icbi-lab / infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
https://infercnvpy.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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rename toggle_string_cache to enable_string_cache #107

Closed christophechu closed 9 months ago

christophechu commented 9 months ago

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when I changed thetoggle_string_cache to enable_string_cache in read_gtf.py , another error occurred scan_csv() got an unexpected keyword argument 'sep'

grst commented 9 months ago

This sounds again like an incompatibility of the gtfparse library with polars. See https://github.com/icbi-lab/infercnvpy/issues/86

christophechu commented 9 months ago

thx, in order not to affect the normal use of other packages, I chose to create a new infercnv-specific environment and specify that the Polars version of 0.15.* is installed and used normally

grst commented 9 months ago

I pinned gtfparse<2 in the latest release which doesn't use polars. This should fix the issue.