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EBISPOT / gwas-sumstats-tools

Apache License 2.0
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[Bug]: NumPy 2.0 #45

Open frahimov opened 3 days ago

frahimov commented 3 days ago

System information

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Description of the Issue

Hello, I installed gwas-sumstats-tools in a conda environment. But I get the following error message when I run gwas_ssf. (gwas-sumstats-tools) rahimfx1@aurora:~> gwas-ssf --help

Traceback (most recent call last): File "/homes/rahimfx1/mambaforge/envs/gwas-sumstats-tools/bin/gwas-ssf", line 5, in from gwas_sumstats_tools.cli import app File "/homes/rahimfx1/mambaforge/envs/gwas-sumstats-tools/lib/python3.10/site-packages/gwas_sumstats_tools/cli.py", line 8, in from gwas_sumstats_tools.validate import validate File "/homes/rahimfx1/mambaforge/envs/gwas-sumstats-tools/lib/python3.10/site-packages/gwas_sumstats_tools/validate.py", line 5, in from pandera import errors File "/homes/rahimfx1/mambaforge/envs/gwas-sumstats-tools/lib/python3.10/site-packages/pandera/init.py", line 34, in from pandera.engines.pandas_engine import ( File "/homes/rahimfx1/mambaforge/envs/gwas-sumstats-tools/lib/python3.10/site-packages/pandera/engines/pandasengine.py", line 693, in np.string, File "/homes/rahimfx1/mambaforge/envs/gwas-sumstats-tools/lib/python3.10/site-packages/numpy/init.py", line 400, in getattr raise AttributeError( AttributeError: np.string_ was removed in the NumPy 2.0 release. Use np.bytes_ instead.

Error Message

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Command used and terminal output

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First 10 Rows of the Input File

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Relevant files

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frahimov commented 3 days ago

A quick update. Downgrading NumPy to version 1.25.0 resolved the issue. This seems to be the latest version supported by Python 3.9-3.11.