Update Python API reference docs based on latest GraphQL schema

[andy-sweet]

The main contribution of this PR is to update the Python API reference docs with the new classes added in the recent schema change (TomogramAuthor and AnnotationFile).

In addition, there are few other documentation related changes.

1. Updated quick start to reflect other API changes (e.g. removing binning keyword argument from download_mrcfile).

2. Added the upgrade option to the napari plugin, so that its dependencies (like the Python client in this repo) are upgraded when there is an existing installation.

3. Fixed the examples in the base model so that they work with the current schema.

4. Fixed some typos and small mistakes in the model docstrings.

5. Enforced a version of Sphinx pre v7 to prevent an error when building the HTML docs.

The error is Reason: UndefinedError("'style' is undefined") and is likely related to the Sphinx RTD theme not supporting Sphinx v7. The corresponding issue should be fixed for v2 of the theme, but I did not find that to be the case.

Related to #278

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (78934ec) 83.71% compared to head (9d8f1ef) 83.71%.
Report is 6 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
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  Coverage   83.71%   83.71%           
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  Files           7        7           
  Lines         565      565           
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  Hits          473      473           
  Misses         92       92           

Flag	Coverage Δ
unittests	83.71% <ø> (ø)

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[jgadling]

Thanks!!