Merge branch 'add_cleaverna' of github.com:reyhaneh-tavakoli/galaxytools into add_cleaverna

Author: reyhaneh-tavakoli

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.1
+  GALAXY_BRANCH: release_26.0
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -105,7 +105,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: --biocontainers --skip version_bumped
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -145,7 +145,7 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v2
+      uses: SimenB/github-actions-cpu-cores@v3
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -162,7 +162,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -181,7 +181,7 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v7
+    - uses: actions/download-artifact@v8
       with:
         path: artifacts
     - uses: actions/setup-python@v6
@@ -200,7 +200,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'All tool test results'
         path: upload

.github/workflows/pr.yaml

@@ -17,7 +17,7 @@ on:
       - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_25.1
+  GALAXY_BRANCH: release_26.0
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 1M
 concurrency:
@@ -167,7 +167,7 @@ jobs:
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
         additional-planemo-options: ${{ env.EXTRA_SKIP }}
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -200,7 +200,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -239,7 +239,7 @@ jobs:
         echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
         git status
         git diff --exit-code | tee rlint_report.txt
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -267,7 +267,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -314,7 +314,7 @@ jobs:
         path: ~/.planemo
         key: planemo_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Get number of CPU cores
-      uses: SimenB/github-actions-cpu-cores@v2
+      uses: SimenB/github-actions-cpu-cores@v3
       id: cpu-cores
     - name: Clean dotnet folder for space
       run: rm -Rf /usr/share/dotnet
@@ -330,8 +330,8 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
-        test_timeout: 1800
-    - uses: actions/upload-artifact@v6
+        test_timeout: 900
+    - uses: actions/upload-artifact@v7
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -350,7 +350,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v7
+    - uses: actions/download-artifact@v8
       with:
         path: artifacts
     - uses: actions/setup-python@v6
@@ -369,7 +369,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v6
+    - uses: actions/upload-artifact@v7
       with:
         name: 'All tool test results'
         path: upload
@@ -393,7 +393,6 @@ jobs:
     needs: [setup, lint, combine_outputs]
     if: ${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
-    environment: toolshed-deployment
     strategy:
       matrix:
         python-version: ['3.11']
@@ -429,9 +428,8 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) }}
+    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'bgruening' }}
     runs-on: ubuntu-latest
-    environment: toolshed-deployment
     steps:
     # report to the PR if deployment failed
     - name: Get PR object

.github/workflows/pr_without_tool_change.yaml

@@ -4,9 +4,13 @@ name: Fallback
 # see https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/troubleshooting-required-status-checks#handling-skipped-but-required-checks
 on:
   pull_request:
+    paths:
+    - 'deprecated/**'
+    - 'docs/**'
+    - '.github/**'
+    - '*'
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
 jobs:
   determine-success:
     name: Check workflow success