deploy: 559e5f7

Author: DriesSchaumont

.github/workflows/create-documentation-pr.yml

@@ -17,11 +17,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           path: openpipelines
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           repository: openpipelines-bio/website
           path: website
@@ -35,32 +35,31 @@ jobs:
           INPUT_TAG="${{ github.event.inputs.version_tag }}"
           TAG_OR_BRANCH_NAME=${INPUT_TAG:-"${{ github.ref_name }}"}
           echo "tag=$TAG_OR_BRANCH_NAME" >> $GITHUB_OUTPUT
-      
-      - name: Remove previous results
-        run: |
-          rm -rf website/components
 
       - uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
         with:
           project_directory: openpipelines
+          src: src
           query: '^(?!workflows|test_workflows)'
           output_dir: ../website/components/modules/
           dest_path: "{namespace}/{name}.qmd"
           viash_pro_token: ${{ secrets.GTHB_PAT }}
           tools_version: main_build
           ref: "${{ steps.get_tag.outputs.tag }}"
-          clean: false
+          clean: true
+
 
       - uses: viash-io/viash-actions/pro/generate-documentation-qmd@v6
         with:
           project_directory: openpipelines
+          src: src
           query: '^workflows'
           output_dir: ../website/components/
           dest_path: "{namespace}/{name}.qmd"
           viash_pro_token: ${{ secrets.GTHB_PAT }}
           tools_version: main_build
           ref: "${{ steps.get_tag.outputs.tag }}"
-          clean: false
+          clean: true
 
       - name: Create Pull Request
         env:

.github/workflows/integration-test.yml

@@ -36,7 +36,7 @@ jobs:
       dest_paths: ${{ steps.cache.outputs.dest_paths }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
 
@@ -55,7 +55,7 @@ jobs:
         component: ${{ fromJson(needs.build.outputs.workflow_matrix) }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
 
@@ -66,7 +66,7 @@ jobs:
       run: |
         git config --global core.symlinks true
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: 'integration_build'
 
@@ -124,7 +124,7 @@ jobs:
         # check if stub runs work
         export NXF_VER=22.04.5
         nextflow run . \
-          -main-script "target/nextflow/${{matrix.component.namespace}}/${{matrix.component.name}}/main.nf" \
+          -main-script "target/${{ matrix.component.scope == 'private' && '_private/' || '' }}nextflow/${{matrix.component.namespace}}/${{matrix.component.name}}/main.nf" \
           -stub -profile no_publish \
           -c src/workflows/utils/integration_tests.config 
 

.github/workflows/main-build.yml

@@ -121,7 +121,7 @@ jobs:
           echo "checkout_branch=$DEPLOY_BRANCH" >> "$GITHUB_OUTPUT"
         fi
   
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ steps.get_checkout_branch.outputs.checkout_branch }}
         fetch-depth: 0
@@ -151,7 +151,11 @@ jobs:
         config_mod: .version := "${{ inputs.version || format('{0}_build', github.ref_name) }}"
         parallel: true
         query: ^workflows
-  
+
+    - name: "Remove test component and workflows from the target folder"
+      run: |
+        rm -r target/_test
+
     - name: Build nextflow schemas
       uses: viash-io/viash-actions/pro/build-nextflow-schemas@v6
       with:
@@ -168,7 +172,7 @@ jobs:
         tools_version: 'main_build'
 
     - name: Deploy to target branch
-      uses: stefanzweifel/git-auto-commit-action@v5
+      uses: stefanzweifel/git-auto-commit-action@v6
       with:
         create_branch: true
         commit_message: "deploy: ${{github.sha}}"
@@ -195,7 +199,7 @@ jobs:
     - name: "Parse JSON output from 'viash ns list' as input for matrix."
       id: set_matrix
       run: |
-        echo "components=$(jq -c '[ .[] | 
+        echo "components=$(jq -c '[ .[] | select(.scope.target != "test") | 
           { 
             "name": .name,
             "namespace_separator": .engines | map(select(.type == "docker"))[0].namespace_separator,
@@ -205,13 +209,14 @@ jobs:
           }
         ] | unique' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT
 
-        echo "workflows=$(jq -c '[ .[] | . as $config | (.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) |
+        echo "workflows=$(jq -c '[ .[]  | select(.scope.target != "test") | . as $config | (.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) |
         { 
           "name": $config.name,
           "namespace": $config.namespace,
           "main_script": (($config.build_info.config | capture("^(?<dir>.*\/)").dir) + "/" + .path),
           "entry": .entrypoint,
-          "config": $config.build_info.config
+          "config": $config.build_info.config,
+          "scope": $config.scope.target
         }
         ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT
 
@@ -233,7 +238,7 @@ jobs:
     # 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: actions/checkout@v5
 
     - uses: viash-io/viash-actions/setup@v6
 

.github/workflows/release-build.yml

@@ -29,7 +29,7 @@ jobs:
       dest_paths: ${{ steps.cache.outputs.dest_paths }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0 
     - uses: viash-io/viash-actions/project/sync-and-cache@v6
@@ -54,7 +54,7 @@ jobs:
       run: |
         git config --global core.symlinks true
 
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: 'release'
 
@@ -112,7 +112,7 @@ jobs:
         # check if stub runs work
         export NXF_VER=22.04.5
         nextflow run . \
-          -main-script "target/nextflow/${{matrix.component.namespace}}/${{matrix.component.name}}/main.nf" \
+          -main-script "target/${{ matrix.component.scope == 'private' && '_private/' || '' }}nextflow/${{matrix.component.namespace}}/${{matrix.component.name}}/main.nf" \
           -stub -profile no_publish \
           -c src/workflows/utils/integration_tests.config
 
@@ -141,7 +141,7 @@ jobs:
     # 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: actions/checkout@v5
 
     - uses: viash-io/viash-actions/setup@v6
 

.github/workflows/viash-test.yml

@@ -14,39 +14,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install Python
         uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff
-        run: ruff check --output-format=github .
-      
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          packages: any::lintr, any::styler, any::roxygen2
-          needs: lint, styler
-
-      - name: Lint
-        run: lintr::lint_dir(path = ".")
-        shell: Rscript {0}
-        env:
-          LINTR_ERROR_ON_LINT: true
-
-      - name: Style
-        run: styler::style_dir(dry = "off")
-        shell: Rscript {0}
-        
+      - run: python -m pip install pre-commit
+        shell: bash
+      - run: python -m pip freeze --local
+        shell: bash
+      - run: pre-commit run --show-diff-on-failure --color=always --all-files
+        shell: bash
+      
 
   # phase 1
   list:
@@ -60,7 +42,7 @@ jobs:
       dest_paths: ${{ steps.cache.outputs.dest_paths }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0 
 
@@ -105,7 +87,7 @@ jobs:
     # 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: actions/checkout@v5
 
     - uses: viash-io/viash-actions/setup@v6
     - uses: viash-io/viash-actions/project/update-docker-engine@v6

.lintr

@@ -0,0 +1,3 @@
+exclusions: list(
+    "README.qmd"
+    )

.pre-commit-config.yaml

@@ -2,9 +2,10 @@
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.1
+  rev: v0.12.1
   hooks:
-    - id: ruff
+    - id: ruff-check
+      args: [ --fix ]
     - id: ruff-format
 - repo: local
   hooks:
@@ -18,6 +19,6 @@ repos:
       - styler
       - knitr
 - repo: https://github.com/lorenzwalthert/precommit
-  rev: v0.4.3 
+  rev: v0.4.3.9012 
   hooks:
     - id: lintr