ";" | |
| diff_relative: true | |
| - id: ns_list | |
| uses: viash-io/viash-actions/ns-list@v4 | |
| with: | |
| platform: docker | |
| format: json | |
| - id: ns_list_filtered | |
| uses: viash-io/viash-actions/project/detect-changed-components@v4 | |
| with: | |
| input_file: "${{ steps.ns_list.outputs.output_file }}" | |
| - id: set_matrix | |
| run: | | |
| echo "matrix=$(jq -c '[ .[] | | |
| { | |
| "name": (.functionality.namespace + "/" + .functionality.name), | |
| "config": .info.config, | |
| "dir": .info.config | capture("^(?<dir>.*\/)").dir | |
| } | |
| ]' ${{ steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT | |
| # 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@v4 | |
| # use cache | |
| - name: Cache resources data | |
| id: restore_cache | |
| uses: actions/cache/restore@v3 | |
| env: | |
| SEGMENT_DOWNLOAD_TIMEOUT_MINS: 5 | |
| with: | |
| path: resources_test | |
| key: ${{ needs.list.outputs.cache_key }} | |
| - name: Sync if caching failed | |
| shell: bash | |
| if: steps.restore_cache.outputs.cache-hit != 'true' | |
| run: | | |
| readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" | jq -r -c '(.info.config | capture("^(?<dir>.*\/)").dir) as $dir | .functionality.test_resources | map(select(.type == "file")) | map($dir + .path) | unique | .[]') | |
| for resource in "${resources[@]}"; do | |
| if [[ $resource == *"resources_test"* ]]; then | |
| relative_path=${resource#*resources_test/} | |
| relative_path_trailing_slash_removed=${relative_path%/} | |
| s3_path="s3://openpipelines-data/$relative_path_trailing_slash_removed" | |
| s3_lookup=$(AWS_EC2_METADATA_DISABLED=true aws s3 ls --no-sign-request "$s3_path" 2>&1) | |
| extra_args=() | |
| if [[ $s3_lookup =~ .*/$ ]]; then | |
| extra_args+=("--recursive") | |
| fi | |
| AWS_EC2_METADATA_DISABLED=true \ | |
| aws s3 cp \ | |
| "$s3_path" \ | |
| "$resource" \ | |
| --no-sign-request \ | |
| "${extra_args[@]}" | |
| fi | |
| done | |
| - name: Remove unused test resources to save space (only when restoring from cache) | |
| if: steps.restore_cache.outputs.cache-hit == 'true' | |
| shell: bash | |
| run: | | |
| readarray -t resources < <(viash config view --format json "${{ matrix.component.config }}" | 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 | |
| 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: ${{ env.NVIDIA_PASSWORD }} | |
| - name: Run test | |
| timeout-minutes: 30 | |
| run: | | |
| viash test \ | |
| "${{ matrix.component.config }}" \ | |
| --cpus 2 \ | |
| --memory "6gb" | |