Add gene annotations to anndata vars

[emdann]

Closes #14

[codecov-commenter]

Codecov Report

Merging #23 (e669b8b) into main (2398977) will decrease coverage by 0.98%.
The diff coverage is 92.98%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #23      +/-   ##
==========================================
- Coverage   93.69%   92.72%   -0.98%     
==========================================
  Files           6        7       +1     
  Lines         333      371      +38     
==========================================
+ Hits          312      344      +32     
- Misses         21       27       +6     

Impacted Files	Coverage Δ
src/genomic_features/annotate.py	89.18% <89.18%> (ø)
src/genomic_features/__init__.py	100.00% <100.00%> (ø)
src/genomic_features/ensembl/ensembldb.py	93.15% <100.00%> (-1.06%)	⬇️

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[emdann]

Outstanding issues:

• Dealing with common column names between var table and annotation table. Throw error?

[lauradmartens]

I found the variable names a bit confusing because in pandas syntax on means that the column is present in both tables. Maybe we could name it left_on and right_on like in pd.merge

[emdann]

I've changed to annotation_on and var_on to match the other params

[lauradmartens]

Looks good! I added a few minor comments :)

[ivirshup]

Yep, looks good.

One comment on the tutorial, can we make it so the AnnData used the same ensembl version as we annotate with? Either by using a different ensembl version, or a different AnnData.

[emdann]

@ivirshup wrt Ensembl version matching, the pbmc3k data was mapped with cellranger 1.1, but I am having a hard time matching this version to a Ensembl release.

I'm gonna use the data from scvi.data.heart_cell_atlas_subsampled which is mapped to cellranger 3.0.1 with hg38 which according to the old release notes corresponds to Ensembl release 93.