Packages

End-to-end workflow for transforming a Qt Designer `.ui` file and a set of CLI
parameters into a complete, runnable GUI/plugin project (MVP architecture).

This module coordinates the full generation pipeline:

1) UI → JSON layout
   Convert the `.ui` file into an internal JSON representation capturing window
   geometry, widget positions, and user-named placeholders.

2) CLI → Input panel injection
   Inspect the target executable (`<exe> --help`) and parse a curated list of
   CLI flags. Insert GUI controls (entries, checkboxes, buttons) into the JSON
   specification according to the selected flags file.
   Optionally, incorporate `update_area_flags.txt` to designate parameters that
   trigger incremental GUI refresh or post-analysis updates.

3) JSON → GUI plugin project
   Generate the final GUI code and directory layout for the requested GUI
   framework:
       - PyQt6 (PyMOL plugin)
       - Tkinter (VMD plugin)
       - Panel (web UI with NGL.js or Three.js back-end)
   Template files are copied, then patched with the generated GUI source code.

This ensures a reproducible, automated UI-generation pipeline for scientific CLI
tools, enabling hybrid computational workflows and GUI deployment across desktop
and web contexts.