Brain-Modulation-Lab · richardkoehler · Apr 20, 2026 · Apr 20, 2026 · Apr 20, 2026
diff --git a/.github/workflows/prepare-release.yml b/.github/workflows/prepare-release.yml
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
     inputs:
       version:
-        description: "Version (X.Y.Z, no v prefix)"
+        description: "PEP 440 version (e.g. 0.4.0 or 0.4.0a1), no v prefix"
         required: true
         type: string
       release_date:

diff --git a/.gitignore b/.gitignore
@@ -68,6 +68,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+# Autosummary stubs (generated by sphinx-build / make html; do not commit)
 docs/_autosummary/
 
 # PyBuilder

diff --git a/.python-version b/.python-version
@@ -1 +1 @@
-3.12
+3.12
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,6 +1,6 @@
-# Contributing to Clinical DBS Annotator
+# Contributing to 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.
+We welcome contributions to DBS Annotator! This document provides guidelines for contributors who want to help improve this open-source software for deep brain stimulation research.
 
 For detailed guidelines, please see the [Contributing Guide](docs/contributing.rst).
 

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2025 BML
+Copyright (c) 2026 Wyss Center
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# Clinical DBS Annotator
+# DBS Annotator
 
 [![CI](https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot/actions/workflows/ci.yml/badge.svg)](https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot/actions/workflows/ci.yml)
 [![Docs Health](https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot/actions/workflows/docs-health.yml/badge.svg)](https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot/actions/workflows/docs-health.yml)
@@ -7,7 +7,7 @@
 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 `dbs_annotator.__version__`
-**Author:** Lucia Poma (lucia.poma@wysscenter.ch)
+**Publisher:** Wyss Center (contact: lucia.poma@wysscenter.ch)
 
 ## For End Users
 
@@ -209,4 +209,4 @@ MIT License — see [LICENSE](LICENSE) for details.
 
 ## Contact
 
-Lucia Poma — lucia.poma@wysscenter.ch
+Wyss Center — lucia.poma@wysscenter.ch
diff --git a/docs/conf.py b/docs/conf.py
@@ -15,8 +15,8 @@
 
 _DIST_NAME = "dbs-annotator"
 
-project = "Clinical DBS Annotator"
-author = "Lucia Poma"
+project = "DBS Annotator"
+author = "Wyss Center"
 release = metadata.version(_DIST_NAME)
 version = ".".join(release.split(".")[:2])
 copyright = f"2025-{datetime.now().year}, {author}"

diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -1,9 +1,9 @@
-Contributing to Clinical DBS Annotator
+Contributing to DBS Annotator
 ======================================
 
-We welcome contributions to the Clinical DBS Annotator! This page is the
-authoritative contributor guide for the repository. The short
-``CONTRIBUTING.md`` at the repository root is a pointer into this page.
+We welcome contributions to DBS Annotator! This page is the authoritative
+contributor guide for the repository. The short ``CONTRIBUTING.md`` at the
+repository root is a pointer into this page.
 
 .. contents::
    :local:
@@ -489,9 +489,8 @@ For data-science contributions:
 Thank You
 ---------
 
-Thank you for considering contributing to the Clinical DBS Annotator! Your
-contributions help make deep brain stimulation research more accessible and
-reproducible.
+Thank you for considering contributing to DBS Annotator! Your contributions
+help make deep brain stimulation research more accessible and reproducible.
 
 For questions about contributing, please open an issue or start a discussion
 on GitHub.
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,16 +1,16 @@
-.. Clinical DBS Annotator documentation master file
+.. DBS Annotator documentation master file
 
-Clinical DBS Annotator
-======================
+DBS Annotator
+=============
 
 .. image:: _static/logo.png
-   :alt: Clinical DBS Annotator
+   :alt: DBS Annotator
    :align: center
    :width: 180px
 
 |
 
-**Clinical DBS Annotator** is a desktop application for recording and analysing
+**DBS Annotator** is a desktop application for recording and analysing
 Deep Brain Stimulation (DBS) clinical programming sessions.  It guides the
 clinician or researcher through the full session workflow — from initial
 electrode configuration and baseline scales, through real-time stimulation

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -1,7 +1,7 @@
 Installation
 ============
 
-Clinical DBS Annotator ships as a **single self-contained executable** — no
+DBS Annotator ships as a **single self-contained executable** — no
 Python, no libraries, no system configuration required.
 
