Merge pull request #31 from richardkoehler/feat/add-typing

Add type checking

Author: Lucia-Poma

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: CI - Lint
+name: CI - Lint and Type Check
 
 on:
   push:
@@ -17,21 +17,21 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v6
 
-      - name: Set up uv with Python
+      - name: Set up uv
         uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57
         with:
           python-version: "3.14"
           enable-cache: true
 
-      - name: Sync dependencies (locked, dev)
+      - name: Sync dependencies
         run: |
           uv sync --locked --dev
 
-      - name: Run ruff (as in pre-commit)
+      - name: Lint
         run: |
           uv run ruff check --exclude tests .
 
-      - name: Run ruff format (check)
+      - name: Format
         run: |
           uv run ruff format --check --exclude tests .
 
@@ -41,3 +41,25 @@ jobs:
       #   run: |
       #     uv run pytest
 
+  type-check:
+    name: Type Check
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@cec208311dfd045dd5311c1add060b2062131d57
+        with:
+          python-version: "3.14"
+          enable-cache: true
+
+      - name: Sync dependencies
+        run: |
+          uv sync --locked --dev
+
+      - name: Type check
+        run: |
+          uv run ty check src
+

.pre-commit-config.yaml

@@ -10,3 +10,11 @@ repos:
       - id: ruff-format
       - id: ruff-check
         args: ["--fix", "--exclude", "tests"]
+
+  - repo: local
+    hooks:
+      - id: ty-check
+        name: ty check (src)
+        entry: uv run ty check src
+        language: system
+        pass_filenames: false

pyproject.toml

@@ -37,6 +37,8 @@ dev = [
     "ruff>=0.1.0",
     # "mypy>=1.8.0",
     "pre-commit>=3.6",
+    "ty>=0.0.30",
+    "pandas-stubs>=3.0.0.260204",
 ]
 build = [
     "pyinstaller>=6.15.0",
@@ -121,3 +123,6 @@ strict_optional = true
 [[tool.mypy.overrides]]
 module = "PySide6.*"
 ignore_missing_imports = true
+
+[tool.ty.rules]
+unresolved-attribute = "ignore"

src/clinical_dbs_annotator/controllers/wizard_controller.py

@@ -476,12 +476,17 @@ def undo_last_session_entry(self, view) -> None:
 
         # Read the TSV file and filter out rows with the last block_id
         file_path = self.session_data.file_path
+        if file_path is None:
+            QMessageBox.warning(
+                view, "Error", "No file path is associated with this session."
+            )
+            return
         rows_to_keep = []
         rows_to_delete = []
 
         with open(file_path, newline="", encoding="utf-8") as f:
             reader = csv.DictReader(f, delimiter="\t")
-            fieldnames = reader.fieldnames
+            fieldnames = list(reader.fieldnames or [])
 
             for row in reader:
                 block_id = row.get("block_id", "")
@@ -528,11 +533,11 @@ def close_session(self, parent) -> None:
             parent,
             "Confirm Close Session",
             "Are you sure you want to close the current session? The session will be saved before closing.",
-            QMessageBox.Ok | QMessageBox.Cancel,
-            QMessageBox.Cancel,
+            QMessageBox.StandardButton.Ok | QMessageBox.StandardButton.Cancel,
+            QMessageBox.StandardButton.Cancel,
         )
 
-        if reply == QMessageBox.Ok:
+        if reply == QMessageBox.StandardButton.Ok:
             self.session_data.close_file()
             parent.close()
 

src/clinical_dbs_annotator/logging_config.py

@@ -5,6 +5,7 @@
 import threading
 from logging.handlers import RotatingFileHandler
 from pathlib import Path
+from types import TracebackType
 
 from PySide6.QtCore import (
     QMessageLogContext,
@@ -21,8 +22,24 @@
 _crash_log_file = None
 
 
+def _safe_exc_info(
+    exc_type: type[BaseException],
+    exc_value: BaseException | None,
+    exc_traceback: TracebackType | None,
+) -> (
+    tuple[type[BaseException], BaseException, TracebackType | None]
+    | tuple[None, None, None]
+):
+    """Normalize exception tuple for logging APIs that require non-optional exception values."""
+    if exc_value is None:
+        return (None, None, None)
+    return (exc_type, exc_value, exc_traceback)
+
+
 def _install_exception_hooks() -> None:
-    def exc_hook(exc_type, exc, tb):
+    def exc_hook(
+        exc_type: type[BaseException], exc: BaseException, tb: TracebackType | None
+    ) -> None:
         logging.getLogger("uncaught").critical(
             "Uncaught exception",
             exc_info=(exc_type, exc, tb),
@@ -33,7 +50,7 @@ def exc_hook(exc_type, exc, tb):
     def thread_exc_hook(args: threading.ExceptHookArgs) -> None:
         logging.getLogger("uncaught").critical(
             "Uncaught thread exception",
-            exc_info=(args.exc_type, args.exc_value, args.exc_traceback),
+            exc_info=_safe_exc_info(args.exc_type, args.exc_value, args.exc_traceback),
         )
 
     threading.excepthook = thread_exc_hook
@@ -42,7 +59,7 @@ def unraisable_hook(args: sys.UnraisableHookArgs) -> None:
         logging.getLogger("uncaught").error(
             "Unraisable exception in %r",
             args.object,
-            exc_info=(args.exc_type, args.exc_value, args.exc_traceback),
+            exc_info=_safe_exc_info(args.exc_type, args.exc_value, args.exc_traceback),
         )
 
