Merge pull request #8 from richardkoehler/feat/cleanup-config

Cleanup project configuration

Author: Lucia-Poma

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.9
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--exclude", "tests"]

.python-version

@@ -1 +1 @@
-3.11.5
+3.11.15

pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "clinical-dbs-annotator"
-version = "0.1.0"
-description = "A PyQt5-based tool for annotating DBS clinical programming sessions"
+description = "A graphical user interface for annotating DBS clinical programming sessions"
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.11,<3.14"
 authors = [
     { name = "Lucia Poma", email = "lpoma@mgh.harvard.edu" }
 ]
 keywords = ["dbs", "clinical", "annotation", "neuroscience", "deep-brain-stimulation"]
+dynamic = ["version"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Healthcare Industry",
@@ -16,14 +16,14 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: MIT License",
     "Environment :: X11 Applications :: Qt",
     "Operating System :: OS Independent",
 ]
-
 dependencies = [
-    "pyqt5==5.15.10",
-    "pyqt5-qt5==5.15.2",
+    "pyqt5",
+    "pyqt5-qt5<=5.15.2",
     "pytz>=2025.2",
     "pandas>=2.1",
     "python-docx>=1.1",
@@ -32,12 +32,11 @@ dependencies = [
     "pyqtgraph>=0.14.0",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 dev = [
     "pytest>=8.0.0",
     "pytest-qt>=4.4.0",
     "pytest-cov>=4.1.0",
-    "black>=24.0.0",
     "ruff>=0.1.0",
     # "mypy>=1.8.0",
     "pre-commit>=3.6",
@@ -47,7 +46,10 @@ build = [
     "opencv-python-headless>=4.12.0.88",
     "nuitka>=4.0.7",
 ]
-docs = ["sphinx", "sphinx-rtd-theme"]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+]
 
 [project.scripts]
 clinical-dbs-annotator = "clinical_dbs_annotator.__main__:main"
@@ -61,6 +63,9 @@ Documentation = "https://github.com/bml/clinical-dbs-annotator/blob/main/README.
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
+[tool.hatch.version]
+path = "src/clinical_dbs_annotator/__init__.py"
+
 [tool.hatch.build.targets.wheel]
 packages = ["src/clinical_dbs_annotator"]
 
@@ -76,25 +81,19 @@ addopts = [
     "--cov-report=term-missing",
 ]
 
-[tool.black]
-line-length = 88
-target-version = ["py311"]
-include = '\.pyi?$'
-extend-exclude = '''
-/(
-  # directories
-  \.eggs
-  | \.git
-  | \.hatch
-  | \.venv
-  | build
-  | dist
-)/
-'''
-
 [tool.ruff]
 line-length = 88
 target-version = "py311"
+extend-exclude = [
+    ".eggs",
+    ".git",
+    ".hatch",
+    ".venv",
+    "build",
+    "dist",
+]
+
+[tool.ruff.lint]
 select = [
     "E",   # pycodestyle errors
     "W",   # pycodestyle warnings
@@ -106,7 +105,7 @@ select = [
     "C4",  # flake8-comprehensions
 ]
 ignore = [
-    "E501",  # line too long (handled by black)
+    "E501",  # line too long (handled by formatter/line-length)
 ]
 
 [tool.mypy]
@@ -125,8 +124,3 @@ strict_optional = true
 [[tool.mypy.overrides]]
 module = "PyQt5.*"
 ignore_missing_imports = true
-
-[dependency-groups]
-dev = [
-    "pyinstaller>=6.15.0",
-]

run.py

@@ -9,6 +9,7 @@
 """
 
 import sys
+
 from clinical_dbs_annotator.__main__ import main
 
 if __name__ == "__main__":

scripts/build_macos.py

@@ -4,11 +4,11 @@
 This script builds a standalone macOS .app bundle with all necessary resources.
 """
 
+import argparse
+import shutil
 import subprocess
 import sys
 from pathlib import Path
-import argparse
-import shutil
 
