Fix notebook bugs and dependency issues

[njmei]

This PR is partially in response to: https://github.com/kaizhang/SnapATAC2/issues/277

Notes:

• I've now run all notebooks except docs/tutorials/atlas.ipynb to ensure they work properly.
  • The atlas.ipynb requires a bit too much data to download for me to test
• Please see individual commit messages for additional details

Questions:

• It looks like there is overlap in terms of how to install dependencies like scanorama>=1.7.3 and harmonypy>=0.0.9. I see them in extra under [project.optional-dependencies] but would it make more sense to remove them from extra and just keep the ones I newly added under recommend? Or would you prefer the opposite (move packages like magic-impute to extra)?
  • It seems like it would be easier to let scanpy maintainers manage these dependences? (See: https://github.com/scverse/scanpy/blob/3ceb740ba37effc44f42ecdb884cef86a38d4346/pyproject.toml#L138-L151) Or are there strong reasons to have snapatac2 manage these dependencies (even under extra)?

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 98.23%. Comparing base (b73dcfd) to head (ca414ce).

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #281 +/- ## ======================================= Coverage 98.23% 98.23% ======================================= Files 4 4 Lines 227 227 ======================================= Hits 223 223 Misses 4 4 ```

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[kaizhang]

Thank you for the pull request! I'll address the extra package issue.