Add check for number of normalized dispersions

[lazappi]

In sc.pp.highly_variable_genes() when flavor='cell_ranger' and n_top_genes is set check that enough normalized dispersions have been calculated and if not raise a warning and set n_top_genes to the number of calculated dispersions.

Fixes #2230

[codecov]

Codecov Report

Merging #2231 (b1b0c31) into master (4623bb7) will increase coverage by 0.02%.
The diff coverage is 100.00%.

❗ Current head b1b0c31 differs from pull request most recent head 29c5505. Consider uploading reports for the commit 29c5505 to get more accurate results

@@            Coverage Diff             @@
##           master    #2231      +/-   ##
==========================================
+ Coverage   71.82%   71.85%   +0.02%     
==========================================
  Files          98       98              
  Lines       11539    11542       +3     
==========================================
+ Hits         8288     8293       +5     
+ Misses       3251     3249       -2     

Impacted Files	Coverage Δ
scanpy/preprocessing/_highly_variable_genes.py	95.38% <100.00%> (+1.11%)	⬆️

[lazappi]

Just noticed this is almost an exact duplicate of #1985 (check the issues but not PRs 🤦🏻 ). Feel free to close this if you want to keep the older one open.

[Zethson]

@lazappi you are now the chosen one :)

Think that using the size attribute like in https://github.com/scverse/scanpy/pull/1985/files is maybe nicer and more explicit. len() could technically be overwritten and return anything. It's less explicit.

Could you maybe add a quick test which covers this case?

Thank you very much!

[lazappi]

Made the .size change and added a test. Not entirely sure I have done the test correctly so let me know if that needs adjusting.

[lazappi]

Sorry, I forgot about this. Not sure why the CI was falling. The only errors I get locally were due to problems with matching images.

[Zethson]

@lazappi no worries! The scanpy CI has always been a little bit flaky and sometimes failures are not the faults of people submitting pull requests. If it fails again, we can dig deeper.

[lazappi]

It looks like the same AssertionError: Error: Image files did not match. error I was getting locally from some of the spatial tests. I haven't touched this so not sure what's going on there.

[Zethson]

@ivirshup this one should be good to go now, right? Do you require release notes for such small things or do you manually add those later?

[ivirshup]

@Zethson, have you reviewed?

[ivirshup]

And yes, should get a bug fix release note.