Merge pull request #12 from richardkoehler/feature/lint

Update python and lint codebase

Author: Lucia-Poma

.python-version

@@ -1 +1 @@
-3.11.15
+3.14

pyproject.toml

@@ -2,7 +2,7 @@
 name = "clinical-dbs-annotator"
 description = "A graphical user interface for annotating DBS clinical programming sessions"
 readme = "README.md"
-requires-python = ">=3.11,<3.14"
+requires-python = ">=3.11"
 authors = [
     { name = "Lucia Poma", email = "lucia.poma@wysscenter.ch" }
 ]
@@ -17,6 +17,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "License :: OSI Approved :: MIT License",
     "Environment :: X11 Applications :: Qt",
     "Operating System :: OS Independent",
@@ -82,7 +83,7 @@ addopts = [
 
 [tool.ruff]
 line-length = 88
-target-version = "py311"
+target-version = "py314"
 extend-exclude = [
     ".eggs",
     ".git",

run.py

@@ -5,7 +5,7 @@
 from Visual Studio or any IDE.
 
 Usage:
-    python run.py 
+    python run.py
 """
 
 import sys

scripts/build_windows_nuitka.py

@@ -140,7 +140,7 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
     # Execute
     try:
         import subprocess
-        result = subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
+        subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
         print("\n✅ Build completed successfully!")
 
         # Show output location

src/clinical_dbs_annotator/config_electrode_models.py

@@ -26,11 +26,11 @@ def add_validator(validator_fn):
     def validate_configuration(contact_states, case_state):
         """
         Validate stimulation configuration according to clinical rules
-        
+
         Args:
             contact_states (dict): Dictionary of {(contact_idx, segment_idx): ContactState}
             case_state (ContactState): State of the case
-            
+
         Returns:
             tuple: (is_valid, error_message)
         """
@@ -73,11 +73,11 @@ def validate_configuration(contact_states, case_state):
     def get_suggested_fix(contact_states, case_state):
         """
         Suggest a fix for invalid configuration
-        
+
         Args:
             contact_states (dict): Dictionary of contact states
             case_state (ContactState): State of the case
-            
+
         Returns:
             str: Suggestion message
         """
@@ -410,10 +410,10 @@ def is_level_directional(self, level_idx):
 def get_model_by_name(name):
     """
     Get electrode model by name
-    
+
     Args:
         name (str): Model name
-        
+
     Returns:
         ElectrodeModel: Electrode model object or None if not found
     """
@@ -423,7 +423,7 @@ def get_model_by_name(name):
 def get_all_model_names():
     """
     Get list of all electrode model names
-    
+
     Returns:
         list: List of model names
     """
@@ -433,10 +433,10 @@ def get_all_model_names():
 def get_models_by_manufacturer(manufacturer):
     """
     Get list of models for a specific manufacturer
-    
+
     Args:
         manufacturer (str): Manufacturer name
-        
+
     Returns:
         list: List of model names for the manufacturer
     """
@@ -446,7 +446,7 @@ def get_models_by_manufacturer(manufacturer):
 def get_all_manufacturers():
     """
     Get list of all manufacturers
-    
+
     Returns:
         list: List of manufacturer names
     """

src/clinical_dbs_annotator/controllers/wizard_controller.py

@@ -422,7 +422,7 @@ def close_session(self, parent) -> None:
     def export_session_word(self, parent, scale_prefs=None, sections=None) -> None:
         """
         Export current session data to Word format.
-        
+
         Args:
             parent: The parent widget for dialogs
             scale_prefs: Scale optimization prefs from the dialog
@@ -434,7 +434,7 @@ def export_session_word(self, parent, scale_prefs=None, sections=None) -> None:
     def export_session_pdf(self, parent, scale_prefs=None, sections=None) -> None:
         """
         Export current session data to PDF format.
-        
+
         Args:
             parent: The parent widget for dialogs
             scale_prefs: Scale optimization prefs from the dialog

src/clinical_dbs_annotator/models/electrode_viewer.py

@@ -5,6 +5,8 @@
 Based on Lead-DBS repository models
 """
 
