Added glm.py examples in docstrings

[pranmod01]

This PR adds examples for the glm.py public-facing commands. I added examples of how the function might be used with different parameters to get different results.

To be discussed: These are my first set of examples for functions. Because I might not thoroughly understand how these examples might be used in the context of neural data, I'm unsure if I should add more details and scenarios of how the functions can be used.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.

Project coverage is 97.23%. Comparing base (6b3a1e8) to head (12a3b16).
Report is 28 commits behind head on development.

Files with missing lines	Patch %	Lines
src/nemos/glm.py	88.88%	2 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development     #249      +/-   ##
===============================================
+ Coverage        97.09%   97.23%   +0.14%     
===============================================
  Files               20       21       +1     
  Lines             1857     1884      +27     
===============================================
+ Hits              1803     1832      +29     
+ Misses              54       52       -2     

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[billbrod]

Pranati was having an issue where running isort locally was giving inconsistent results with the CI and with my local machine. Turned out the issue was PyCQA/isort#1790: there was a local folder named jax in her nemos directory, which made isort consider jax as an internal package, and changing how it was sorted. jax was a git submodule, and we're unsure how it ended up there. Deleting the directory caused isort to behave as expected.

[BalzaniEdoardo]

This is almost good to go but we should have an example in the fit method of PopulationGLM, since it overrides the GLM one.

[pranmod01]

Updates made:

1. Added example to the fit method of PopulationGLM
2. Changed some wording based on Edoardo's comments
3. Removed the basis example that overlapped with this branch to keep this branch clean of only GLM examples
4. Regular formatting tox fixes

[billbrod]

This looks good! Couple more user-facing functions need examples, though @BalzaniEdoardo maybe some of these can be made private?

• cast_to_jax
• initialize_state

General notes:

• While it's fine to have the imports in the examples right above where they get used, I think it's more standard to have all imports at the top (that's how scripts and notebooks are generally written) -- any particular reason you didn't do it that way?

[pranmod01]

For the comment about ordering the import statements -- I didn't put them all at the top and instead put them in the order that they are called just because I thought it would be easier for someone who didn't really understand the imports to see exactly how they are being used. But because the examples aren't too lengthy or technical, I can change the imports to the regular standard. Let me know!

Added an example to initialize_state but not cast_to_jax because the latter seems to be only used internally. Other than that, everything else is fixed from my end.

[BalzaniEdoardo]

Last very small round of comments, and then this is good to be merged. Thanks Pranati, very good job on this

[billbrod]

I still think the definition of size for Xnew should be changed, but otherwise this looks good to me!

[BalzaniEdoardo]

This looks good! Couple more user-facing functions need examples, though @BalzaniEdoardo maybe some of these can be made private?

• cast_to_jax
• initialize_state

General notes:

• While it's fine to have the imports in the examples right above where they get used, I think it's more standard to have all imports at the top (that's how scripts and notebooks are generally written) -- any particular reason you didn't do it that way?

Let's make 'cast_to_jax' private, keep 'initialize_state' public since batching as we have it now requires the user to call the method, if you check the relative how to guide in the docs.

[billbrod]

All looks good to me, thanks for your work on this Pranati!

@BalzaniEdoardo should we open an issue about making cast_to_jax private? (doing that probably doesn't belong here)

[BalzaniEdoardo]

Thanks @pranmod01!