feat: Ubuntu 26.04 support — install script + Wayland/napari rendering + desktop launcher fixes

[hongquanli]

Summary

Makes Squid run on Ubuntu 26.04 LTS (system Python 3.14, GNOME/Mutter Wayland). Three parts:

1. software/setup_26.04.sh — install script adapted from setup_22.04.sh.
2. Wayland/napari rendering fix (main_hcs.py, control/gui_hcs.py) — stops the GUI going black on acquisition.
3. Desktop launcher fix (setup_26.04.sh) — the shortcut now uses ptyxis instead of the removed gnome-terminal.

1. Install script (setup_26.04.sh)

Ubuntu 26.04 ships Python 3.14, which breaks the 22.04 script two ways: PEP 668 (externally-managed system pip) and pinned deps with no 3.14 wheels.

• pip3 install --break-system-packages — system Python 3.14 is externally-managed (PEP 668). Non-sudo install keeps packages in the user site, leaving apt-managed packages intact.
• numpy<2 → numpy — NumPy 1.x has no Python 3.14 wheels (1.26 caps at 3.12).
• napari==0.5.4 → napari — the old pin predates 3.14 (this now resolves to napari 0.7.1; see the rendering fix below).
• Dropped aicsimageio + basicpy — only imported by control/stitcher.py, which nothing loads (active stitcher is the ImageJ-based tools/stitcher.py). These were the main 3.14 blocker.
• Qt stays via apt (python3-pyqt5*, python3-pyqtgraph) — apt packages aren't subject to PEP 668.
• Removed the 22.04-only pip-upgrade step.

Version-agnostic steps (Daheng/Toupcam drivers, udev rules, dialout group, kernel-hold, desktop shortcut) are unchanged.

2. Wayland/napari black-screen fix

On a Wayland session, napari 0.7.1's napari/_wayland_fix.py runs on import and forces QT_QPA_PLATFORM=xcb + PYOPENGL_PLATFORM=glx on Nvidia hardware, assuming XWayland+GLX is more stable. On recent hardware/drivers (tested: RTX 5070 Ti Blackwell + driver 595 + Mutter) it's backwards:

• xcb → napari's vispy GL surface renders black the moment acquisition switches to a napari tab.
• glx → PyOpenGL context tracking fails (Attempt to retrieve context when no valid context), so image layers never draw.

Live View is unaffected because it uses pyqtgraph (raster), which is why only acquisition went black.

Fix: napari applies those defaults with os.environ.setdefault, so presetting both QT_QPA_PLATFORM=wayland and PYOPENGL_PLATFORM=egl before napari is imported neutralizes the workaround and keeps the proven-good native Wayland + EGL path. Guarded to Linux Wayland sessions and respects explicit overrides → no-op on X11/macOS/Windows. Because it lives in main_hcs.py/gui_hcs.py, it applies on pull without re-running setup.

3. Desktop launcher fix

Ubuntu 26.04 dropped gnome-terminal (default terminal is now ptyxis) and removed the -e "cmd" syntax, so the generated .desktop did nothing when double-clicked. Now uses ptyxis --new-window --working-directory=… -- … with Terminal=false.

Testing

✅ Runtime-tested on Ubuntu 26.04 (Python 3.14, Mutter Wayland, RTX 5070 Ti Blackwell + Intel, driver 595):

• Acquisition renders in the napari mosaic/multichannel view with no black window and no OpenGL context errors (verified end-to-end reproducing the embedded-napari tab-switch + repaint path: 0 errors).
• Desktop launcher opens a ptyxis window and starts the GUI.

⚠️ A clean end-to-end run of setup_26.04.sh on a fresh 26.04 box still recommended to confirm apt package availability and full pip resolution.

🤖 Generated with Claude Code