Update ir_mex_build to build penalty_mex file

[kristinazvolanek]

Description of changes:

1. Added mex/ to MATLAB path in setup.m to ensure mex source files are available
2. Added irt_mex_make to ir_mex_build.m so it is run as part of standard build
3. Updated directory handling in irt_mex_make so the script runs when called from ir_mex_build
   Note: this means there would be an error when running irt_mex_make from the mex/src directory, so there might be a more elegant solution
4. Edited mex build command for penalty_mex to reflect current directory structure. Note that it no longer saves to the mex/v7 folder.

[JeffFessler]

thanks for the PR!
see what you think of my suggestions in your environment?
you might need to tweak further.

[kristinazvolanek]

Added a comment about the mex/v7 directory. Let me know if you prefer a different message!

[kristinazvolanek]

Automatically create the mex/local directory if it doesn't exist

[kristinazvolanek]

Thanks for the review!
I edited the setup file to create the mex/local directory automatically and tested in my environment. ir_mex_build runs and creates a compiled penalty_mex file in mex/local.

[JeffFessler]

Thanks for the updates and I appreciate you testing them.
So you could compile penalty_mex but I assume the memory issue you reported at the outset is still an open problem on apple cpu?

I've made a couple (hopefully final) suggestions based on #33.
I could just commit them but I wanted to give you the chance to counter if you think I'm overlooking something.

[kristinazvolanek]

Thanks for the additional suggestions. I re-tested in my environment and they look good on my end.

I can successfully compile penalty_mex, but I still see the same error ("array exceeds the maximum possible variable size"). I haven't confirmed if this is specific to Apple, but I am seeing it on an M4 Pro with MATLAB 2025b and 2024b.