Refactor Pipeline code

[rachelstephlee]

See #45 for more information.

Generally, the issue is that there are a lot of functions that are duplicated across. We need to refactor to clean up the code.

Copying Alex's description here:

In this capsule: https://codeocean.allenneuraldynamics.org/capsule/9216710/tree (NWB-Packaging-FiberPhotometry-Base-Capsule)

• The functions in util should live in a library that can be imported, otherwise its very difficult to run these functions outside of code ocean, and if we want to re-use those functions in another capsule we have to copy the code manually.
  • In fact, code is already being manually copied into https://github.com/AllenNeuralDynamics/aind-fip-dff ! We should absolutely not have the exact same functions in two capsules in the same pipeline.
• The code in util.aligned_fiber_to_nwb.py has lots of commented out blocks of code, and needs a general cleaning/linting

In this repo https://github.com/AllenNeuralDynamics/aind-fip-dff, there are a lot of mentions of "old" and "new" processing methods. These should be replaced with descriptive versions of how the code works. No one will remember in a year what old and new mean.

[alexpiet]

• [ ] Util functions should be moved to this repo: https://github.com/AllenNeuralDynamics/aind-fib-utils
• [ ] aind-fib-utils should be pip installable

[Ahad-Allen]

I've moved NWB util functions to the util repo, I am not sure if preprocessing functions should exist here or stay within the dff capsule, however. Should be easy to move them in either case.

[Ahad-Allen]

I recall @rachelstephlee did some work on the utils after my PR was merged, is my help still needed on this?

[rachelstephlee]

I didn't touch this, so if you think all the refactoring is completed, we can close this.