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morrislab / pairtree

Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
MIT License
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pairtree requires older version of numpy #40

Closed agorelick closed 6 months ago

agorelick commented 1 year ago

Hi, pairtree does not work with the latest version of numpy. This appears to be the same issue as mentioned here in the pyclone-vi github issues: https://github.com/Roth-Lab/pyclone-vi/issues/28.

To fix this, I edited the requirements.txt file so that version 1.23.5 of numpy is used: numpy = 1.23.5, then re-installed: conda remove --name pairtree --all conda create -c conda-forge -n pairtree --file requirements.txt --yes

oghzzang commented 10 months ago

I'm not a developer. But I used the pairtree recently. It worked well! My python version is 3.11.7, and my numpy version is 1.26.3.

I installed it like you using conda. I think you can try to define the python version when you install conda.

alexanderchang1 commented 8 months ago

I think it would be a good idea for the requirement.txt file to specify version number to avoid this issue. Scipy and Numba aren't updated in lockstep and these breaks will become only more common as time goes on.

ethanumn commented 7 months ago

I've updated the requirements.txt file with the latest versions that do not seem to cause any dependency issues. Please let me know if this works on your end.