Code Refactor

[MitchLahm]

No description provided.

[nlk36701]

Hey @MitchLahm, while reviewing this refactor I noticed a few targeted improvements that might be worth incorporating:

I've committed symmetry functionality enhancements and test updates here: nlk36701@c1fa4ab

Changes include:

Restored symmetry functionality in cma.py (make_proj integration)
Fixed deprecated np.row_stack() → np.vstack() calls in symmetry.py (matches your refactor)
Updated symmetry pytest with corrected test data
Added sisyphus_template.py for eventual Sisyphus-cluster support. I dropped this into submit.py so that I could test on my own infrastructure. I think we need to look at the current submission method a little more carefully to appeal to users other than you and I.

Let me know if you'd like me to incorporate these into this PR, or if you'd prefer to review them separately after merging. I can also adjust the changes to align with the refactoring direction.

[nlk36701]

Thanks for the refactor! This is a substantial cleanup and I appreciate the effort here.

I think there are a few changes to be made before merge to improve portability for users outside our current computing environments (e.g. Sapelo2, Vulcan, Sisyphus):

Requested Changes

1. I think the current approach to submission "templates" still requires new users to hardcode their own scheduler-specific solution into the code path. Could we make templates user-provided/configurable so users can pass in their own PBS/Slurm (etc.) template without changing core logic?

2. Could you either (a) merge my symmetry fix and Sisyphus template addition commit into this PR, or (b) cherry-pick the relevant changes you want to keep? I'm fine with either as long as the symmetry behavior is corrected before the merge. We can hash out the details of the submission script changes later.