Update GitHub action versions

Also:
- Use Python 3.12 in GitHub workflows
- Use `check` subcommand of ruff
- Update ruff settings for 0.2.0 deprecations

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
     outputs:
       recipes_found: ${{ steps.recipes_changes.outputs.recipes_found }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       # The range of commits to check for changes is:
@@ -58,7 +58,7 @@ jobs:
               recipes_found=false
           fi
           echo "recipes_found=$recipes_found" >> $GITHUB_OUTPUT
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: recipe_list
           path: recipe_list.txt
@@ -71,11 +71,11 @@ jobs:
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
-      - uses: actions/download-artifact@v3
+          python-version: '3.12'
+      - uses: actions/download-artifact@v4
         with:
           name: recipe_list
           path: ../workflow_artifacts/
@@ -86,9 +86,9 @@ jobs:
           while read -r folder; do
               python3 wheel_builder.py "$folder";
           done < ../workflow_artifacts/recipe_list.txt
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: wheelhouse
+          name: wheelhouse-{{ matrix.os }}
           path: wheelhouse/
 
   deploy:
@@ -97,13 +97,14 @@ jobs:
     if: ${{ github.ref == 'refs/heads/main' && github.event_name == 'push' && github.repository_owner == 'galaxyproject' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: wheelhouse
+          merge-multiple: true
+          name: wheelhouse-*
           path: wheelhouse/
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
       - name: Setup deploy environment
         run: python3 -m pip install s3pypi
       - name: Deploy wheels

.github/workflows/lint.yaml

@@ -19,15 +19,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
         run: pip install tox
       - name: Run tox
         run: tox
       - uses: psf/black@stable
-      - uses: isort/isort-action@master
+      - uses: isort/isort-action@v1

pyproject.toml

@@ -7,8 +7,10 @@ include = '\.pyi?$'
 isort = true
 
 [tool.ruff]
-select = ["E", "F", "B", "UP"]
 target-version = "py38"
+
+[tool.ruff.lint]
+select = ["E", "F", "B", "UP"]
 # Exceptions:
 # B9 flake8-bugbear opinionated warnings
 # E501 is line length (delegated to black)

tox.ini

@@ -6,7 +6,7 @@ skipsdist = True
 
 [testenv]
 commands =
-    lint: ruff .
+    lint: ruff check .
     lint: flake8 .
     mypy: mypy .
 deps =