Chore/update logo

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2026 Wyss Center
+Copyright (c) 2026 Wyss Center for Bio and Neuroengineering
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -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__`
-**Publisher:** Wyss Center (contact: lucia.poma@wysscenter.ch)
+**Publisher:** Wyss Center for Bio and Neuroengineering (contact: lucia.poma@wysscenter.ch)
 
 ## For End Users
 
@@ -98,7 +98,7 @@ App_ClinicalDBSAnnot/
 │   ├── config.py                 #   App configuration and constants
 │   └── config_electrode_models.py #  Electrode model definitions
 ├── styles/                       # QSS theme files (Briefcase + dev; see resource_path)
-├── icons/                        # Application icons
+├── icons/                        # Application icons (e.g. logosimple/ bundle)
 ├── scripts/                      # Utility scripts
 └── pyproject.toml                # Project configuration and dependencies
 ```
@@ -132,19 +132,19 @@ uv run briefcase package windows -p zip    # avoids WiX; omit -p (MSI) when WiX
 
 `macOS` builds on Apple Silicon produce **arm64** artifacts when `universal_build = false` is set under `[tool.briefcase.app.dbs_annotator.macOS]` in `pyproject.toml`.
 
-**Windows Briefcase quirks:** keep `[tool.briefcase].version` in sync with `dbs_annotator.__version__` (Briefcase does not use Hatch’s dynamic `[project]` version). If `briefcase build` fails at **“Setting stub app details”** / RCEdit with **“Unable to commit changes”**, exclude the repo or `build\` from real-time antivirus scanning and retry (see [Briefcase issue #1530](https://github.com/beeware/briefcase/issues/1530)).
+**Windows Briefcase quirks:** keep `[tool.briefcase].version` in sync with `dbs_annotator.__version__` (Briefcase does not use Hatch’s dynamic `[project]` version). Bump both in one step with `uv run python scripts/release_prepare.py <version>` (or `--bump …`). If `briefcase build` fails at **“Setting stub app details”** / RCEdit with **“Unable to commit changes”**, exclude the repo or `build\` from real-time antivirus scanning and retry (see [Briefcase issue #1530](https://github.com/beeware/briefcase/issues/1530)).
 
 The Windows stub binary is named **`DBSAnnotator.exe`** (from `[tool.briefcase.app.dbs_annotator].formal_name`). After changing that field, run **`briefcase create windows app`** again (or delete `build\dbs_annotator\windows`) before **`briefcase build`**.
 
-Icons for the **stub**, **MSI/ZIP**, and **Qt** (`QApplication` / window chrome) come from **`icons/logoneutral.ico`** and **`icons/logoneutral.png`** at the **repository root** (`icon = "icons/logoneutral"` in `pyproject.toml`). That folder is also listed as a Briefcase **`sources`** entry so a sibling `icons\` directory is shipped next to the app package inside the bundle. Runtime lookup uses `resource_path()` (package dir, then `src\icons`, then repo-root `icons\`).
+Icons for the **stub**, **MSI/ZIP**, and **Qt** (`QApplication` / window chrome) live under **`icons/logosimple/`**: **`logosimple.ico`**, **`logosimple.png`**, plus **`logosimple-{16,32,64,128,256,512}.png`** for **Linux system** (BeeWare copies them into the Freedesktop hicolor tree; all six are listed in the upstream `briefcase-linux-system-template`). **`logosimple.icns`** is for macOS (build with `iconutil` on a Mac; see `scripts/build_app_icons.py`). Configure with `icon = "icons/logosimple/logosimple"` in `pyproject.toml`. The repo-root **`icons/`** tree is a Briefcase **`sources`** entry and is shipped next to the app package; runtime lookup uses `resource_path()` (package dir, then `src/icons`, then repo-root `icons/`).
 
 **Inventory (for packaging):**
 
 | Area | Notes |
 | --- | --- |
 | App type | Qt **GUI** (`console_app` is false by default). |
 | Heavy deps | `PySide6`, `matplotlib`, `pandas`, `python-docx`, `docx2pdf` (Windows: `pywin32`; macOS: `appscript` via `docx2pdf`). |
-| Data files | JSON presets under `src/dbs_annotator/config/`; QSS and SVG under repo-root **`styles/`** (also a Briefcase **`sources`** entry); **`icons/logoneutral.{ico,png}`** at repo root (Briefcase + Qt). |
+| Data files | JSON presets under `src/dbs_annotator/config/`; QSS and SVG under repo-root **`styles/`** (also a Briefcase **`sources`** entry); app icons under **`icons/logosimple/`** (Briefcase + Qt). |
 | macOS entitlements | Add an entitlements plist only if you enable the Hardened Runtime and need extra capabilities (network is usually fine without custom entitlements). |
 
 ### Release signing (distribution outside store)
@@ -209,4 +209,4 @@ MIT License — see [LICENSE](LICENSE) for details.
