Update GHA and pyproject to run more tools via ruff

.github/workflows/lint-code.yml

@@ -1,94 +1,58 @@
 name: lint-code
 on: [push]
 jobs:
+  # Use ruff to check for code style violations
   ruff-check:
-    # Use ruff to check for code style violations
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.10"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install ruff
       - name: ruff --> Check for style violations
-        # The following style violations will be ignored
-        # ==============================================
-        # E402: Module level import not at top of file
-        # E722: Do not use bare 'except'
-        # E741: Ambiguous variable name
-        run: ruff check --ignore E402,E722,E741 --unsafe-fixes .
-
-  isort-check:
-    # Use isort to check that imports are ordered according to best practice
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.7"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install isort
-      - name: isort --> Check for best-practice sorting of imports
-        run: isort --check .
+        # Configured in pyproject.toml
+        run: ruff check .
 
+  # Use ruff to check code formatting
   ruff-format:
-    # Use ruff to check code formatting
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.10"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install ruff
       - name: ruff --> Check code formatting
         run: ruff format --check .
 
+  # Use mypy for static type checking
   mypy-check:
-    # Use mypy for static type checking
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.10"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install mypy
+      # Start by installing type stubs
       - name: mypy --> Install stubs
-        run: echo -e "y" | mypy --install-types --ignore-missing-imports --follow-imports=skip --exclude build . || exit 0
+        run: echo -e "y" | mypy --install-types || exit 0
       - name: mypy --> Static type checking
-        run: mypy --ignore-missing-imports --follow-imports=skip --exclude build .
-
-  pyupgrade-check:
-    # Use pyupgrade to check for outdated syntax
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.7"
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install pyupgrade
-      - name: pyupgrade --> Check for outdated syntax
-        run: pyupgrade **/*.py
+        # Configured in pyprojet.toml
+        run: mypy **/*.py

pyproject.toml

@@ -1,21 +1,27 @@
 title = "scilifelab_epps"
 
-[tool.ruff.lint]
 
+[tool.ruff.lint]
 select =[
-    # === Ruff defaults ===
+    #         Ruff default rules
+    # ------------------------------
     "E4",   # pycodestyle Imports
-    "E7",   # pycodestyle Statement
-    "E9",   # pycodestyle Runstyle
+    "E7",   # pycodestyle Statements
+    "E9",   # pycodestyle Runtime
     "F",    # Pyflakes
-    # === Additional ===
-    "I",    # isort
-    "UP",   # pyupgrade
-]
 
+    #         Additional    Comment
+    # ------------------------------------------------------
+    "I",    # isort         Best-practice sorting of imports
+    "UP",   # pyupgrade     Make sure syntax is up-to-date
+]
 ignore = [
     "E402", # Module level import not at top of file
     "E722", # Do not use bare 'except'
     "E741", # Ambiguous variable name
-    ]
+]
+
 
+[tool.mypy]
+ignore_missing_imports = true
+follow_imports = 'skip'