Merge branch 'main' into get-sbml-model

.github/workflows/ci.yaml

@@ -28,7 +28,7 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -44,11 +44,11 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -88,11 +88,11 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -104,7 +104,7 @@ jobs:
         mode: lint
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -136,11 +136,11 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -163,7 +163,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -182,14 +182,14 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -200,7 +200,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
@@ -211,7 +211,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

.github/workflows/pr.yaml

@@ -61,17 +61,17 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -118,11 +118,11 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -144,7 +144,7 @@ jobs:
         fail-level: ${{ env.FAIL_LEVEL }}
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -164,11 +164,11 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -181,7 +181,7 @@ jobs:
       run: |
         echo "Repository list:"
         echo "${{ needs.setup.outputs.repository-list }}"
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -204,7 +204,7 @@ jobs:
       with:
         r-version: ${{ matrix.r-version }}
     - name: Cache R packages
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
@@ -240,7 +240,7 @@ jobs:
         }
         quit(status = status)
       shell: Rscript {0}
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -267,7 +267,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -298,17 +298,17 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
     - name: Cache .planemo
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -331,7 +331,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -350,14 +350,14 @@ jobs:
       matrix:
         python-version: ['3.7']
     steps:
-    - uses: actions/download-artifact@v3
+    - uses: actions/download-artifact@v4
       with:
         path: artifacts
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -368,7 +368,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: 'All tool test results'
         path: upload
@@ -384,11 +384,11 @@ jobs:
           exit 1
         fi
 
-  # deploy the tools to the toolsheds (first TTS for testing)
+  # deploy the tools to the toolsheds (first TTS for testing), github.event.pull_request.merged == true
   deploy:
     name: Deploy
     needs: [setup, lint, combine_outputs]
-    if: ${{ github.ref == 'refs/heads/main' && github.repository_owner == 'brsynth' && github.event.pull_request.merged == true }}
+    if: ${{ github.ref == 'refs/heads/main' && github.repository_owner == 'brsynth'}}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -397,11 +397,11 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -430,12 +430,12 @@ jobs:
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
-      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      uses: 8BitJonny/gh-get-current-pr@3.0.0
       id: getpr
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         issue-number: ${{ steps.getpr.outputs.number }}
         body: |

.github/workflows/release.yml

@@ -19,7 +19,7 @@ jobs:
       - name: "Check diff"
         id: set-diff
         run: |
-          nb=$(git diff --shortstat stable..origin/main | cut -f2 -d ' ')
+          nb=$(git diff --name-only stable..origin/main | grep -E "^tools|^workflows" | wc -l | tr -d " ")
           echo "Find diff: ${nb}"
           echo "nb=${nb}" >> "${GITHUB_OUTPUT}"
 
@@ -77,7 +77,7 @@ jobs:
           echo "$USER $PROJECT"
           github_changelog_generator --user "$USER" --project "$PROJECT" --no-unreleased
       - name: 'Upload Artifact Changelog'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: changelog-artifact
           path: CHANGELOG.md
@@ -95,7 +95,7 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
       - name: 'Download Artifact Changelog'
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: changelog-artifact
       # Commit

.github/workflows/update.yml

@@ -34,7 +34,7 @@ jobs:
           token: ${{ secrets.USER_TOKEN }}
           ref: main
       - name: "Setup python"
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip' # caching pip dependencies

.tt_skip

@@ -1,5 +1,5 @@
 tools/neo4jsbml
-tools/retropath2_wrapper
+tools/retropath2
 tools/rpbasicdesign
 tools/partsgenie
 workflows/retrosynthesis_workflow