Merge branch 'main' of github.com:viash-hub/biobox into seqtk_sample

.github/workflows/test.yaml

@@ -3,114 +3,7 @@ name: Component Testing
 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:
-           GH_TOKEN: ${{ github.token }}
-
-  # phase 1
-  list:
-    needs: run_ci_check_job
-    runs-on: ubuntu-latest
-    if: ${{ needs.run_ci_check_job.outputs.run_ci == 'true' }}
-
-    outputs:
-      matrix: ${{ steps.set_matrix.outputs.matrix }}
-
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-
-    - name: Get head git commit message
-      id: get_head_commit_message
-      run: echo "HEAD_COMMIT_MESSAGE=$(git show -s --format=%s ${{ github.event.pull_request.head.sha || github.sha }})" >> "$GITHUB_OUTPUT"
-
-    - uses: viash-io/viash-actions/setup@v5
-
-    - name: Check if all config can be parsed if there is no unicode support
-      run: |
-        LANG=C viash ns list > /dev/null
-
-    # see https://github.com/viash-io/viash/issues/654
-    # and https://github.com/viash-io/viash-actions/pull/27
-    # - name: Get changed files
-    #   id: changed-files
-    #   uses: tj-actions/changed-files@v42
-    #   with:
-    #     separator: ";"
-    #     diff_relative: true
-    # - id: ns_list
-    #   uses: viash-io/viash-actions/ns-list@v5
-    #   with:
-    #     platform: docker
-    #     format: json
-    #     query: ^(?!workflows)
-    # - id: ns_list_filtered
-    #   uses: viash-io/viash-actions/project/detect-changed-components@v5
-    #   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
-    #       }
-    #     ]' ${{ contains(steps.get_head_commit_message.outputs.HEAD_COMMIT_MESSAGE, 'ci force') && steps.ns_list.outputs.output_file || steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT
-
-
-    - id: set_matrix
-      run: |
-        viash ns list --format json > ns_list.json
-        echo "matrix=$(jq -c '[ .[] | 
-          { 
-            "name": (.namespace + "/" + .name),
-            "config": .build_info.config,
-            "dir": .build_info.config | capture("^(?<dir>.*\/)").dir
-          }
-        ]' ns_list.json )" >> $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: ${{ fromJson(needs.list.outputs.matrix) }}
-
-    steps:
-    # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.'
-    - uses: data-intuitive/reclaim-the-bytes@v2
-
-    - uses: actions/checkout@v4
-
-    - uses: viash-io/viash-actions/setup@v5
-
-    - name: Run test
-      timeout-minutes: 30
-      run: |
-        viash test \
-          "${{ matrix.component.config }}" \
-          --cpus 2 \
-          --memory "6gb"
+  test:
+    uses: viash-hub/toolbox/.github/workflows/test.yaml@main

.gitignore

@@ -3,6 +3,7 @@
 
 # IDE ignores
 .idea/
+.vscode/
 
 # R specific ignores
 .Rhistory