update project_name to dbs_annotator

Author: Lucia-Poma

README.md

@@ -2,7 +2,7 @@
 
 A desktop application for annotating Deep Brain Stimulation (DBS) clinical programming sessions. Built for clinicians and researchers working with DBS systems (Medtronic Percept and others).
 
-**Version:** derived from `clinical_dbs_annotator.__version__`
+**Version:** derived from `dbs_annotator.__version__`
 **Author:** Lucia Poma (lucia.poma@wysscenter.ch)
 
 ## For End Users
@@ -79,14 +79,14 @@ pip install -e .
 ```bash
 python run.py
 # or
-python -m clinical_dbs_annotator
+python -m dbs_annotator
 ```
 
 ### Project Structure
 
 ```
 App_ClinicalDBSAnnot/
-├── src/clinical_dbs_annotator/   # Application source code
+├── src/dbs_annotator/   # Application source code
 │   ├── models/                   #   Data models (session, scales, stimulation, electrode)
 │   ├── views/                    #   Qt views (step0-3, annotations, wizard window)
 │   ├── controllers/              #   Business logic (wizard controller)

dist/ClinicalDBSAnnot_Windows_v0_3_testing.exe

@@ -3,7 +3,7 @@
 from datetime import datetime
 from importlib import metadata
 
-_DIST_NAME = "clinical-dbs-annotator"
+_DIST_NAME = "dbs-annotator"
 
 project = "Clinical DBS Annotator"
 author = "Lucia Poma"

docs/conf.py

@@ -1,5 +1,5 @@
 [project]
-name = "clinical-dbs-annotator"
+name = "dbs-annotator"
 description = "A graphical user interface for annotating DBS clinical programming sessions"
 readme = "README.md"
 requires-python = ">=3.14"
@@ -51,22 +51,22 @@ docs = [
 ]
 
 [project.scripts]
-clinical-dbs-annotator = "clinical_dbs_annotator.__main__:main"
+dbs-annotator = "dbs_annotator.__main__:main"
 
 [project.urls]
-Homepage = "https://github.com/bml/clinical-dbs-annotator"
-Repository = "https://github.com/bml/clinical-dbs-annotator"
-Documentation = "https://github.com/bml/clinical-dbs-annotator/blob/main/README.md"
+Homepage = "https://github.com/bml/dbs-annotator"
+Repository = "https://github.com/bml/dbs-annotator"
+Documentation = "https://github.com/bml/dbs-annotator/blob/main/README.md"
 
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.version]
-path = "src/clinical_dbs_annotator/__init__.py"
+path = "src/dbs_annotator/__init__.py"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/clinical_dbs_annotator"]
+packages = ["src/dbs_annotator"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -75,7 +75,7 @@ python_classes = ["Test*"]
 python_functions = ["test_*"]
 addopts = [
     "--verbose",
-    "--cov=clinical_dbs_annotator",
+    "--cov=dbs_annotator",
     "--cov-report=html",
     "--cov-report=term-missing",
 ]

pyproject.toml

@@ -10,7 +10,7 @@
 
 import sys
 
-from clinical_dbs_annotator.__main__ import main
+from dbs_annotator.__main__ import main
 
 if __name__ == "__main__":
     sys.exit(main())

run.py

@@ -5,59 +5,57 @@
 #define AppName "ClinicalDBSAnnotator"
 #define AppVersion "0.3.0"
 #define AppPublisher "Brain Modulation Lab"
-#define AppURL "https://github.com/bml/clinical-dbs-annotator"
+#define AppURL "https://github.com/bml/dbs-annotator"
