Rework mitochondrial gene detection #3981
Workflow file for this run
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: 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" | |