bump workflows

.github/workflows/ci.yaml

@@ -7,7 +7,7 @@ on:
     types: [run-all-tool-tests-command]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_22.05
+  GALAXY_BRANCH: release_23.1
   MAX_CHUNKS: 40
 jobs:
   setup:
@@ -112,6 +112,8 @@ jobs:
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     # TODO this is only temporary and only for OpenMS
     - name: create test data
       run: |

.github/workflows/pr.yaml

@@ -1,8 +1,23 @@
 name: Galaxy Tool Linting and Tests for push and PR
-on: [push, pull_request]
+on:
+  pull_request:
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
+  push:
+    branches:
+      - main
+      - master
+    paths-ignore:
+      - '.github/**'
+      - 'deprecated/**'
+      - 'docs/**'
+      - '*'
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_22.05
+  GALAXY_BRANCH: release_23.1
   MAX_CHUNKS: 4
   MAX_FILE_SIZE: 2M
 concurrency:
@@ -189,7 +204,7 @@ jobs:
     - name: lintr
       run: |
         library(lintr)
-        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
+        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_name_linter = NULL)
         con <- file("repository_list.txt", "r")
         status <- 0
         while (TRUE) {
@@ -299,6 +314,8 @@ jobs:
     - name: Get number of CPU cores
       uses: SimenB/github-actions-cpu-cores@v1
       id: cpu-cores
+    - name: Clean dotnet folder for space
+      run: rm -Rf /usr/share/dotnet
     - name: Planemo test
       uses: galaxyproject/planemo-ci-action@v1
       id: test
@@ -325,7 +342,7 @@ jobs:
   combine_outputs:
     name: Combine chunked test results
     needs: [setup, test]
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -358,6 +375,12 @@ jobs:
       id: check
       with:
         mode: check
+    - name: Check if all test chunks succeeded
+      run: |
+        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
+          exit 1
+        fi
 
   # deploy the tools to the toolsheds (first TTS for testing)
   deploy:
@@ -397,6 +420,28 @@ jobs:
         shed-target: toolshed
         shed-key: ${{ secrets.TS_API_KEY }}
 
+  deploy-report:
+    name: Report deploy status
+    needs: [deploy]
+    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    runs-on: ubuntu-latest
+    steps:
+    # report to the PR if deployment failed
+    - name: Get PR object
+      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      id: getpr
+      with:
+        sha: ${{ github.event.after }}
+    - name: Create comment
+      uses: peter-evans/create-or-update-comment@v2
+      with:
+        token: ${{ secrets.PAT }}
+        issue-number: ${{ steps.getpr.outputs.number }}
+        body: |
+          Attention: deployment ${{ needs.deploy.result }}!
+
+          https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+
   determine-success:
     name: Check workflow success
     needs: [setup, lint, flake8, lintr, file_sizes, combine_outputs]

.github/workflows/pr_without_tool_change.yaml

@@ -0,0 +1,17 @@
+name: Galaxy Tool Linting and Tests for push and PR
+# Fallback workflow that provides a succeeding "Check workflow success" job
+# as this is a requirement for being able to merge a PR
+# 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:
+concurrency:
+  # Group runs by PR, but keep runs on the default branch separate
+  # because we do not want to cancel ToolShed uploads
+  group: pr-${{ (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main') && github.run_number || github.ref }}
+  cancel-in-progress: true
+jobs:
+  determine-success:
+    name: Check workflow success
+    runs-on: ubuntu-latest
+    steps:
+      -  run: 'echo "No tool tests required for this PR"'