ci: ruff format, isort, and lint

.github/workflows/check-styles.yml

@@ -0,0 +1,60 @@
+# Check ruff format and isort applied correctly
+
+name: Style checking
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  ruff-format:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install ruff
+        run: |
+          pip3 install ruff --break-system-packages
+      - name: Run ruff
+        run: |
+          set +e  # Do not exit shell on ruff failure
+          out=$(ruff format --check --diff . 2> app_stderr.txt)
+
+          exit_code=$?
+          err=$(<app_stderr.txt)
+
+          # Display the raw output in the step
+          echo "${out}"
+          echo "${err}"
+
+          # Display the Markdown output in the job summary
+          { echo "\`\`\`diff"; echo "${out}"; echo "${err}"; echo "\`\`\`"; } >> "$GITHUB_STEP_SUMMARY"
+
+          # Exit with the exit-code returned by ruff
+          exit ${exit_code}
+
+  ruff-isort:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install ruff
+        run: |
+          pip3 install ruff --break-system-packages
+      - name: Run ruff
+        run: |
+          set +e  # Do not exit shell on ruff failure
+          out=$(ruff check --select I --diff . 2> app_stderr.txt)
+
+          exit_code=$?
+          err=$(<app_stderr.txt)
+
+          # Display the raw output in the step
+          echo "${out}"
+          echo "${err}"
+
+          # Display the Markdown output in the job summary
+          { echo "\`\`\`diff"; echo "${out}"; echo "${err}"; echo "\`\`\`"; } >> "$GITHUB_STEP_SUMMARY"
+
+          # Exit with the exit-code returned by ruff
+          exit ${exit_code}

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'noci')"
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ['3.11']
 
     steps:
       - uses: actions/checkout@v4
@@ -26,18 +26,16 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black flake8 pytest coverage
-          pip install -e .
-          pip install -e .[test]
-      - name: Lint with flake8
+          pip install -e '.[test]'
+      - name: Lint with ruff
         run: |
           # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          ruff check . --config=ruff_essential.toml --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --statistics
+          ruff check . --exit-zero --statistics
       - name: Test with pytest and coverage
         run: |
-          coverage run --source=pdb2pqr -m pytest
+          coverage run -m pytest
           coverage report -m | tee coverage.txt
           coverage html
       - name: Upload coverage results