small changes to process data #239
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| # name: Test | |
| # on: | |
| # push: | |
| # branches: [ main ] | |
| # pull_request: | |
| # jobs: | |
| # build: | |
| # uses: openproblems-bio/actions/.github/workflows/test.yml@main | |
| name: test | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| # phase 1 | |
| list: | |
| env: | |
| s3_bucket: s3://openproblems-data/resources_test/grn/ | |
| runs-on: ubuntu-latest | |
| 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@v6 | |
| - uses: viash-io/viash-actions/project/sync-and-cache-s3@v6 | |
| id: cache | |
| with: | |
| s3_bucket: $s3_bucket | |
| dest_path: resources_test | |
| cache_key_prefix: resources__ | |
| - id: ns_list | |
| uses: viash-io/viash-actions/ns-list@v6 | |
| with: | |
| platform: docker | |
| format: json | |
| - id: ns_list_filtered | |
| uses: viash-io/viash-actions/project/detect-changed-components@v6 | |
| with: | |
| input_file: "${{ steps.ns_list.outputs.output_file }}" | |
| - id: set_matrix | |
| run: | | |
| echo "matrix=$(jq -c '[ .[] | | |
| { | |
| "name": (.functionality.namespace + "/" + .functionality.name), | |
| "config": .info.config | |
| } | |
| ]' ${{ 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@v6 | |
| # use cache | |
| - name: Cache resources data | |
| uses: actions/cache@v4 | |
| timeout-minutes: 10 | |
| with: | |
| path: resources_test | |
| key: ${{ needs.list.outputs.cache_key }} | |
| - name: Run test | |
| timeout-minutes: 30 | |
| run: | | |
| VIASH_TEMP=$RUNNER_TEMP/viash viash test \ | |
| "${{ matrix.component.config }}" \ | |
| --cpus 2 \ | |
| --memory "5gb" | |