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Bioconda installs numpy >= 2.0 which is incompativle with HATCHet #229

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simozacca opened this issue Oct 15, 2024 · 3 comments
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Bioconda installs numpy >= 2.0 which is incompativle with HATCHet #229

simozacca opened this issue Oct 15, 2024 · 3 comments
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@simozacca
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Bioconda installs HATCHet with the new version of numpy >= 2.0 which is however incompatible with the current version of HATCHet and most of the used packages.

Temporary solution is to force the installation of an older version of numpy:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

conda create -n hatchet hatchet "bcftools==1.19" "samtools==1.19" "numpy<=1.26"

Note that bcftools and samtools versions are neede as per #227

For a permanent fix, @mmyers1 could you please update accordingly the version of numpy in the Bioconda recipe?

@vineetbansal
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@simozacca - I'm opening up PR #230 for this. It might be a few iterations before its ready to be reviewed. I'll mark it ready for review when it is.

@vineetbansal
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HATCHeT 2.1.0 is now available on bioconda with the correct pinning of numpy

@simozacca
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Wonderful, thank you!

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