 
 ## Contact
 
-Wyss Center — lucia.poma@wysscenter.ch
+Wyss Center for Bio and Neuroengineering — lucia.poma@wysscenter.ch

docs/conf.py

@@ -15,11 +15,13 @@
 
 _DIST_NAME = "dbs-annotator"
 
+from dbs_annotator.config import APP_LEAD_AUTHOR, ORGANIZATION_PUBLISHER
+
 project = "DBS Annotator"
-author = "Wyss Center"
+author = APP_LEAD_AUTHOR
 release = metadata.version(_DIST_NAME)
 version = ".".join(release.split(".")[:2])
-copyright = f"2025-{datetime.now().year}, {author}"
+copyright = f"2025-{datetime.now().year}, {ORGANIZATION_PUBLISHER}"
 
 extensions = [
     "sphinx.ext.autodoc",

docs/faq.rst

@@ -159,4 +159,5 @@ Contact & Support
 
 For bug reports, feature requests, or questions:
 
+| **Wyss Center for Bio and Neuroengineering**
 | **Lucia Poma** — lucia.poma@wysscenter.ch

docs/index.rst

@@ -19,7 +19,8 @@ adjustments, to the automatic generation of structured Word and PDF reports.
 Developed at the **Brain Modulation Lab, Massachusetts General Hospital**.
 
 .. note::
-   Version |release|. Contact: lucia.poma@wysscenter.ch
+   Version |release|. Publisher: Wyss Center for Bio and Neuroengineering.
+   Contact: lucia.poma@wysscenter.ch
 
 ----
 

newsfragments/66.changed.md

@@ -0,0 +1 @@
+Consolidate branding under `icons/logosimple/` for Briefcase and Qt, add `scripts/build_app_icons.py` to generate platform icon sizes from a single source PNG, and document Linux `linux system` icon requirements.

pyproject.toml

@@ -116,6 +116,7 @@ select = [
 ]
 
 [tool.ruff.lint.per-file-ignores]
+"docs/conf.py" = ["E402"]
 "src/dbs_annotator/views/wizard_window.py" = ["E501"]
 
 [tool.codespell]
@@ -140,6 +141,7 @@ quiet = false
 
 [tool.uv]
 exclude-newer = "1 week"
+exclude-newer-package = { lxml = false }
 
 [tool.towncrier]
 package = "dbs_annotator"
@@ -178,7 +180,7 @@ bundle = "ch.wysscenter.dbsannotator"
 # Briefcase requires a static version here even when [project] uses dynamic version
 version = "0.4.0a1"
 license = { file = "LICENSE" }
-author = "WyssCenter"
+author = "Lucia Poma"
 author_email = "lucia.poma@wysscenter.ch"
 url = "https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot"
 
@@ -193,8 +195,8 @@ It supports clinicians and researchers by organizing session information,
 tracking stimulation settings, and generating standardized exports and reports.
 """
 sources = ["src/dbs_annotator", "icons", "styles"]
-icon = "icons/logoneutral"
-installer_icon = "icons/logoneutral"
+icon = "icons/logosimple/logosimple"
+installer_icon = "icons/logosimple/logosimple"
 requirement_installer_args = [
     "--index-url",
     "https://pypi.org/simple",

scripts/build_app_icons.py

@@ -0,0 +1,212 @@
+#!/usr/bin/env python3
+"""Build desktop icon assets (Briefcase + Qt) from a single **square-ish** source PNG.
+
+**Output directory** defaults to ``icons/logosimple/`` so all app-icon files for one
+mark live together.
+
+**Linux (``linux system`` / .deb):** BeeWare’s template lists exactly six PNGs:
+``icon.16`` … ``icon.512`` in ``briefcase.toml``; Briefcase copies them from
+``{icon}-{size}.png`` into ``usr/share/icons/hicolor/<size>/apps/<bundle id>.png``.
+All six sizes are required (missing files keep the template placeholder).
+
+**Windows:** one multi-size ``.ico`` (16, 32, 48, 64, 256).
+
+**macOS .icns:** Apple’s ``iconutil`` reads a ``.iconset`` folder (fixed PNG names and
+pixel sizes) and writes a **single** ``.icns`` binary. That is the only portable way
+to produce a valid ``.icns``; run ``iconutil`` on macOS (or copy the ``.iconset`` to
+a Mac). The ``.iconset`` is build input only — you can delete it after ``.icns`` exists.
+
+**Source:** prefer ≥512 px for clean downscales.
+
+Requires Pillow (pulled in via project deps e.g. matplotlib).