 ----
@@ -26,7 +26,7 @@ Steps
    b. Follow the on-screen prompts (Next → Next → Finish).
    c. A shortcut appears on your Desktop and in the Start Menu.
 
-3. **If you received a standalone** ``ClinicalDBSAnnot.exe`` **file:**
+3. **If you received a standalone** ``DBSAnnotator.exe`` **file:**
 
    a. Copy the file to any folder you prefer (e.g. ``C:\Users\YourName\DBS_Tool\``).
    b. Double-click to launch — no further steps needed.
@@ -62,7 +62,7 @@ macOS
    below assume a ``.dmg`` disk image has been provided.
 
 1. Open the ``.dmg`` file.
-2. Drag **ClinicalDBSAnnot** to your *Applications* folder.
+2. Drag **DBSAnnotator** to your *Applications* folder.
 3. On first launch, right-click the app icon → **Open** → **Open** again in the
    dialog.  This is required once because the app is not notarised.
 

diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -9,7 +9,7 @@ choosing the right workflow for your needs.
 Launching the Application
 --------------------------
 
-Double-click **ClinicalDBSAnnot.exe** (or the Desktop shortcut).  The main
+Double-click **DBSAnnotator.exe** (or the Desktop shortcut).  The main
 window opens, showing the **Home screen**.
 
 .. image:: _static/home_screen.png

diff --git a/docs/releasing.rst b/docs/releasing.rst
@@ -11,7 +11,8 @@ Version sources
 Keep these in sync whenever you cut a release:
 
 - ``__version__`` in ``src/dbs_annotator/__init__.py`` — Hatch reads this as the
-  ``dbs-annotator`` distribution version.
+  ``dbs-annotator`` distribution version (PEP 440: stable ``X.Y.Z`` or prereleases
+  such as ``X.Y.Za1``, ``X.Y.Zb2``, ``X.Y.Zrc1``).
 - ``version`` under ``[tool.briefcase]`` in ``pyproject.toml`` (Briefcase requires a static string)
 
 The automation below updates both, then runs `Towncrier`_ to fold Markdown fragments
@@ -55,8 +56,23 @@ Option A — Prepare the release PR locally
    .. code-block:: bash
 
       uv sync --dev
-      uv run python scripts/release_prepare.py X.Y.Z --dry-run
-      uv run python scripts/release_prepare.py X.Y.Z --commit
+      uv run python scripts/release_prepare.py 0.4.0 --dry-run
+      uv run python scripts/release_prepare.py 0.4.0rc1 --commit
+
+   Instead of typing the next version explicitly, derive it from the current
+   ``__version__`` with ``--bump``:
+
+   .. code-block:: bash
+
+      uv run python scripts/release_prepare.py --bump alpha --dry-run
+      uv run python scripts/release_prepare.py --bump beta --dry-run
+      uv run python scripts/release_prepare.py --bump rc --dry-run
+      uv run python scripts/release_prepare.py --bump stable --dry-run
+      uv run python scripts/release_prepare.py --bump patch --dry-run
+
+   ``alpha`` / ``beta`` / ``rc`` advance the prerelease train; ``stable`` drops
+   prerelease labels (``0.4.0rc2`` → ``0.4.0``). ``patch`` / ``minor`` / ``major``
+   apply only when there is **no** prerelease segment (run ``--bump stable`` first).
 
    Use ``--date YYYY-MM-DD`` if the Towncrier release date should not be “today”.
    Use ``--skip-towncrier`` only in exceptional cases (changelog skipped).
@@ -69,8 +85,9 @@ Option B — Prepare the release PR from GitHub Actions
 
 1. In GitHub: **Actions** → **CD - Prepare release PR** → **Run workflow**.
 
-2. Enter **Version** (``X.Y.Z`` without a ``v`` prefix). Optionally set **Release date**
-   (``YYYY-MM-DD``); otherwise UTC “today” is used.
+2. Enter **Version** (PEP 440 string without a ``v`` prefix, e.g. ``0.4.0`` or
+   ``0.4.0a1``). Optionally set **Release date** (``YYYY-MM-DD``); otherwise UTC
+   “today” is used.
 
