Installation error about cnvkit HOT 3 OPEN

You may have fixed this but I'll post here for posterity. See jmschrei/pomegranate#1052, jmschrei/pomegranate#1057 for more information about what's going on here.

Long story short is that cnvkit asks for pomegranate 0.14.8 or 0.14.9, but those versions of pomegranate ask for numpy versions >=1.20.0. the issue here is that the numpy 2.0.0 release is not backwards compatible, so when you install, it tries to use the most recent (but incompatible) version, causing the error you posted.

The fix in jmschrei/pomegranate#1052 hasn't been pushed. If it ever does get pushed/released, there may still be problems if they release it under 0.14.10 since cnvkit asks for pomegranate >= 0.14.8, <=0.14.9.

The fastest fix is to download a version of pomegranate labelled as release 0.14.9 that asks for numpy <2.0.0. This repo I made does precisely that. I was able to install cnvkit by making sure I downloaded old versions of the problematic dependencies (cython, numpy) and then the "new" pomegranate.

Try doing

pip uninstall cython numpy -y
pip install cython==0.29.17 numpy==1.26.4 -y
git clone -b v0.14.9 --single-branch https://github.com/tiwalayo/pomegranate.git
pip install -e pomegranate/

from cnvkit.

I have the same issue on x86_64.

from cnvkit.

Thank you tiwalayo It works like a charm. You saved me a lot of time. Thank you! :)

from cnvkit.