     sys.unraisablehook = unraisable_hook

src/clinical_dbs_annotator/models/session_data.py

@@ -128,7 +128,7 @@ def open_file_append(
         try:
             with open(file_path, newline="", encoding="utf-8") as f:
                 reader = csv.DictReader(f, delimiter="\t")
-                existing_fieldnames = reader.fieldnames
+                existing_fieldnames = list(reader.fieldnames or [])
         except Exception:
             logger.warning(
                 "Failed to read existing TSV headers, using defaults: %s",
@@ -388,7 +388,7 @@ def open_simple_file_append(self, filepath: str) -> None:
             try:
                 with open(filepath, newline="", encoding="utf-8") as f:
                     reader = csv.DictReader(f, delimiter="\t")
-                    fieldnames = reader.fieldnames
+                    fieldnames = list(reader.fieldnames or [])
             except Exception:
                 logger.warning(
                     "Failed reading annotation TSV headers, using defaults: %s",

src/clinical_dbs_annotator/ui/widgets.py

@@ -7,7 +7,7 @@
 
 import typing
 
-from PySide6.QtCore import QEvent, QSize, Qt, Signal
+from PySide6.QtCore import QByteArray, QEvent, QSize, Qt, Signal
 from PySide6.QtGui import QIcon, QPixmap
 from PySide6.QtWidgets import (
     QFrame,
@@ -168,10 +168,10 @@ def _create_arrow_button(self, direction: str, double: bool) -> QPushButton:
         """
         btn = QPushButton()
         btn.setIcon(create_arrow_icon(direction, double))
-        btn.setIconSize(QSize(*ICON_SIZES["increment"]))
-        btn.setFixedSize(
-            BUTTON_SIZES["increment"]["width"], BUTTON_SIZES["increment"]["height"]
-        )
+        icon_width, icon_height = typing.cast(tuple[int, int], ICON_SIZES["increment"])
+        btn.setIconSize(QSize(icon_width, icon_height))
+        increment_size = typing.cast(dict[str, int], BUTTON_SIZES["increment"])
+        btn.setFixedSize(increment_size["width"], increment_size["height"])
         btn.setCursor(Qt.PointingHandCursor)
         btn.setStyleSheet(
             """
@@ -353,7 +353,7 @@ def _create_lr_arrow_icon(self, direction: str, double: bool) -> QIcon:
                 """
 
         pixmap = QPixmap()
-        pixmap.loadFromData(bytes(svg, encoding="utf-8"), "SVG")
+        pixmap.loadFromData(QByteArray(svg.encode("utf-8")))
         return QIcon(pixmap)
 
     def _create_x_icon(self) -> QIcon:
@@ -366,7 +366,7 @@ def _create_x_icon(self) -> QIcon:
         </svg>
         """
         pixmap = QPixmap()
-        pixmap.loadFromData(bytes(svg, encoding="utf-8"), "SVG")
+        pixmap.loadFromData(QByteArray(svg.encode("utf-8")))
         return QIcon(pixmap)
 
     @typing.override
@@ -437,26 +437,22 @@ def _toggle_disabled(self) -> None:
             self.valueChanged.emit(self._value)
 
     # Public API (mirrors old InteractiveProgressBar)
-    @typing.override
-    def setMinimum(self, value: int) -> None:
+    def setMinimum(self, value: int) -> None:  # noqa: N802
         """Set the minimum internal value."""
         self._minimum = int(value)
         self.progress_bar.setMinimum(int(value))
 
-    @typing.override
-    def setMaximum(self, value: int) -> None:
+    def setMaximum(self, value: int) -> None:  # noqa: N802
         """Set the maximum internal value."""
         self._maximum = int(value)
         self.progress_bar.setMaximum(int(value))
 
-    @typing.override
-    def setValue(self, value: int) -> None:
+    def setValue(self, value: int) -> None:  # noqa: N802
         """Set the current value and update the progress bar."""
         self._value = int(value)
         self.progress_bar.setValue(int(value))
 
-    @typing.override
-    def setFormat(self, format_str: str) -> None:
+    def setFormat(self, format_str: str) -> None:  # noqa: N802
         """Set the text format displayed on the progress bar."""
         self.progress_bar.setFormat(format_str)
 
@@ -477,8 +473,7 @@ def value(self) -> int:
         """Return the current internal value."""
         return self._value
 
-    @typing.override
-    def isDisabled(self) -> bool:
+    def isDisabled(self) -> bool:  # noqa: N802
         """Return True if the widget is in disabled state."""
         return self._disabled
 

src/clinical_dbs_annotator/utils/graphics.py

@@ -5,7 +5,7 @@
 and button animations.
 """
 
-from PySide6.QtCore import QRectF, Qt, QTimer
+from PySide6.QtCore import QByteArray, QRectF, Qt, QTimer
 from PySide6.QtGui import QIcon, QPainter, QPainterPath, QPixmap
 
 from ..config import BUTTON_PULSE_COUNT, BUTTON_PULSE_DURATION
@@ -54,7 +54,7 @@ def create_arrow_icon(direction: str = "up", double: bool = False) -> QIcon:
             """
 
     pixmap = QPixmap()
-    pixmap.loadFromData(bytes(svg, encoding="utf-8"), "SVG")
+    pixmap.loadFromData(QByteArray(svg.encode("utf-8")))
     return QIcon(pixmap)