 #define AppExeName "ClinicalDBSAnnotator_Windows_0_3_0.exe"
 
 [Setup]
-AppId={{{{A1B2C3D4-E5F6-7890-ABCD-EF1234567890}}}}
-AppName={{{{#AppName}}}}
-AppVersion={{{{#AppVersion}}}}
-AppPublisher={{{{#AppPublisher}}}}
-AppPublisherURL={{{{#AppURL}}}}
-AppSupportURL={{{{#AppURL}}}}
-AppUpdatesURL={{{{#AppURL}}}}
-DefaultDirName={{{{autopf}}}}\{{{{{#AppName}}}}}
-DefaultGroupName={{{{#AppName}}}}
+AppId={{A1B2C3D4-E5F6-7890-ABCD-EF1234567890}
+AppName={#AppName}
+AppVersion={#AppVersion}
+AppPublisher={#AppPublisher}
+AppPublisherURL={#AppURL}
+AppSupportURL={#AppURL}
+AppUpdatesURL={#AppURL}
+DefaultDirName={autopf}\{#AppName}
+DefaultGroupName={#AppName}
 AllowNoIcons=yes
 OutputDir=installer_output
-OutputBaseFilename={{{{#AppName}}}}_Setup_{{{{{#AppVersion}}}}_Windows
+OutputBaseFilename={#AppName}_Setup_{#AppVersion}_Windows
 Compression=lzma2/max
 SolidCompression=yes
 WizardStyle=Modern
-WizardImageFile=..\icons\logoneutral.bmp
-WizardSmallImageFile=..\icons\logoneutral-small.bmp
 SetupIconFile=..\icons\logoneutral.ico
-UninstallDisplayIcon={{{{app}}}}\{{{{{#AppExeName}}}}}
+UninstallDisplayIcon={app}\{#AppExeName}
 ChangesAssociations=yes
 
 [Languages]
 Name: "english"; MessagesFile: "compiler:Default.isl"
 Name: "italian"; MessagesFile: "compiler:Languages\Italian.isl"
 
 [Tasks]
-Name: "desktopicon"; Description: "{{{{cm:CreateDesktopIcon}}}}"; GroupDescription: "{{{{cm:AdditionalIcons}}}}"
-Name: "quicklaunchicon"; Description: "{{{{cm:CreateQuickLaunchIcon}}}}"; GroupDescription: "{{{{cm:AdditionalIcons}}}}"; OnlyBelowVersion: 6.1
+Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"
+Name: "quicklaunchicon"; Description: "{cm:CreateQuickLaunchIcon}"; GroupDescription: "{cm:AdditionalIcons}"; OnlyBelowVersion: 6.1
 
 [Files]
 ; Main application files from PyInstaller onedir build
-Source: "dist\ClinicalDBSAnnotator_Windows_0_3_0\*"; DestDir: "{{{{app}}}}"; Flags: ignoreversion recursesubdirs createallsubdirs
+Source: "dist\ClinicalDBSAnnotator_Windows_0_3_0\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
 ; Icon file for shortcuts
-Source: "..\icons\logoneutral.ico"; DestDir: "{{{{app}}}}"; Flags: ignoreversion
+Source: "..\icons\logoneutral.ico"; DestDir: "{app}"; Flags: ignoreversion
 
 [Icons]
-Name: "{{{{group}}}}\{{{{{#AppName}}}}"; Filename: "{{{{app}}}}\{{{{{#AppExeName}}}}"; IconFilename: "{{{{app}}}}\logoneutral.ico"
-Name: "{{{{commondesktop}}}}\{{{{{#AppName}}}}"; Filename: "{{{{app}}}}\{{{{{#AppExeName}}}}"; IconFilename: "{{{{app}}}}\logoneutral.ico"; Tasks: desktopicon
-Name: "{{{{userappdata}}}}\Microsoft\Internet Explorer\Quick Launch\{{{{{#AppName}}}}"; Filename: "{{{{app}}}}\{{{{{#AppExeName}}}}"; IconFilename: "{{{{app}}}}\logoneutral.ico"; Tasks: quicklaunchicon
+Name: "{group}\{#AppName}"; Filename: "{app}\{#AppExeName}"; IconFilename: "{app}\logoneutral.ico"
+Name: "{commondesktop}\{#AppName}"; Filename: "{app}\{#AppExeName}"; IconFilename: "{app}\logoneutral.ico"; Tasks: desktopicon
+Name: "{userappdata}\Microsoft\Internet Explorer\Quick Launch\{#AppName}"; Filename: "{app}\{#AppExeName}"; IconFilename: "{app}\logoneutral.ico"; Tasks: quicklaunchicon
 
 [Run]
-Filename: "{{{{app}}}}\{{{{{#AppExeName}}}}"; Description: "{{{{cm:LaunchProgram,{{{{#StringChange(AppName, '&', '&&')}}}}}}"; Flags: nowait postinstall skipifsilent
+Filename: "{app}\{#AppExeName}"; Description: "{cm:LaunchProgram,{#StringChange(AppName, '&', '&&')}}"; Flags: nowait postinstall skipifsilent
 
 [Registry]
 ; File association for .tsv annotation files
 Root: HKCR; Subkey: ".tsv\OpenWithProgids"; ValueType: string; ValueName: "ClinicalDBSAnnotator.tsv"; ValueData: ""; Flags: uninsdeletevalue
 Root: HKCR; Subkey: "ClinicalDBSAnnotator.tsv"; ValueType: string; ValueName: ""; ValueData: "Clinical DBS Annotator File"; Flags: uninsdeletekey
-Root: HKCR; Subkey: "ClinicalDBSAnnotator.tsv\DefaultIcon"; ValueType: string; ValueName: ""; ValueData: "{{{{app}}}}\logoneutral.ico,0"
-Root: HKCR; Subkey: "ClinicalDBSAnnotator.tsv\shell\open\command"; ValueType: string; ValueName: ""; ValueData: '"{{{{app}}}}\{{{{{#AppExeName}}}}" "%1"'
+Root: HKCR; Subkey: "ClinicalDBSAnnotator.tsv\DefaultIcon"; ValueType: string; ValueName: ""; ValueData: "{app}\logoneutral.ico,0"
+Root: HKCR; Subkey: "ClinicalDBSAnnotator.tsv\shell\open\command"; ValueType: string; ValueName: ""; ValueData: ""{app}\{#AppExeName}" "%1""
 
 [UninstallDelete]
-Type: filesandordirs; Name: "{{{{app}}}}
+Type: filesandordirs; Name: "{app}"

scripts/ClinicalDBSAnnotator.iss

@@ -23,7 +23,7 @@
 
 
 def _read_version() -> str:
-    init_path = SRC_DIR / "clinical_dbs_annotator" / "__init__.py"
+    init_path = SRC_DIR / "dbs_annotator" / "__init__.py"
     text = init_path.read_text(encoding="utf-8")
     m = re.search(
         r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE
@@ -72,7 +72,7 @@ def build_macos_app(*, console: bool, onefile: bool):
     name = f"{APP_NAME}_{PLATFORM}_{VERSION.replace('.', '_')}"
     entrypoint = PROJECT_ROOT / "run.py"
     styles_dir = PROJECT_ROOT / "styles"
-    config_dir = SRC_DIR / "clinical_dbs_annotator" / "config"
+    config_dir = SRC_DIR / "dbs_annotator" / "config"
 
     icon_icns = ICONS_DIR / "logoneutral.icns"
     icon_fallback = ICONS_DIR / "logoneutral.ico"
@@ -98,11 +98,11 @@ def build_macos_app(*, console: bool, onefile: bool):
         "--hidden-import=pandas",
         "--hidden-import=openpyxl",
         "--hidden-import=xlrd",
-        "--hidden-import=PySide6.QtCore",
-        "--hidden-import=PySide6.QtGui",
-        "--hidden-import=PySide6.QtWidgets",
+        "--hidden-import=dbs_annotator",
+        "--collect-all=PySide6",
         "--exclude-module=PySide6.QtWebEngineWidgets",
         "--exclude-module=PySide6.QtWebEngineCore",
+        "--osx-bundle-identifier=com.bml.dbs-annotator",
         # Add data files (macOS uses : separator)
         f"--add-data={ICONS_DIR / 'logoneutral.ico'}:icons",
         f"--add-data={ICONS_DIR / 'logoneutral.png'}:icons",
@@ -124,6 +124,16 @@ def build_macos_app(*, console: bool, onefile: bool):
     else:
         cmd.append("--windowed")
 
+    # Add package metadata for version detection (macOS venv layout)
+    venv_lib = PROJECT_ROOT / ".venv" / "lib"
+    if venv_lib.exists():
+        # macOS: .venv/lib/pythonX.Y/site-packages
+        dist_info_dirs = list(
+            venv_lib.glob("python*/site-packages/dbs_annotator*.dist-info")
+        )
+        if dist_info_dirs:
+            cmd.append(f"--add-data={dist_info_dirs[0]}:.")
+
     # Run PyInstaller
     try:
         subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
@@ -168,8 +178,8 @@ def main():
         ICONS_DIR / "logoneutral.png",
         PROJECT_ROOT / "styles" / "dark_theme.qss",
         PROJECT_ROOT / "styles" / "light_theme.qss",
-        SRC_DIR / "clinical_dbs_annotator" / "config" / "clinical_presets.json",
-        SRC_DIR / "clinical_dbs_annotator" / "config" / "session_scales_presets.json",
+        SRC_DIR / "dbs_annotator" / "config" / "clinical_presets.json",
+        SRC_DIR / "dbs_annotator" / "config" / "session_scales_presets.json",
     ]
 
     for path in required_files:

scripts/build_macos.py

@@ -21,7 +21,7 @@
 
 
 def _read_version() -> str:
-    init_path = SRC_DIR / "clinical_dbs_annotator" / "__init__.py"
+    init_path = SRC_DIR / "dbs_annotator" / "__init__.py"
     text = init_path.read_text(encoding="utf-8")
     m = re.search(
         r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE
@@ -41,7 +41,7 @@ def build_windows_exe(*, console: bool, onefile: bool) -> bool:
     name = f"{APP_NAME}_{PLATFORM}_{VERSION.replace('.', '_')}"
     entrypoint = PROJECT_ROOT / "run.py"
     styles_dir = PROJECT_ROOT / "styles"
-    config_dir = SRC_DIR / "clinical_dbs_annotator" / "config"
+    config_dir = SRC_DIR / "dbs_annotator" / "config"
 
     cmd = [
         sys.executable,
@@ -58,6 +58,7 @@ def build_windows_exe(*, console: bool, onefile: bool) -> bool:
         "--hidden-import=pandas",
         "--hidden-import=openpyxl",
         "--hidden-import=xlrd",
+        "--hidden-import=dbs_annotator",
     ]
 
     if onefile:
@@ -84,6 +85,13 @@ def build_windows_exe(*, console: bool, onefile: bool) -> bool:
         ]
     )
 
+    # Add package metadata for version detection
+    venv_site_packages = PROJECT_ROOT / ".venv" / "Lib" / "site-packages"
+    dist_info_dirs = list(venv_site_packages.glob("dbs_annotator*.dist-info"))
+    if dist_info_dirs:
+        dist_info = dist_info_dirs[0]
+        cmd.append(f"--add-data={dist_info};.")
+
     try:
         subprocess.run(cmd, check=True, cwd=PROJECT_ROOT)
         print("\n✓ Build successful!")

scripts/build_windows.py

@@ -25,14 +25,14 @@
 BUILD_DIR = PROJECT_ROOT / "build"
 ICONS_DIR = PROJECT_ROOT / "icons"
 STYLES_DIR = PROJECT_ROOT / "styles"
-CONFIG_DIR = SRC_DIR / "clinical_dbs_annotator" / "config"
+CONFIG_DIR = SRC_DIR / "dbs_annotator" / "config"
 
 NAME = "ClinicalDBSAnnotator"
 ENTRYPOINT = PROJECT_ROOT / "run.py"
 
 
 def _read_version() -> str:
-    init_path = SRC_DIR / "clinical_dbs_annotator" / "__init__.py"
+    init_path = SRC_DIR / "dbs_annotator" / "__init__.py"
     text = init_path.read_text(encoding="utf-8")
     m = re.search(
         r'^__version__\s*=\s*["\']([^"\']+)["\']\s*$', text, flags=re.MULTILINE