Merge pull request #6184 from bernt-matthias/topic/skip_lint

Add linter exceptions for all linters that are currently failing

Author: mvdbeek

.github/workflows/ci.yaml

@@ -75,7 +75,7 @@ jobs:
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
   lint:
-    name: Check for missing containers
+    name: Lint tool-list
     needs: setup
     if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
     runs-on: ubuntu-latest
@@ -101,9 +101,10 @@ jobs:
       id: lint
       with:
         mode: lint
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-        additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion
+        additional-planemo-options: --biocontainers
     - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:

.github/workflows/pr.yaml

@@ -123,21 +123,12 @@ jobs:
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
-
-    - name: Set fail level for pull request
-      if: ${{ github.event_name == 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
-    - name: Set fail level for merge
-      if: ${{ github.event_name != 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
-        fail-level: ${{ env.FAIL_LEVEL }}
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
     - uses: actions/upload-artifact@v4

data_managers/data_manager_bowtie2_index_builder/.lint_skip

@@ -0,0 +1,2 @@
+CitationsMissing
+XMLOrder

data_managers/data_manager_bowtie_index_builder/.lint_skip

@@ -0,0 +1 @@
+TestsMissing

data_managers/data_manager_build_kma_index/.lint_skip

@@ -0,0 +1 @@
+HelpEmpty

data_managers/data_manager_build_kraken_database/.lint_skip

@@ -0,0 +1,2 @@
+HelpEmpty
+TestsMissing

data_managers/data_manager_bwa_mem_index_builder/.lint_skip

@@ -0,0 +1 @@
+CitationsMissing

data_managers/data_manager_fetch_gene_annotation/.lint_skip

@@ -0,0 +1,3 @@
+CitationsMissing
+HelpEmpty
+TestsMissing

data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip

@@ -0,0 +1 @@
+CitationsMissing

data_managers/data_manager_fetch_index_maf/.lint_skip

@@ -0,0 +1,2 @@
+CitationsMissing
+TestsMissing