+import typing
+
 from PySide6.QtCore import QPointF, QRectF, Qt
 from PySide6.QtGui import (
     QBrush,
@@ -188,7 +190,7 @@ def set_ring_state(self, ring_idx, state):
                 new_states[contact_id] = state
 
         self._apply_change_if_valid(new_states, self.case_state)
-
+    @typing.override
     def mousePressEvent(self, event):
         """Handle clicks on contacts, rings and case"""
         if event.button() == Qt.LeftButton:
@@ -223,6 +225,7 @@ def mousePressEvent(self, event):
                 self.cycle_case_state()
                 return
 
+    @typing.override
     def mouseMoveEvent(self, event):
         """Handle hover over contacts, rings and case"""
         old_hovered_contact = self.hovered_contact
@@ -260,6 +263,7 @@ def get_state_color(self, state, is_hovered=False):
 
         return base_color, border_color, border_width
 
+    @typing.override
     def paintEvent(self, event):
         """Render the electrode lead, contacts, case, and labels."""
         if not self.model:
@@ -336,7 +340,7 @@ def paintEvent(self, event):
         contact_height_px = self.model.contact_height * scale
         # E0 is the last contact (index 0), positioned after all other contacts and their spacing
         e0_y_position = start_y + 2 * scale  # Initial offset
-        for i in range(self.model.num_contacts - 1):  # All contacts except E0
+        for _ in range(self.model.num_contacts - 1):  # All contacts except E0
             e0_y_position += contact_height_px + (self.model.contact_spacing + 1.0) * scale
 
         # Lead body end position depends on electrode type
@@ -445,7 +449,7 @@ def paintEvent(self, event):
                 self.ring_rects[contact_idx] = ring_cap_rect
 
                 #  Directional electrode with 3D metallic segments
-                segment_width = lead_width * 0.5
+                lead_width * 0.5
                 extension = base_extension
 
                 # Helper function to draw 3D segment
@@ -784,6 +788,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
             painter.drawText(ring_cap_rect, Qt.AlignCenter, "Ring")
 
 
+    @typing.override
     def resizeEvent(self, event):
         """Redraw when window is resized"""
         super().resizeEvent(event)

src/clinical_dbs_annotator/models/session_data.py

@@ -130,14 +130,6 @@ def open_file_append(self, file_path: str, start_block_id: int | None = None) ->
             pass
         self.session_start_time = datetime.now()
 
-    def is_file_open(self) -> bool:
-        """
-        Check if a TSV file is currently open.
-
-        Returns:
-            True if file is open, False otherwise
-        """
-        return self.tsv_file is not None and self.tsv_writer is not None
 
     def close_file(self) -> None:
         """Close the TSV file if it's open."""

src/clinical_dbs_annotator/models/stimulation.py

@@ -52,7 +52,7 @@ def to_dict(self) -> dict:
         }
 
     @classmethod
-    def from_dict(cls, data: dict) -> "StimulationParameters":
+    def from_dict(cls, data: dict) -> StimulationParameters:
         """Create StimulationParameters from a dictionary."""
         return cls(
             left_frequency=data.get("left_stim_freq"),
@@ -67,7 +67,7 @@ def from_dict(cls, data: dict) -> "StimulationParameters":
             right_pulse_width=data.get("right_pulse_width"),
         )
 
-    def copy(self) -> "StimulationParameters":
+    def copy(self) -> StimulationParameters:
         """Create a copy of the stimulation parameters."""
         return StimulationParameters(
             left_frequency=self.left_frequency,

src/clinical_dbs_annotator/ui/amplitude_split_widget.py

@@ -277,7 +277,7 @@ def _refresh_ma_values(self) -> None:
 
     def update_main_amplitude_from_split(self, split_text: str) -> None:
         """Update the main amplitude field to show the sum of split values.
-        
+
         When loading a file with split amplitude (e.g., "2.5_2.5"),
         this method calculates the sum and updates the main field.
         """
@@ -297,7 +297,7 @@ def update_main_amplitude_from_split(self, split_text: str) -> None:
 
     def set_amplitude_from_split(self, split_text: str) -> None:
         """Set amplitude from split values and update percentages.
-        
+
         When loading a file with split amplitude (e.g., "2.5_2.5"),
         this method:
         1. Updates the main amplitude field to show the sum