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theislab / scCODA

A Bayesian model for compositional single-cell data analysis
BSD 3-Clause "New" or "Revised" License
141 stars 23 forks source link

conda compatibility #75

Closed Nusob888 closed 1 year ago

Nusob888 commented 1 year ago

Hi,

Is there any possibility of submitting sccoda to conda?

I am having a lot of compatibility issues with sccoda compatibility. It appears to break my scanpy installations when installed via pip.

Many thanks for your consideration

johannesostner commented 1 year ago

Hi @Nusob888! We've recently released a complete reimplementation of scCODA as part of the scverse package pertpy. Please check it out - you will hopefully run into less compatibility issues there!

Nusob888 commented 1 year ago

Hi thanks for the feedback,

sadly, still dependency issues and I am only using scverse tools in my conda environment. It would be great if the scverse packages could all have conda implementations to avoid conflicts caused by pip and conda if possible.

johannesostner commented 1 year ago

That's unfortunate - I'm also using conda environments and never had any problems with installing scCODA or pertpy via pip.
Is there a specific dependency that causes these compatibility issues? What error message do you get?

Zethson commented 1 year ago

@Nusob888 please open an issue at pertpy if you're having installation troubles. Happy to help you over there.