Merge branch 'master' into fix_msconvert_defaults

Author: bgruening

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_24.0
+  GALAXY_BRANCH: release_24.1
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -32,7 +32,7 @@ jobs:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
         comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
-        reaction-type: hooray
+        reactions: hooray
     - name: Set galaxy fork and branch
       id: get-fork-branch
       run: |
@@ -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

@@ -15,7 +15,7 @@ on:
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_24.0
+  GALAXY_BRANCH: release_24.1
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -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

.github/workflows/slash.yaml

@@ -8,7 +8,7 @@ jobs:
     steps:
       - name: Slash Command Dispatch
         if: github.repository_owner == 'galaxyproteomics'
-        uses: peter-evans/slash-command-dispatch@v3
+        uses: peter-evans/slash-command-dispatch@v4
         with:
           token: ${{ secrets.PAT }}
           commands: |