Allow plugins to add morphometrics subcommands via entry points

[bbarad]

What

Lets third-party packages installed in the same environment contribute morphometrics subcommands by advertising a morphometrics.commands entry point. The immediate motivation is the napari GUI (surface-morphometrics-gui#41), which will expose morphometrics gui once it declares the matching entry point — without the pipeline taking a hard dependency on it.

Changes

• surface_morphometrics/cli.py — LazyGroup now discovers commands from the morphometrics.commands entry-point group:
  • list_commands unions in discovered plugin names.
  • get_command falls back to EntryPoint.load(), wrapping failures in a clean ClickException (e.g. when the plugin is installed but its GUI deps aren't).
  • _short_help resolves plugin help so they render in --help.
  • Discovery reads package metadata only, so morphometrics --help stays fast and never imports napari/Qt. Plugin commands appear under "Other commands".
• pyproject.toml — adds an optional gui extra pointing at the GUI's git repo (PyPI line left commented for when it's published):

  gui = ["surface-morphometrics-gui @ git+https://github.com/baradlab/surface-morphometrics-gui.git"]

Behavior

State	Result
No GUI installed	--help and command list unchanged
pip install surface-morphometrics[gui]	morphometrics gui appears and launches the GUI
GUI installed but import fails	Friendly Error: Could not load the 'gui' command …

Testing

• Full suite passes (38 passed).
• Verified end-to-end against a simulated plugin: discovery, listing under "Other commands", invocation, and the load-failure error path.

The GUI-side half (a thin import-light click command + the entry-point declaration) lands separately on surface-morphometrics-gui#41.

🤖 Generated with Claude Code

[bbarad]

@hemanthkapa this is the pipeline side update to allow surface morphometrics GUI to use morphometrics gui