 # Get project root directory
 PROJECT_ROOT = Path(__file__).parent.parent
@@ -113,7 +113,7 @@ def build_macos_app(*, console: bool, onefile: bool):
     # Run PyInstaller
     try:
         subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
-        print(f"\n✓ Build successful!")
+        print("\n✓ Build successful!")
         if onefile:
             artifact_path = DIST_DIR / f"{name}.app"
             print(f"  Expected app bundle: {artifact_path}")

scripts/build_quick.py

@@ -38,17 +38,17 @@ def run_command(cmd, cwd=None):
         # Nuitka: onefile, no console
         cmd = [sys.executable, "scripts/build_windows_nuitka.py", "--onefile"]
         run_command(cmd, cwd=PROJECT_ROOT)
-    
+
     elif target == "windows-debug":
         # Nuitka: onedir, with console
         cmd = [sys.executable, "scripts/build_windows_nuitka.py", "--console"]
         run_command(cmd, cwd=PROJECT_ROOT)
-    
+
     elif target == "windows-pyinstaller":
         # Fallback to PyInstaller
         cmd = [sys.executable, "scripts/build_windows.py"]
         run_command(cmd, cwd=PROJECT_ROOT)
-    
+
     else:
         print(f"Unknown target: {target}")
         sys.exit(1)

scripts/build_windows.py

@@ -4,10 +4,10 @@
 This script builds a standalone Windows executable with all necessary resources.
 """
 
+import argparse
 import subprocess
 import sys
 from pathlib import Path
-import argparse
 
 # Get project root directory
 PROJECT_ROOT = Path(__file__).parent.parent
@@ -76,7 +76,7 @@ def build_windows_exe(*, console: bool, onefile: bool) -> bool:
     # Run PyInstaller
     try:
         subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
-        print(f"\n✓ Build successful!")
+        print("\n✓ Build successful!")
         if onefile:
             exe_path = DIST_DIR / f"{name}.exe"
         else:

scripts/build_windows_nuitka.py

@@ -14,7 +14,6 @@
 """
 
 import argparse
-import os
 import sys
 from pathlib import Path
 
@@ -143,19 +142,19 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
         import subprocess
         result = subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
         print("\n✅ Build completed successfully!")
-        
+
         # Show output location
         if onefile:
             exe_path = DIST_DIR / f"{NAME}.exe"
         else:
             exe_path = DIST_DIR / f"{NAME}.dist" / f"{NAME}.exe"
-        
+
         if exe_path.exists():
             print(f"📦 Executable: {exe_path}")
             print(f"📊 Size: {exe_path.stat().st_size / (1024*1024):.1f} MB")
         else:
             print("⚠️  Executable not found at expected location")
-            
+
     except subprocess.CalledProcessError as e:
         print(f"\n❌ Build failed with exit code {e.returncode}")
         sys.exit(1)
@@ -166,16 +165,16 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
 # -------------------------------------------------------------------------
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Build Windows executable with Nuitka")
-    parser.add_argument("--console", action="store_true", 
+    parser.add_argument("--console", action="store_true",
                        help="Include console window (useful for debugging)")
-    parser.add_argument("--onefile", action="store_true", 
+    parser.add_argument("--onefile", action="store_true",
                        help="Create single .exe file (default: directory bundle)")
-    
+
     args = parser.parse_args()
-    
+
     print("=== Clinical DBS Annotator Nuitka Build ===")
     print(f"Console: {'Yes' if args.console else 'No'}")
     print(f"Onefile: {'Yes' if args.onefile else 'No'}")
     print()
-    
+
     build_nuitka(console=args.console, onefile=args.onefile)

src/clinical_dbs_annotator/__init__.py

@@ -1,11 +1,11 @@
 """
 Clinical DBS Annotator - A tool for annotating DBS clinical programming sessions.
 
-This package provides a PyQt5-based GUI application for recording and managing
+This package provides a GUI for recording and managing
 clinical data during Deep Brain Stimulation programming sessions.
 """
 
-__version__ = "0.3_testing"
+__version__ = "0.3.0-beta"
 __app_name__ = "Clinical DBS Annotator"
 __author__ = "BML"
 

src/clinical_dbs_annotator/__main__.py

@@ -5,10 +5,10 @@
 and main window creation.
 """
 
-import sys
-import traceback
 import os
+import sys
 import tempfile
+import traceback
 
 from PyQt5.QtCore import Qt
 from PyQt5.QtWidgets import QApplication
@@ -57,8 +57,8 @@ def main() -> int:
 
         # Run application
         return app.exec_()
-        
-    except Exception as e:
+
+    except Exception:
         print("FATAL ERROR:")
         traceback.print_exc()
         try: