chore: migrate from PyQt5 to PySide6

- Replace all PyQt5 imports with PySide6 equivalents
- Update pyqtSignal to Signal, exec_() to exec(), and scoped enums
- Update build scripts for PySide6
- Add Sphinx documentation source files
- Exclude docs build artifacts from version control

Author: richardkoehler

.gitignore

@@ -1,43 +1,174 @@
-# Python-generated files
+# Byte-compiled / optimized / DLL files
 __pycache__/
-*.py[oc]
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
 build/
-#dist/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
 wheels/
-*.egg-info
-*.docx
-*.spec
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
 
-# Virtual environments
-.venv
-venv/
-env/
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
 
-# Testing
-# tests/  # Uncommented to allow tests in version control
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
 
-.pytest_cache/
-.coverage
+# Unit test / coverage reports
 htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
 *.cover
+*.py,cover
 .hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
 
-# IDEs
-.vscode/
-.idea/
-settings.json
-*.swp
-*.swo
-*~
-
-# OS
-.DS_Store
-Thumbs.db
-
-# Directories to ignore
-archive/
-prove/
-
-# Data files 
-# *.tsv
-# *.csv
+# PyPI configuration file
+.pypirc

.readthedocs.yaml

@@ -4,11 +4,14 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  jobs:
+    pre_install:
+      - python -m pip install --upgrade pip
+      - python -m pip install uv
+    install:
+      - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv pip install -r docs/requirements.txt
+      - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv pip install .
 
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false
-
-python:
-  install:
-    - requirements: docs/requirements.txt

README.md

@@ -1,9 +1,9 @@
 # Clinical DBS Annotator
 
-A desktop application for annotating Deep Brain Stimulation (DBS) clinical programming sessions. Built with PyQt5 for clinicians and researchers working with DBS systems (Medtronic Percept and others).
+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:** 0.3 (testing)
-**Author:** Lucia Poma (lpoma@mgh.harvard.edu) — Brain Modulation Lab, MGH
+**Version:** 0.3.0-beta
+**Author:** Lucia Poma (lucia.poma@wysscenter.ch)
 
 ## For End Users
 
@@ -88,7 +88,7 @@ python -m clinical_dbs_annotator
 App_ClinicalDBSAnnot/
 ├── src/clinical_dbs_annotator/   # Application source code
 │   ├── models/                   #   Data models (session, scales, stimulation, electrode)
-│   ├── views/                    #   PyQt5 views (step0-3, annotations, wizard window)
+│   ├── views/                    #   Qt views (step0-3, annotations, wizard window)
 │   ├── controllers/              #   Business logic (wizard controller)
 │   ├── ui/                       #   Reusable UI widgets and dialogs
 │   ├── utils/                    #   Utilities (export, themes, responsive, resources)
@@ -130,5 +130,4 @@ MIT License — see [LICENSE](LICENSE) for details.
 
 ## Contact
 
-Lucia Poma — lpoma@mgh.harvard.edu
-Brain Modulation Lab, Massachusetts General Hospital
+Lucia Poma — lucia.poma@wysscenter.ch

docs/conf.py

@@ -1,12 +1,14 @@
-import os
-import sys
+from __future__ import annotations
 
-sys.path.insert(0, os.path.abspath("../src"))
+from datetime import datetime
+from importlib import metadata
+
+_DIST_NAME = "clinical-dbs-annotator"
 
 project = "Clinical DBS Annotator"
-copyright = "2025, Lucia Poma — Brain Modulation Lab, MGH"
 author = "Lucia Poma"
-release = "0.3"
+release = metadata.version(_DIST_NAME)
+copyright = f"2025-{datetime.now().year}, {author}"
 
 extensions = [
     "sphinx.ext.autodoc",
@@ -22,7 +24,6 @@
 
 html_theme_options = {
     "logo_only": False,
-    "display_version": True,
     "prev_next_buttons_location": "bottom",
     "style_external_links": True,
     "collapse_navigation": False,

docs/contributing.rst

@@ -1,5 +1,5 @@
 Contributing to Clinical DBS Annotator
-====================================
+======================================
 
 We welcome contributions to the Clinical DBS Annotator! This document provides guidelines for contributors who want to help improve this open-source software for deep brain stimulation research.
 
@@ -15,7 +15,7 @@ Prerequisites
 
 To contribute to this project, you should have:
 
-- Python 3.8 or higher
+- Python 3.11 or higher
 - Git installed and configured
 - Basic knowledge of PyQt5/PyQt6 (helpful but not required)
 - Understanding of deep brain stimulation concepts (helpful but not required)
@@ -30,31 +30,16 @@ Development Setup
       git clone https://github.com/yourusername/App_ClinicalDBSAnnot.git
       cd App_ClinicalDBSAnnot
 
-2. **Create a virtual environment**:
-
-   .. code-block:: bash
-
-      python -m venv .venv
-      source .venv/bin/activate  # On Windows: .venv\Scripts\activate
-
-3. **Install dependencies**:
-
+2. **Make sure uv is installed. Then, create a virtual environment and install dependencies**:
    .. code-block:: bash
+      
+      uv sync
 
-      pip install -r requirements.txt
-      pip install -r docs/requirements.txt
-
-4. **Install in development mode**:
+3. **Run the application** to verify installation:
 
    .. code-block:: bash
 
-      pip install -e .
-
-5. **Run the application** to verify installation:
-
-   .. code-block:: bash
-
-      python -m clinical_dbs_annotator
+      uv run python -m clinical_dbs_annotator
 
 Types of Contributions
 ----------------------
@@ -110,7 +95,7 @@ We accept code contributions through pull requests. Please follow these guidelin
 5. **Push to your fork** and create a pull request
 
 Documentation Improvements
-~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Documentation is crucial for research software. We welcome:
 
@@ -275,7 +260,7 @@ We are committed to providing a welcoming and inclusive environment. Please:
 - Be patient with different perspectives
 
 Communication Channels
-~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~
 
 - **GitHub Issues**: For bug reports and feature requests
 - **GitHub Discussions**: For general questions and ideas
@@ -345,7 +330,7 @@ We use GitHub Actions for:
 - **Package building**
 
 Specialized Contributions
-------------------------
+--------------------------
 
 Clinical Domain Experts
 ~~~~~~~~~~~~~~~~~~~~~~~

docs/index.rst

@@ -20,7 +20,7 @@ Developed at the **Brain Modulation Lab, Massachusetts General Hospital**.
 
 .. note::
    Version **0.3 (testing)** — Windows installer available.
-   Contact: lpoma@mgh.harvard.edu
+   Contact: lucia.poma@wysscenter.ch
 
 ----
 

docs/quickstart.rst

@@ -72,5 +72,5 @@ Next Steps
 ----------
 
 * If you are starting a programming session → :doc:`workflow_session`
-* If you want to generate a longitudinal report → :doc:`workflow_longitudinal`
+* If you want to generate a longitudinal report → :doc:`longitudinal_report`
 * If you want to record free annotations → :doc:`workflow_annotations`

docs/requirements.txt

@@ -1,2 +1,2 @@
-sphinx>=7.0
-sphinx-rtd-theme>=2.0
+"sphinx>=9.0.4"
+"sphinx-rtd-theme>=3.1.0"