Run ruff format changes and finalize indentation and lint fixes.

scripts/analyze_themes.py

@@ -1,16 +1,21 @@
 #!/usr/bin/env python3
 """Test script to analyze all theme header colors."""
+# ruff: noqa: E402
 
 import sys
 import tkinter as tk
 from pathlib import Path
 
-from init import logger
-from theme_manager import ThemeManager
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
 
-# Add src directory to Python path
-src_path = Path(__file__).parent / "src"
-sys.path.insert(0, str(src_path))
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def analyze_all_themes():

scripts/integration_test.py

@@ -3,18 +3,23 @@
 Integration test for TheChart export system
 Tests the complete export workflow without GUI dependencies
 """
+# ruff: noqa: E402
 
 import sys
 from pathlib import Path
 
-# Add src to path
-sys.path.insert(0, "src")
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
 
-from data_manager import DataManager
-from export_manager import ExportManager
-from init import logger
-from medicine_manager import MedicineManager
-from pathology_manager import PathologyManager
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.data import DataManager
+from thechart.export import ExportManager
+from thechart.managers import MedicineManager, PathologyManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 class MockGraphManager:

scripts/test_arc_darker.py

@@ -1,17 +1,25 @@
 #!/usr/bin/env python3
 """Test the darker header text for Arc theme."""
 
+# ruff: noqa: E402
+#!/usr/bin/env python3
+"""Test the darker header text for Arc theme."""
+
 import sys
 import tkinter as tk
 from pathlib import Path
 from tkinter import ttk
 
-from init import logger
-from theme_manager import ThemeManager
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
 
-# Add src directory to Python path
-src_path = Path(__file__).parent / "src"
-sys.path.insert(0, str(src_path))
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def test_arc_darker_headers():

scripts/test_arc_headers.py

@@ -1,13 +1,22 @@
 #!/usr/bin/env python3
 """Test script to check table header visibility in Arc theme."""
+# ruff: noqa: E402
 
 import sys
 import tkinter as tk
 from pathlib import Path
 from tkinter import ttk
 
-from init import logger
-from theme_manager import ThemeManager
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
+
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 # Add src directory to Python path
 src_path = Path(__file__).parent / "src"

scripts/test_dose_parsing.py

@@ -2,16 +2,22 @@
 """
 Test the complete dose tracking flow: load -> display -> add -> save
 """
+# ruff: noqa: E402
 
 import os
 import sys
 from datetime import datetime
 
-# Add the src directory to Python path
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "src"))
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = os.path.join(os.path.dirname(__file__), "..", "src")
+if SRC_DIR not in sys.path:
+    sys.path.insert(0, SRC_DIR)
 
-from init import logger
-from ui_manager import UIManager
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import UIManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def test_dose_parsing():

scripts/test_dose_tracking_ui.py

@@ -3,20 +3,28 @@
 Test script for dose tracking UI in edit window.
 Tests the specific issue where adding new doses replaces existing ones.
 """
+# ruff: noqa: E402
 
-import os
 import sys
 import tkinter as tk
 from datetime import datetime
+from pathlib import Path
 
-# Add the src directory to Python path
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", "src"))
 
-from init import logger
-from medicine_manager import MedicineManager
-from pathology_manager import PathologyManager
-from theme_manager import ThemeManager
-from ui_manager import UIManager
+def _ensure_src_on_path() -> None:
+    src_dir = Path(__file__).resolve().parent.parent / "src"
+    if str(src_dir) not in sys.path:
+        sys.path.insert(0, str(src_dir))
+
+
+_ensure_src_on_path()
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.managers import Medicine, MedicineManager, PathologyManager
+from thechart.ui import ThemeManager
+from thechart.ui.ui_manager import UIManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def test_dose_tracking():
@@ -39,8 +47,6 @@ def test_dose_tracking():
     # Add a test medicine if none exist
     medicines = medicine_manager.get_all_medicines()
     if not medicines:
-        from medicine_manager import Medicine
-
         test_medicine = Medicine(
             key="bupropion",
             display_name="Bupropion",

scripts/test_improved_headers.py

@@ -1,13 +1,22 @@
 #!/usr/bin/env python3
 """Test the improved header visibility fix."""
+# ruff: noqa: E402
 
 import sys
 import tkinter as tk
 from pathlib import Path
 from tkinter import ttk
 
-from init import logger
-from theme_manager import ThemeManager
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
+
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 # Add src directory to Python path
 src_path = Path(__file__).parent / "src"

scripts/test_theme_changing.py

@@ -1,57 +1,73 @@
 #!/usr/bin/env python3
-"""Test script to verify theme changing functionality works without errors."""
+"""Quick smoke test for ThemeManager: iterate and apply available themes.
 
+This script can be run standalone. It ensures the local ``src`` is on sys.path
+so the ``thechart`` package is importable without installation. It also hides
+the Tk window and gracefully skips if no display is available.
+"""
+
+from __future__ import annotations
+
+import contextlib
 import sys
 import tkinter as tk
 from pathlib import Path
 
-from init import logger
-from theme_manager import ThemeManager
 
-# Add src directory to Python path
-src_path = Path(__file__).parent.parent / "src"
-sys.path.insert(0, str(src_path))
+def _ensure_src_on_path() -> None:
+    """Add the repository's ``src`` dir to sys.path when running locally."""
+    repo_root = Path(__file__).resolve().parents[1]
+    src_dir = repo_root / "src"
+    if str(src_dir) not in sys.path:
+        sys.path.insert(0, str(src_dir))
 
 
-def test_theme_changes():
-    """Test changing between different themes to ensure no errors occur."""
+def main() -> int:
+    _ensure_src_on_path()
+
+    # Imports after path fix
+    from thechart.core.constants import LOG_LEVEL
+    from thechart.core.logger import init_logger
+    from thechart.ui import ThemeManager
+
+    logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
+
     print("Testing theme changing functionality...")
 
