rename count_file in internal API to counts_file

[flying-sheep]

Description

rename the count_file argument in the internal _read_counts to match the counts_file (with “s”) in the public API.

This changes the error message when it’s wrongly specified from

TypeError: squidpy.read._utils._read_counts() got multiple values for keyword argument 'count_file'

to

TypeError: squidpy.read._read.visium() got an unexpected keyword argument 'count_file'. Did you mean 'counts_file'?

How has this been tested?

CI

Closes

Fixes #940, but let’s wait for @alexanderchang1 to confirm

[alexanderchang1]

Hi, sorry, the conversation got mixed up between the Issue and the pull request. This probably fixes this bug, and looks good to me.

But a broader function I need is for Squidpy to read in Antibody Capture Data as well, which 10x Genomics offers for their Visium platform and is developing for their Visium HD platform. I reviewed the Squidpy function and the kwargs seem to now correctly being passed all the way back to the read_10x_h5 function pulled from Scanpy. Previously the Scanpy version of read visium did not. The previous PR I put in fixed that issue, I can test it once this goes through.

[flying-sheep]

squidpy.read.visium(counts_file=..., gex_only=False) should work already with the released version of squidpy!

[alexanderchang1]

Thank you so much! I will update my squidpy. Thanks again for all your help.

[timtreis]

Hey @alexanderchang1, does it work?

But a broader function I need is for Squidpy to read in Antibody Capture Data as well, which 10x Genomics offers for their Visium platform and is developing for their Visium HD platform.

Generally, we're working towards making SpatialData the default container that Squidpy uses and are therefore pivoting a lot of the reading capabilities into https://spatialdata.scverse.org/projects/io/en/latest/

[timtreis]

lgtm

[alexanderchang1]

@timtreis It does! Will the old scanpy spatial plotting functions still be compatible with SpatialData objects? We have a paper going in that uses Scanpy and Anndata to demonstrate a lot of the package utility.