AttributeError: module 'numpy' has no attribute 'int'

[narzouni]

Hello,
When I try to run IDR on two replicates, it gives me the following attribute error:

AttributeError: module 'numpy' has no attribute 'int'

This is the command I am using for IDR:

idr --samples Rep1.narrowPeak Rep2.narrowPeak --input-file-type narrowPeak --rank p.value --output-file ELSIdr56 --plot --log-output-file ELSIDR56.log

Thanks,

[KMt9WT]

I suggest using a combination of numpy version 1.19.5 and idr, as using numpy version 1.20.0 or higher may cause inconsistencies with idr due to the deprecation of built-in type aliases like np.int .

https://numpy.org/doc/stable/release/1.20.0-notes.html#using-the-aliases-of-builtin-types-like-np-int-is-deprecated

[The1stMartian]

I was able to fix this issue by editing idr.py lines 305 and 306 from "numpy.int" to "numpy.int_"

[Nanderson246]

To fix the numpy.int issue use this change in docker file

sed -i 's/numpy.int/int/g' idr.py will replace all numpy.int instances with int, which is safe in this case, since that's the fix.
The --break-system-packages flag is only needed in Ubuntu 22.04+ with pip ≥23. Ensure your base image requires it.

Install IDR 2.0.4.2 and patch numpy.int usage

RUN apt-get update && apt-get install -y wget tar python3-pip build-essential python3-dev cython

WORKDIR /opt
RUN wget https://github.com/kundajelab/idr/archive/refs/tags/2.0.4.2.tar.gz &&
tar -xvf 2.0.4.2.tar.gz &&
cd idr-2.0.4.2/idr &&
sed -i 's/numpy.int/int/g' idr.py &&
cd .. &&
pip install . --break-system-packages &&
rm -rf /opt/idr-2.0.4.2 /opt/2.0.4.2.tar.gz