P/init install cleanup

[peterhollender]

This is a fairly major change to the project, designed to address issues #8 and #10

• Trims unnecessary parts of the project, including
  • legacy scripts
  • the io module (now covered in openlifu-sdk)
  • unused parts of Database (gridweights)
• Reorganizes virtual_fit module into seg
• Eliminates "eager" imports in openlifu.__init__, to prevent the many-seconds-long importing when accessing any submodule.
• Moves importing of heavier-weight packages (which are being made optional by this branch) into the methods that call them, so that the objects can be partially-used without having those dependencies imported.
• Introduces sets of optional-dependencies to pyproject.toml that allow for reduced dependency installation. The openlifu-test-app project, for example, can package only the hardware-communication required dependencies by using the [io] option. The base application as used in Slicer should now be installed with the [app] option.

Code that touches openlifu.virtual_fit needs to be refactored to use openlifu.seg.virtualfit, and code that used things like openlifu.Transducer will need to be changed to use openlifu.xdc.Transducer

[peterhollender]

Interesting - the CI virtual environment isn't picking up the right dependencies (because the "no-option" version grabs a super-minimal set that won't have full functionality). Not sure how to address this? I'd really like pip install openlifu to get the primary dependencies with the [app] option, but I'm not sure how to make pyproject.toml do that

[ebrahimebrahim]

Interesting - the CI virtual environment isn't picking up the right dependencies (because the "no-option" version grabs a super-minimal set that won't have full functionality). Not sure how to address this? I'd really like pip install openlifu to get the primary dependencies with the [app] option, but I'm not sure how to make pyproject.toml do that

I think this is not possible, to make pip install openlifu default to pip install openlifu[app]. It will always be the minimal thing.

But that is completely fine, in my opinion. It is very reasonable to make the CI ofr example install pip install openlifu[app] or whatever we want, and to make the primary instructions be pip install openlifu[app] or wahtever. This is common and reasonable.

One way to achieve something like what you are saying is to rename this package to openlifu-core and make a new package called openlifu that thinly wraps it and that depends on openlifu-core[app]. But... eh.