Merge pull request #24 from richardkoehler/feat/format-code

feat: format code

Author: Lucia-Poma

.github/workflows/ci.yml

@@ -31,6 +31,10 @@ jobs:
         run: |
           uv run ruff check --exclude tests .
 
+      - name: Run ruff format (check)
+        run: |
+          uv run ruff format --check --exclude tests .
+
       # Tests are temporarily disabled in CI until they are ready.
       # To re-enable, uncomment the step below once tests are stable.
       # - name: Run pytest

.pre-commit-config.yaml

@@ -1,6 +1,12 @@
 repos:
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.11.5
+    hooks:
+      - id: uv-lock
+      
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.15.9
     hooks:
+      - id: ruff-format
       - id: ruff-check
         args: ["--fix", "--exclude", "tests"]

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"
+requires-python = ">=3.14"
 authors = [
     { name = "Lucia Poma", email = "lucia.poma@wysscenter.ch" }
 ]
@@ -14,9 +14,6 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
     "Programming Language :: Python :: 3",
-    "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",

scripts/build_macos.py

@@ -21,10 +21,13 @@
 APP_NAME = "ClinicalDBSAnnot"
 PLATFORM = "macOS"
 
+
 def _read_version() -> str:
     init_path = SRC_DIR / "clinical_dbs_annotator" / "__init__.py"
     text = init_path.read_text(encoding="utf-8")
-    m = re.search(r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE)
+    m = re.search(
+        r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE
+    )
     if not m:
         raise RuntimeError(f"Could not determine version from {init_path}")
     return m.group(1)
@@ -141,8 +144,14 @@ def build_macos_app(*, console: bool, onefile: bool):
 def main():
     """Main entry point."""
     parser = argparse.ArgumentParser()
-    parser.add_argument("--console", action="store_true", help="Build with console window")
-    parser.add_argument("--onedir", action="store_true", help="Build as a folder (onedir) instead of a single bundle (onefile)")
+    parser.add_argument(
+        "--console", action="store_true", help="Build with console window"
+    )
+    parser.add_argument(
+        "--onedir",
+        action="store_true",
+        help="Build as a folder (onedir) instead of a single bundle (onefile)",
+    )
     parser.add_argument(
         "--mac-logo-png",
         type=Path,

scripts/build_quick.py

@@ -14,6 +14,7 @@
 
 PROJECT_ROOT = Path(__file__).resolve().parent.parent
 
+
 def run_command(cmd, cwd=None):
     """Run a command and handle errors."""
     print(f"Running: {' '.join(cmd)}")
@@ -24,6 +25,7 @@ def run_command(cmd, cwd=None):
         print(f"❌ Failed with exit code {e.returncode}")
         sys.exit(1)
 
+
 if __name__ == "__main__":
     if len(sys.argv) < 2:
         print("Usage: python scripts/build_quick.py <target>")

scripts/build_windows.py

@@ -19,10 +19,13 @@
 APP_NAME = "ClinicalDBSAnnotator"
 PLATFORM = "Windows"
 
+
 def _read_version() -> str:
     init_path = SRC_DIR / "clinical_dbs_annotator" / "__init__.py"
     text = init_path.read_text(encoding="utf-8")
-    m = re.search(r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE)
+    m = re.search(
+        r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE
+    )
     if not m:
         raise RuntimeError(f"Could not determine version from {init_path}")
     return m.group(1)
@@ -41,7 +44,9 @@ def build_windows_exe(*, console: bool, onefile: bool) -> bool:
     config_dir = SRC_DIR / "clinical_dbs_annotator" / "config"
 
     cmd = [
-        sys.executable, "-m", "PyInstaller",
+        sys.executable,
+        "-m",
+        "PyInstaller",
         "--noconfirm",
         "--clean",
         f"--name={name}",
@@ -97,8 +102,14 @@ def build_windows_exe(*, console: bool, onefile: bool) -> bool:
 def main():
     """Main entry point."""
     parser = argparse.ArgumentParser()
-    parser.add_argument("--console", action="store_true", help="Build with console window")
-    parser.add_argument("--onedir", action="store_true", help="Build as a folder (onedir) instead of a single exe (onefile)")
+    parser.add_argument(
+        "--console", action="store_true", help="Build with console window"
+    )
+    parser.add_argument(
+        "--onedir",
+        action="store_true",
+        help="Build as a folder (onedir) instead of a single exe (onefile)",
+    )
     args = parser.parse_args()
 
     if not (ICONS_DIR / "logoneutral.ico").exists():

scripts/build_windows_nuitka.py

@@ -30,10 +30,13 @@
 NAME = "ClinicalDBSAnnotator"
 ENTRYPOINT = PROJECT_ROOT / "run.py"
 
+
 def _read_version() -> str:
     init_path = SRC_DIR / "clinical_dbs_annotator" / "__init__.py"
     text = init_path.read_text(encoding="utf-8")
-    m = re.search(r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE)
+    m = re.search(
+        r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE
+    )
     if not m:
         raise RuntimeError(f"Could not determine version from {init_path}")
     return m.group(1)
@@ -80,6 +83,7 @@ def _base_version(version: str) -> str:
     "imageformats",
 ]
 
+
 def build_nuitka(console: bool = False, onefile: bool = False) -> None:
     """Build the executable with Nuitka."""
     DIST_DIR.mkdir(exist_ok=True)
@@ -118,20 +122,24 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
 
     cmd.append("--follow-imports")
 