-    # Create a test tkinter window
-    root = tk.Tk()
-    root.withdraw()  # Hide the window
+    # Create a test tkinter root; skip gracefully if headless
+    try:
+        root = tk.Tk()
+    except tk.TclError as exc:
+        print(f"Skipping: no display available ({exc})")
+        return 0
 
-    # Initialize theme manager
-    theme_manager = ThemeManager(root, logger)
+    try:
+        root.withdraw()  # Hide the window
 
-    # Test all available themes
-    available_themes = theme_manager.get_available_themes()
-    print(f"Available themes: {available_themes}")
+        theme_manager = ThemeManager(root, logger)
+        available_themes = theme_manager.get_available_themes()
 
-    for theme in available_themes:
-        print(f"Testing theme: {theme}")
-        try:
-            success = theme_manager.apply_theme(theme)
-            if success:
-                print(f"  ✓ {theme} applied successfully")
+        for theme in available_themes:
+            print(f"Testing theme: {theme}")
+            try:
+                success = theme_manager.apply_theme(theme)
+                if success:
+                    print(f"  ✓ {theme} applied successfully")
 
-                # Test getting theme colors (this is where the error was occurring)
-                colors = theme_manager.get_theme_colors()
-                print(f"  ✓ Theme colors retrieved: {list(colors.keys())}")
+                    colors = theme_manager.get_theme_colors()
+                    print(f"  ✓ Theme colors retrieved: {list(colors.keys())}")
 
-                # Test getting menu colors
-                menu_colors = theme_manager.get_menu_colors()
-                print(f"  ✓ Menu colors retrieved: {list(menu_colors.keys())}")
-
-            else:
-                print(f"  ✗ Failed to apply {theme}")
-        except Exception as e:
-            print(f"  ✗ Error with {theme}: {e}")
-
-    # Clean up
-    root.destroy()
-    print("Theme testing completed!")
+                    menu_colors = theme_manager.get_menu_colors()
+                    print(f"  ✓ Menu colors retrieved: {list(menu_colors.keys())}")
+                else:
+                    print(f"  ✗ Failed to apply {theme}")
+            except Exception as e:  # pragma: no cover - smoke test resilience
+                print(f"  ✗ Error applying {theme}: {e}")
+        return 0
+    finally:
+        with contextlib.suppress(Exception):
+            root.destroy()
 
 
 if __name__ == "__main__":
-    test_theme_changes()
+    raise SystemExit(main())

scripts/test_white_headers.py

@@ -1,17 +1,22 @@
 #!/usr/bin/env python3
 """Test the improved header visibility with white text."""
+# ruff: noqa: E402
 
 import sys
 import tkinter as tk
 from pathlib import Path
 from tkinter import ttk
 
-from init import logger
-from theme_manager import ThemeManager
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
 
-# Add src directory to Python path
-src_path = Path(__file__).parent / "src"
-sys.path.insert(0, str(src_path))
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def test_white_headers():

scripts/verify_headers.py

@@ -1,16 +1,21 @@
 #!/usr/bin/env python3
 """Verify header visibility across all themes."""
+# ruff: noqa: E402
 
 import sys
 import tkinter as tk
 from pathlib import Path
 
-from init import logger
-from theme_manager import ThemeManager
+# Ensure the 'src' directory is on sys.path so 'thechart' package is importable
+SRC_DIR = Path(__file__).resolve().parent.parent / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
 
-# Add src directory to Python path
-src_path = Path(__file__).parent / "src"
-sys.path.insert(0, str(src_path))
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def verify_all_themes():
@@ -56,7 +61,6 @@ def verify_all_themes():
         darker = min(bg_lum, fg_lum)
         contrast_ratio = (lighter + 0.05) / (darker + 0.05)
 
-        # Determine status
         if contrast_ratio >= 4.5:
             status = "✅ EXCELLENT"
         elif contrast_ratio >= 3.0:

scripts/verify_themes.py

@@ -1,16 +1,24 @@
 #!/usr/bin/env python3
 """Verify that other themes still work correctly with Arc-specific change."""
+# ruff: noqa: E402
 
 import sys
 import tkinter as tk
 from pathlib import Path
 
-from init import logger
-from theme_manager import ThemeManager
 
-# Add src directory to Python path
-src_path = Path(__file__).parent / "src"
-sys.path.insert(0, str(src_path))
+def _ensure_src_on_path() -> None:
+    src_dir = Path(__file__).resolve().parent.parent / "src"
+    if str(src_dir) not in sys.path:
+        sys.path.insert(0, str(src_dir))
+
+
+_ensure_src_on_path()
+from thechart.core.constants import LOG_LEVEL
+from thechart.core.logger import init_logger
+from thechart.ui import ThemeManager
+
+logger = init_logger(__name__, testing_mode=(LOG_LEVEL == "DEBUG"))
 
 
 def verify_other_themes():