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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Bug: python3.12 incompatible due to numpy<1.24 restriction #598

Closed jowodo closed 10 months ago

jowodo commented 10 months ago

Describe the bug numpy<1.26 does not work with python3.12 and macs3 needs numpy<1.24

Is it planned to upgrade the dependency of numpy so that macs3 can be used with python3.12?

taoliu commented 10 months ago

We will work on it. Thanks for the report!

philippadoherty commented 10 months ago

Hi @jowodo our requirements don't actually specify numpy<1.24, we only specify numpy >= 1.19. We tested this with Python version 3.12 and this works and passes our tests. MACS3 now supports Python versions 3.9, 3.10, 3.11, and 3.12 (x86_64). We are working on releasing a formal MACS 3.0.0 version soon, so keep an eye out for that.

Please let us know if this is not resolved. Thanks

jowodo commented 10 months ago

My bad! I've added the numpy<1.24 previously to the installation procedure. I removed it now. I tried to install macs3.0.0b3 with python3.9 as a test and it installed. Installing macs3.0.0b3 with python3.12 gives me these errors log.txt err.txt

philippadoherty commented 10 months ago

Hi @jowodo, just to clarify, support for Python 3.12 will be available with the next release (3.0.0) that we are working on right now (not with macs3 3.0.0b3) - sorry for the confusion!

jowodo commented 10 months ago

aaah thanks for the clarification!

philippadoherty commented 10 months ago

no problem! We just released MACS3 v3.0.0 if you would like to try.

jowodo commented 10 months ago

installation was successful for python 3.9, 3.10, 3.11, 3.12 😎