Unable to successfully install vcf2gwas in new conda environment - numpy dependency version problems

[TobyBaril]

Hi,

I am following the instructions on the installation page. The environment is created properly with no conflicts, but I think there is an issue with the conda recipe, as an incompatible version of NumPy is installed, and I cannot install the correct version to satisfy the dependency:

vcf2gwas -v test

vcf2gwas v0.8.8 

Initialising..

Copying example input files to current working directory..
Copying README and LICENSE files..
/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/seaborn/utils.py:10: UserWarning: A NumPy version >=1.22.4 and <2.3.0 is required for this version of SciPy (detected version 1.20.3)
  from scipy import stats
Traceback (most recent call last):
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/starter.py", line 23, in <module>
    from vcf2gwas.utils import *
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/utils.py", line 54, in <module>
    import seaborn as sns
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/seaborn/__init__.py", line 2, in <module>
    from .rcmod import *  # noqa: F401,F403
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/seaborn/rcmod.py", line 7, in <module>
    from . import palettes
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/seaborn/palettes.py", line 9, in <module>
    from .utils import desaturate, get_color_cycle
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/seaborn/utils.py", line 10, in <module>
    from scipy import stats
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/__init__.py", line 134, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/stats/__init__.py", line 606, in <module>
    from ._stats_py import *
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 37, in <module>
    from scipy import sparse
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/__init__.py", line 134, in __getattr__
    return _importlib.import_module(f'scipy.{name}')
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/sparse/__init__.py", line 294, in <module>
    from ._base import *
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/sparse/_base.py", line 5, in <module>
    from scipy._lib._util import VisibleDeprecationWarning
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/_lib/_util.py", line 18, in <module>
    from scipy._lib._array_api import array_namespace
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/_lib/_array_api.py", line 17, in <module>
    from scipy._lib.array_api_compat import (
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/_lib/array_api_compat/numpy/__init__.py", line 16, in <module>
    __import__(__package__ + '.linalg')
  File "/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/scipy/_lib/array_api_compat/numpy/linalg.py", line 2, in <module>
    from numpy.linalg import __all__ as linalg_all
ImportError: cannot import name '__all__' from 'numpy.linalg' (/data/toby/mambaforge/envs/vcf2gwas/lib/python3.9/site-packages/numpy/linalg/__init__.py)

[TobyBaril]

As an extra note, it seems the recipe specifies a compatible version (numpy=1.23), but the environment consistently installs v1.20.3 for some reason...

[tottlefields]

I am having the same issue. I love this package and would really like to get it to work for me again, please!

[TobyBaril]

A long time later but activating the env and then installing numpy 1.23 manually with pip works!

pip install numpy==1.23

It will throw a warning that it could not successfully parse the requirements of vcf2gwas which I think is what is causing the issues in the first place, but the test then completes successfully!

WARNING: Error parsing dependencies of vcf2gwas: Expected matching RIGHT_PARENTHESIS for LEFT_PARENTHESIS, after version specifier
    numpy (==1.20*)