Fix use_raw=None in scanpy.tl.score_genes

[michalk8]

This PR fixes the case when use_raw=None in scanpy.tl.score_genes. It causes to first fetch var_names from adata.var_names, but later a subset on adata.raw can happen, which can have different gene names.
Also fixes the type of use_raw and adds a ValueError if gene_pool is empty (otherwise, crashes with non-informative error message).

related issue: theislab/cellrank#746

[codecov]

Codecov Report

Merging #1999 (046c34e) into master (5acf8cb) will increase coverage by 0.01%.
The diff coverage is 100.00%.

❗ Current head 046c34e differs from pull request most recent head de7e7ca. Consider uploading reports for the commit de7e7ca to get more accurate results

@@            Coverage Diff             @@
##           master    #1999      +/-   ##
==========================================
+ Coverage   71.63%   71.64%   +0.01%     
==========================================
  Files          92       92              
  Lines       11248    11250       +2     
==========================================
+ Hits         8057     8060       +3     
+ Misses       3191     3190       -1     

Impacted Files	Coverage Δ
scanpy/tools/_score_genes.py	85.71% <100.00%> (+1.56%)	⬆️

[ivirshup]

LGTM, just needs a release note

[ivirshup]

Could the note be a little more descriptive? Without a specific issue linked to this it's hard to tell what incorrect behavior was changed.

[ivirshup]

Great, thanks!

We do have the CI checks as required for merging, unfortunately.

Question for you about the pre-commit CI. Do you know what's going on here with the extra service? Do we no longer need the github actions pre-commit check? Can also figure this out on Friday.

[ivirshup]

Heads up, I'm going to make an empty commit to re-trigger the CI.

[michalk8]

We do have the CI checks as required for merging, unfortunately.

Ok, didn't wanted to waste the resources and thought you can just merge manually even if checks don't pass.

Question for you about the pre-commit CI. Do you know what's going on here with the extra service? Do we no longer need the github actions pre-commit check? Can also figure this out on Friday.

Yes, afaik this was enabled a few weeks back for the whole organization.