-    cmd.extend([
-        "--enable-plugin=pyside6",
-    ])
+    cmd.extend(
+        [
+            "--enable-plugin=pyside6",
+        ]
+    )
 
     icon_path = ICONS_DIR / "logoneutral.ico"
     if icon_path.exists():
         cmd.append(f"--windows-icon-from-ico={icon_path}")
 
-    cmd.extend([
-        "--windows-company-name=Brain Modulation Lab",
-        "--windows-product-name=Clinical DBS Annotator",
-        f"--windows-file-version={BASE_VERSION}",
-        f"--windows-product-version={BASE_VERSION}",
-    ])
+    cmd.extend(
+        [
+            "--windows-company-name=Brain Modulation Lab",
+            "--windows-product-name=Clinical DBS Annotator",
+            f"--windows-file-version={BASE_VERSION}",
+            f"--windows-product-version={BASE_VERSION}",
+        ]
+    )
 
     cmd.append(str(ENTRYPOINT))
 
@@ -141,6 +149,7 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
 
     try:
         import subprocess
+
         subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
         print("\n✅ Build completed successfully!")
 
@@ -151,7 +160,7 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
 
         if exe_path.exists():
             print(f"📦 Executable: {exe_path}")
-            print(f"📊 Size: {exe_path.stat().st_size / (1024*1024):.1f} MB")
+            print(f"📊 Size: {exe_path.stat().st_size / (1024 * 1024):.1f} MB")
         else:
             print("⚠️  Executable not found at expected location")
 
@@ -162,12 +171,19 @@ def build_nuitka(console: bool = False, onefile: bool = False) -> None:
         print("\n❌ Nuitka not found. Install it with: pip install nuitka")
         sys.exit(1)
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Build Windows executable with Nuitka")
-    parser.add_argument("--console", action="store_true",
-                       help="Include console window (useful for debugging)")
-    parser.add_argument("--onefile", action="store_true",
-                       help="Create single .exe file (default: directory bundle)")
+    parser.add_argument(
+        "--console",
+        action="store_true",
+        help="Include console window (useful for debugging)",
+    )
+    parser.add_argument(
+        "--onefile",
+        action="store_true",
+        help="Create single .exe file (default: directory bundle)",
+    )
 
     args = parser.parse_args()
 

src/clinical_dbs_annotator/config.py

@@ -27,8 +27,8 @@
 
 # Responsive window size ratios based on screen size
 RESPONSIVE_WINDOW_RATIOS = {
-    "small": {"width": 0.9, "height": 0.85},   # < 1400px width
-    "medium": {"width": 0.85, "height": 0.8}, # 1400-1919px width
+    "small": {"width": 0.9, "height": 0.85},  # < 1400px width
+    "medium": {"width": 0.85, "height": 0.8},  # 1400-1919px width
     "large": {"width": 0.75, "height": 0.75},  # >= 1920px width
 }
 
@@ -99,33 +99,34 @@
 
 CLINICAL_SCALES_PRESETS: dict[str, list[str]] = {
     "OCD": [
-        "Y-BOCS",   # Yale–Brown Obsessive–Compulsive Scale
-        "Y-BOCS-o", "Y-BOCS-c",
-        "MADRS",    # Montgomery–Åsberg Depression Rating Scale
-        "OCI-R",    # Obsessive–Compulsive Inventory – Revised
+        "Y-BOCS",  # Yale–Brown Obsessive–Compulsive Scale
+        "Y-BOCS-o",
+        "Y-BOCS-c",
+        "MADRS",  # Montgomery–Åsberg Depression Rating Scale
+        "OCI-R",  # Obsessive–Compulsive Inventory – Revised
     ],
     "MDD": [
-        "MADRS",    # Montgomery–Åsberg Depression Rating Scale
-        "HAM-D",    # Hamilton Depression Rating Scale
-        "BDI-II",   # Beck Depression Inventory – Second Edition
+        "MADRS",  # Montgomery–Åsberg Depression Rating Scale
+        "HAM-D",  # Hamilton Depression Rating Scale
+        "BDI-II",  # Beck Depression Inventory – Second Edition
     ],
     "PD": [
         "MDS-UPDRS",  # Movement Disorder Society – Unified Parkinson’s Disease Rating Scale
         "UPDRS-III",  # Unified Parkinson’s Disease Rating Scale part III
-        "PDQ-39",     # Parkinson’s Disease Questionnaire (39-item)
-        "UDysRS",     # Unified Dyskinesia Rating Scale
+        "PDQ-39",  # Parkinson’s Disease Questionnaire (39-item)
+        "UDysRS",  # Unified Dyskinesia Rating Scale
     ],
     "ET": [
         "FTM-TRS",  # Fahn–Tolosa–Marin Tremor Rating Scale
-        "TETRAS",   # The Essential Tremor Rating Assessment Scale
+        "TETRAS",  # The Essential Tremor Rating Assessment Scale
     ],
     "Dystonia": [
         "BFMDRS",  # Burke–Fahn–Marsden Dystonia Rating Scale
         "TWSTRS",  # Toronto Western Spasmodic Torticollis Rating Scale
     ],
     "TS": [
-        "YGTSS",   # Yale Global Tic Severity Scale
-        "PUTS",    # Premonitory Urge for Tics Scale
+        "YGTSS",  # Yale Global Tic Severity Scale
+        "PUTS",  # Premonitory Urge for Tics Scale
         "TS-CGI",  # Tourette Syndrome Clinical Global Impression
         "Y-BOCS",  # Yale–Brown Obsessive–Compulsive Scale
     ],