+"""
+
+from __future__ import annotations
+
+import argparse
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+from PIL import Image
+
+# Windows stub / MSI (BeeWare Windows icon format)
+WIN_ICO_SIZES = (16, 32, 48, 64, 256)
+# Linux system: briefcase-linux-system-template briefcase.toml path_index
+LINUX_PNG_SIZES = (16, 32, 64, 128, 256, 512)
+# macOS .icns: logical pixel size -> PNG file (same as `iconutil` / .iconset)
+# Each tuple: (filename, width_px, height_px)
+MACOS_ICONSET = (
+    ("icon_16x16.png", 16, 16),
+    ("icon_16x16@2x.png", 32, 32),
+    ("icon_32x32.png", 32, 32),
+    ("icon_32x32@2x.png", 64, 64),
+    ("icon_128x128.png", 128, 128),
+    ("icon_128x128@2x.png", 256, 256),
+    ("icon_256x256.png", 256, 256),
+    ("icon_256x256@2x.png", 512, 512),
+    ("icon_512x512.png", 512, 512),
+    ("icon_512x512@2x.png", 1024, 1024),
+)
+
+
+def _load_rgba(path: Path) -> Image.Image:
+    img = Image.open(path).convert("RGBA")
+    return img
+
+
+def _letterbox_rgba(src: Image.Image) -> Image.Image:
+    """Square canvas: transparent padding (canvas side = max of width, height)."""
+    w, h = src.size
+    m = max(w, h)
+    canvas = Image.new("RGBA", (m, m), (0, 0, 0, 0))
+    canvas.paste(src, ((m - w) // 2, (m - h) // 2), src)
+    return canvas
+
+
+def build_icons(
+    source: Path,
+    out_dir: Path,
+    name: str,
+    master_px: int,
+    *,
+    write_master: bool,
+) -> None:
+    out_dir = out_dir.resolve()
+    out_dir.mkdir(parents=True, exist_ok=True)
+    src = _load_rgba(source)
+    src_sq = _letterbox_rgba(src)
+
+    master = src_sq.copy()
+    if max(master.size) != master_px:
+        master = master.resize((master_px, master_px), Image.Resampling.LANCZOS)
+
+    master_path = out_dir / f"{name}.png"
+    if source.resolve() == master_path.resolve() and not write_master:
+        print(
+            f"Skip {master_path} (same as --source; "
+            f"use --write-master to re-encode to {master_px}px)",
+            file=sys.stderr,
+        )
+    else:
+        master.save(master_path, format="PNG", optimize=True)
+        print(f"Wrote {master_path}", file=sys.stderr)
+
+    # Windows .ico (one file, multiple embedded sizes)
+    ico_images: list[Image.Image] = []
+    for px in WIN_ICO_SIZES:
+        ico_img = src_sq.copy()
+        ico_img = ico_img.resize((px, px), Image.Resampling.LANCZOS)
+        ico_images.append(ico_img)
+    ico_path = out_dir / f"{name}.ico"
+    ico_images[0].save(
+        ico_path,
+        format="ICO",
+        sizes=[(i.width, i.height) for i in ico_images],
+        append_images=ico_images[1:],
+    )
+    print(f"Wrote {ico_path} sizes={list(WIN_ICO_SIZES)}", file=sys.stderr)
+
+    # Linux AppImage PNGs
+    for px in LINUX_PNG_SIZES:
+        li = src_sq.copy()
+        li = li.resize((px, px), Image.Resampling.LANCZOS)
+        p = out_dir / f"{name}-{px}.png"
+        li.save(p, format="PNG", optimize=True)
+    print(
+        f"Wrote {len(LINUX_PNG_SIZES)} Linux PNGs: {name}-<size>.png",
+        file=sys.stderr,
+    )
+
+    # macOS .iconset
+    iconset_dir = out_dir / f"{name}.iconset"
+    if iconset_dir.is_dir():
+        shutil.rmtree(iconset_dir)
+    iconset_dir.mkdir(parents=True)
+    for fname, w, h in MACOS_ICONSET:
+        im = src_sq.copy()
+        im = im.resize((w, h), Image.Resampling.LANCZOS)
+        im.save(iconset_dir / fname, format="PNG", optimize=True)
+    print(f"Wrote {iconset_dir}/ ({len(MACOS_ICONSET)} files)", file=sys.stderr)
+
+    icns_path = out_dir / f"{name}.icns"
+    if sys.platform == "darwin":
+        try:
+            # Writes ``{name}.icns`` next to ``{name}.iconset`` (overwrites if present).