 3. The workflow creates branch ``chore/release-prep-X.Y.Z``, runs the same steps as
    ``scripts/release_prepare.py``, pushes it, and opens a pull request.

diff --git a/newsfragments/62.changed.md b/newsfragments/62.changed.md
@@ -0,0 +1 @@
+Ship ``0.4.0a1`` alpha, space-free data/install paths (``WyssCenter`` / ``DBSAnnotator``), optional GitHub release update checks, upgrade-safe user config locations, and ``release_prepare.py --bump`` for prerelease and semver bumps.
diff --git a/pyproject.toml b/pyproject.toml
@@ -11,7 +11,6 @@ authors = [
 keywords = ["dbs", "annotation", "neuroscience", "deep-brain-stimulation"]
 dynamic = ["version"]
 classifiers = [
-    "Development Status :: 4 - Beta",
     "Intended Audience :: Healthcare Industry",
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Medical Science Apps.",
@@ -29,14 +28,15 @@ dependencies = [
     "pydantic>=2.0",
     "pyside6>=6.11.0",
     "matplotlib>=3.5",
+    "packaging>=23.0",
 ]
 
 [dependency-groups]
 dev = [
-    "pytest>=9.0.3",
-    "pytest-qt>=4.5.0",
-    "pytest-timeout>=2.4.0",
-    "pytest-cov>=7.1.0",
+    "pytest>=8.0.0",
+    "pytest-qt>=4.4.0",
+    "pytest-timeout>=2.3.0",
+    "pytest-cov>=4.1.0",
     "ruff>=0.1.0",
     "pre-commit>=3.6",
     "pre-commit-uv>=4.2.1",
@@ -119,11 +119,7 @@ select = [
 "src/dbs_annotator/views/wizard_window.py" = ["E501"]
 
 [tool.codespell]
-# `vas` is the clinical abbreviation for "Visual Analog Scale"; without this
-# it is reported as a misspelling of "was". Add further domain terms as they
-# come up.
 ignore-words-list = "vas"
-# Skip binary assets, generated build output, lockfiles, and logs.
 skip = "uv.lock,.venv,build,dist,htmlcov,docs/_build,*.svg,*.ico,*.png,*.pdf,*.log,*.min.js"
 
 [tool.doc8]
@@ -132,7 +128,6 @@ ignore = ["D004"]
 ignore-path = ["docs/_build", "docs/_templates"]
 
 [tool.interrogate]
-# Starting floor; raise as coverage improves.
 fail-under = 85
 ignore-init-module = true
 ignore-magic = true
@@ -177,19 +172,19 @@ directory = "docs"
 name = "Documentation"
 showcontent = true
 
-# BeeWare Briefcase: native installers (Windows MSI / macOS .app + DMG).
-# App entrypoint: `python -m dbs_annotator` (see src/dbs_annotator/__main__.py).
-# Project [project] metadata (version via Hatch, dependencies) is merged by Briefcase.
 [tool.briefcase]
-project_name = "DBS Annotator"
+project_name = "DBSAnnotator"
 bundle = "ch.wysscenter.dbsannotator"
-# Briefcase requires a static version here even when [project] uses dynamic version from Hatch.
-version = "0.3.0"
+# Briefcase requires a static version here even when [project] uses dynamic version
+version = "0.4.0a1"
 license = { file = "LICENSE" }
+author = "WyssCenter"
+author_email = "lucia.poma@wysscenter.ch"
+url = "https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot"
 
 [tool.briefcase.app.dbs_annotator]
 formal_name = "DBSAnnotator"
-description = "An application for annotating clinical programming sessions."
+description = "A graphical user interface for annotating DBS clinical programming sessions"
 long_description = """
 DBS Annotator is a desktop application used to structure and review
 deep-brain stimulation programming sessions in a reproducible workflow.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Ship ``0.4.0a1`` alpha, space-free data/install paths (``WyssCenter`` / ``DBSAnnotator``), optional GitHub release update checks, upgrade-safe user config locations, and ``release_prepare.py --bump`` for prerelease and semver bumps.