Merge branch 'main' into enh/reports-graphics

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/__main__.py

@@ -11,10 +11,12 @@
 import PySide6.QtSvg  # noqa: F401 - required to enable SVG rendering in QSS
 from PySide6.QtWidgets import QApplication
 
-from .logging_config import setup_logging
+from .logging_config import setup_bootstrap_logging, setup_logging
 from .utils import get_theme_manager
 from .views import WizardWindow
 
+logger = logging.getLogger(__name__)
+
 
 def main() -> int:
     """
@@ -23,23 +25,28 @@ def main() -> int:
     Returns:
         Exit code (0 for success)
     """
-    app = QApplication(sys.argv)
+    setup_bootstrap_logging()
+    try:
+        app = QApplication(sys.argv)
 
-    app.setApplicationName("Clinical DBS Annotator")
-    app.setOrganizationName("BML")
+        app.setApplicationName("Clinical DBS Annotator")
+        app.setOrganizationName("BML")
 
-    setup_logging(app)
+        setup_logging(app)
 
-    theme_manager = get_theme_manager()
-    try:
-        theme_manager.apply_theme(theme_manager.get_current_theme(), app)
-    except Exception as e:
-        logging.warning("Could not load theme: %s", e)
+        theme_manager = get_theme_manager()
+        try:
+            theme_manager.apply_theme(theme_manager.get_current_theme(), app)
+        except Exception:
+            logger.exception("Could not load current theme")
 
-    window = WizardWindow(app)
-    window.show()
+        window = WizardWindow(app)
+        window.show()
 
-    return app.exec()
+        return app.exec()
+    except Exception:
+        logger.critical("Fatal startup failure", exc_info=True)
+        return 1
 
 
 if __name__ == "__main__":

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

@@ -1,9 +1,11 @@
+import faulthandler
 import logging
 import platform
 import sys
 import threading
 from logging.handlers import RotatingFileHandler
 from pathlib import Path
+from types import TracebackType
 
 from PySide6.QtCore import (
     QMessageLogContext,
@@ -17,10 +19,69 @@
 
 _configured = False
 _log_file_path: Path | None = None
+_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: type[BaseException], exc: BaseException, tb: TracebackType | None
+    ) -> None:
+        logging.getLogger("uncaught").critical(
+            "Uncaught exception",
+            exc_info=(exc_type, exc, tb),
+        )
+
+    sys.excepthook = exc_hook
+
+    def thread_exc_hook(args: threading.ExceptHookArgs) -> None:
+        logging.getLogger("uncaught").critical(
+            "Uncaught thread exception",
+            exc_info=_safe_exc_info(args.exc_type, args.exc_value, args.exc_traceback),
+        )
+
+    threading.excepthook = thread_exc_hook
+
+    def unraisable_hook(args: sys.UnraisableHookArgs) -> None:
+        logging.getLogger("uncaught").error(
+            "Unraisable exception in %r",
+            args.object,
+            exc_info=_safe_exc_info(args.exc_type, args.exc_value, args.exc_traceback),
+        )
+
+    sys.unraisablehook = unraisable_hook
+
+
+def setup_bootstrap_logging() -> None:
+    root = logging.getLogger()
+    if root.handlers:
+        _install_exception_hooks()
+        return
+
+    fmt = logging.Formatter("%(asctime)s ¦ %(levelname)s ¦ %(name)s ¦ %(message)s")
+    sh = logging.StreamHandler(sys.stderr)
+    sh.setLevel(logging.INFO)
+    sh.setFormatter(fmt)
+    root.setLevel(logging.DEBUG)
+    root.addHandler(sh)
+    _install_exception_hooks()
 
 
 def setup_logging(_app: QApplication) -> Path:
-    global _configured, _log_file_path
+    global _configured, _log_file_path, _crash_log_file
     if _configured:
         assert _log_file_path is not None
         return _log_file_path
@@ -53,21 +114,7 @@ def setup_logging(_app: QApplication) -> Path:
         sh.setFormatter(fmt)
         root.addHandler(sh)
 
-    def exc_hook(exc_type, exc, tb):
-        logging.getLogger("uncaught").critical(
-            "Uncaught exception",
-            exc_info=(exc_type, exc, tb),
-        )
-
-    sys.excepthook = exc_hook
-
-    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),
-        )
-
-    threading.excepthook = thread_exc_hook
+    _install_exception_hooks()
 
     def qt_handler(mode: QtMsgType, context: QMessageLogContext, message: str) -> None:
         if mode == QtMsgType.QtDebugMsg:
@@ -86,6 +133,19 @@ def qt_handler(mode: QtMsgType, context: QMessageLogContext, message: str) -> No
         logging.getLogger("qt").log(level, "%s%s", message, suffix)
 
     qInstallMessageHandler(qt_handler)
+    _app.aboutToQuit.connect(
+        lambda: logging.getLogger("clinical_dbs_annotator").info("Application shutdown")
+    )
+
+    crash_log_path = log_dir / "clinical-dbs-annotator-crash.log"
+    try:
+        _crash_log_file = open(crash_log_path, "a", encoding="utf-8")
+        faulthandler.enable(file=_crash_log_file, all_threads=True)
+    except Exception:
+        logging.getLogger("clinical_dbs_annotator").exception(
+            "Failed to enable faulthandler with crash log %s",
+            crash_log_path,
+        )
 
     logging.getLogger("clinical_dbs_annotator").info(
         "Started v%s Python %s | %s | log=%s",