+            subprocess.run(
+                ["iconutil", "-c", "icns", f"{name}.iconset", "-o", f"{name}.icns"],
+                check=True,
+                capture_output=True,
+                text=True,
+                cwd=out_dir,
+            )
+            print(f"Wrote {icns_path} (iconutil)", file=sys.stderr)
+        except (subprocess.CalledProcessError, FileNotFoundError) as e:
+            print(
+                f"iconutil failed: {e}; on a Mac, run (cwd = output dir above):\n"
+                f"  iconutil -c icns {name}.iconset -o {name}.icns",
+                file=sys.stderr,
+            )
+    else:
+        print(
+            f"Skip {icns_path} (not macOS). On macOS (cwd = {out_dir}):\n"
+            f"  iconutil -c icns {name}.iconset -o {name}.icns",
+            file=sys.stderr,
+        )
+
+
+def main() -> None:
+    root = Path(__file__).resolve().parents[1]
+    p = argparse.ArgumentParser(description=__doc__)
+    p.add_argument(
+        "--source",
+        type=Path,
+        default=root / "icons" / "logosimple" / "logosimple.png",
+        help="Source PNG (master artwork)",
+    )
+    p.add_argument(
+        "--out-dir",
+        type=Path,
+        default=root / "icons" / "logosimple",
+        help="Output directory (default: ./icons/logosimple)",
+    )
+    p.add_argument(
+        "--name",
+        default="logosimple",
+        help="Base filename without extension (default: logosimple)",
+    )
+    p.add_argument(
+        "--master-px",
+        type=int,
+        default=512,
+        help="Pixel size of {name}.png (default: 512)",
+    )
+    p.add_argument(
+        "--write-master",
+        action=argparse.BooleanOptionalAction,
+        default=None,
+        help=(
+            "Write {name}.png from source. If --source is that file, default is skip "
+            "re-encoding; use --write-master to replace."
+        ),
+    )
+    args = p.parse_args()
+    if not args.source.is_file():
+        sys.exit(f"Not found: {args.source.resolve()}")
+    master_path = (args.out_dir / f"{args.name}.png").resolve()
+    if args.write_master is None:
+        write_master = args.source.resolve() != master_path
+    else:
+        write_master = args.write_master
+    build_icons(
+        source=args.source,
+        out_dir=args.out_dir,
+        name=args.name,
+        master_px=args.master_px,
+        write_master=write_master,
+    )
+
+
+if __name__ == "__main__":
+    main()

src/dbs_annotator/__init__.py

@@ -7,7 +7,10 @@
 
 __version__ = "0.4.0a1"
 __app_name__ = "DBS Annotator"
-__author__ = "Wyss Center"
+
+from .config import APP_LEAD_AUTHOR
+
+__author__ = APP_LEAD_AUTHOR
 
 from .models import ClinicalScale, SessionData, SessionScale, StimulationParameters
 from .views import WizardWindow

src/dbs_annotator/config.py

@@ -13,25 +13,29 @@
 APP_NAME = "DBS Annotator"
 APP_VERSION = get_version()
 
-# Legal / marketing organization label (not used for on-disk paths).
-ORGANIZATION_NAME = "Wyss Center"
+# Publisher (UI, About, docs). Not used for on-disk paths.
+ORGANIZATION_PUBLISHER = "Wyss Center for Bio and Neuroengineering"
+
+# Lead author (About; list same person first in package metadata).
+APP_LEAD_AUTHOR = "Lucia Poma"
 
 # Qt application identity for :func:`QStandardPaths` and :class:`QSettings`.
 # Use ASCII without spaces so per-user directories never contain spaces
 # (``%LOCALAPPDATA%\\<org>\\<app>\\``, Application Support on macOS, etc.).
-FS_ORG_NAME = "WyssCenter"
+FS_ORG_NAME = "WyssGeneva"
 FS_APP_NAME = "DBSAnnotator"
 
 # Canonical upstream (releases + issue tracker; keep aligned with updater repo slug).
 APP_REPOSITORY_URL = "https://github.com/Brain-Modulation-Lab/App_ClinicalDBSAnnot"
 APP_ISSUES_URL = f"{APP_REPOSITORY_URL}/issues"
+# Primary contact for feedback (same person as APP_LEAD_AUTHOR).
 UPDATE_FEEDBACK_EMAIL = "lucia.poma@wysscenter.ch"
 
 # File paths (relative to executable)
-ICON_FILENAME = "logoneutral.png"
-ICO_FILENAME = "logoneutral.ico"
+ICON_FILENAME = "logosimple.png"
+ICO_FILENAME = "logosimple.ico"
 STYLE_FILENAME = "style.qss"
-ICONS_DIR = "icons"
+ICONS_DIR = "icons/logosimple"
 
 # Window size ratios for responsive design
 WINDOW_SIZE_RATIO = {