Convert models to macro templates

[dbirman]

This PR overhauls the aind-data-schema-models repository to use jinja2 templates.

The entry point is the run_all.sh script, which pulls the templates from the _generators/templates folder. The name of each template file is used to get the corresponding data from the models folder. The templates then parse each row, generating the corresponding classes, and merge them into the ALL/ONE_OF patterns that we use. It's not super easy to write the templates so I almost certainly made a typo somewhere, especially in the docstrings appreciate a close eye on them.

Some additional utility functions were added to support this and tests to coverage the new code.

Overall I'm happy with this approach, it's super simple and the templates are pretty understandable except for some weird edge cases with how empty columns are treated by pandas. This should be backward compatible with our existing repos, but we need to check carefully before merging this.

Also the mouse_anatomy file is massive, although it's only really a few MB so not a big deal to keep it. I vote that we merge this in some form and then revisit how to handle large vocabularies with this issue #80 in the future.

[dbirman]

Closes #73

[dbirman]

Closes #63

[dbirman]

FYI to get this to run I had to manually change the acronym of the "cranial nerve" region in the brain atlas. I'm not sure what to do about this. The acronyms are case sensitive apparently (ugh) which breaks some of the templating code. I need to go back and do something custom to handle this but not sure what/how to implement it.

[jtyoung84]

Seems good to me. I want to import this branch into a few repos and run the unit tests in those to see if everything passes.

[jtyoung84]

The pid_names module seems to have been removed in this PR. It raises a few errors in aind-data-schema

ModuleNotFoundError: No module named 'aind_data_schema_models.pid_names'

[jtyoung84]

The sub-lists in the Organizations are missing. Stuff like DETECTOR_MANUFACTURERS, SUBJECT_SOURCES, etc.: https://github.com/AllenNeuralDynamics/aind-data-schema-models/blob/main/src/aind_data_schema_models/organizations.py

[dbirman]

The sub-lists in the Organizations are missing. Stuff like DETECTOR_MANUFACTURERS, SUBJECT_SOURCES, etc.: https://github.com/AllenNeuralDynamics/aind-data-schema-models/blob/main/src/aind_data_schema_models/organizations.py

Whoops thanks for catching that, I'll add a test too so we don't lose them again...

[jtyoung84]

I think it should be good to go. There was one small issue where a warning message was displaying
Union[_Callithrix_Jacchus, _Homo_Sapiens,...]
instead of
Union[CALLITHRIX_JACCHUS, HOMO_SAPIENS,...]
but I think that should be okay.

[dbirman]

I think it should be good to go. There was one small issue where a warning message was displaying Union[_Callithrix_Jacchus, _Homo_Sapiens,...] instead of Union[CALLITHRIX_JACCHUS, HOMO_SAPIENS,...] but I think that should be okay.

I think I changed the class names by accident, but the dynamically generated classes probably shouldn't have been named in all caps anyways...