[Bug]: NumPy 2.0

[frahimov]

System information

No response

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/pandas_engine.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

No response

Command used and terminal output

No response

First 10 Rows of the Input File

No response

Relevant files

No response

[frahimov]

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.

[twillis209]

I'm not sure this adds much but @frahimov's post helped me install gwas-sff.

I tried installing into this conda environment:

channels:
- conda-forge
dependencies:
  - python=3.10
  - pip
  - pip:
      - gwas-sumstats-tools

I got this error:

tomw@toms-tpd:~/cam/serum_ig_pipeline$ gwas-ssf
Traceback (most recent call last):
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/bi
n/gwas-ssf", line 5, in <module>
    from gwas_sumstats_tools.cli import app
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/gwas_sumstats_tools/cli.py", line 8, in <module>
    from gwas_sumstats_tools.validate import validate
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/gwas_sumstats_tools/validate.py", line 3, in <module>
    import pandas as pd
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/pandas/__init__.py", line 22, in <module>
    from pandas.compat import is_numpy_dev as _is_numpy_dev  # pyright: ignore # noqa:F401
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/pandas/compat/__init__.py", line 18, in <module>
    from pandas.compat.numpy import (
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/pandas/compat/numpy/__init__.py", line 4, in <module>
    from pandas.util.version import Version
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/pandas/util/__init__.py", line 2, in <module>
    from pandas.util._decorators import (  # noqa:F401
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/pandas/util/_decorators.py", line 14, in <module>
    from pandas._libs.properties import cache_readonly
  File "/home/tomw/cam/serum_ig_pipeline/.snakemake/conda/8156fc3390a64db761657dd1a3ad2cc0_/li
b/python3.10/site-packages/pandas/_libs/__init__.py", line 13, in <module>
    from pandas._libs.interval import Interval
  File "pandas/_libs/interval.pyx", line 1, in init pandas._libs.interval
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C 
header, got 88 from PyObject

Stipulating numpy=1.25.0 like so allowed me to install the program correctly:

channels:
- conda-forge
dependencies:
  - python=3.10
  - numpy=1.25.0
  - pip
  - pip:
      - gwas-sumstats-tools

Thanks @frahimov! Thanks also to you folks at the EBISPOT team for working on this tool and the harmoniser, beats having to roll your own.