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rename count_file in internal API to counts_file #944

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rename count_file in internal API to counts_file #944

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

@alexanderchang1
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Thank you so much! I will update my squidpy. Thanks again for all your help.

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Successfully merging this pull request may close these issues.

Can't read in protein antibody capture data
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@flying-sheep @alexanderchang1