Bgen

[SantiDu]

Two changes were made here:

1. Conda/Mamba and Pixi seem to install numpy>=2 even though the yaml file states numpy=1.26, but scipy requires numpy<2:

/home/j/jidu/MetaXcan-0.8.1/software/metax/gwas/GWAS.py:5: UserWarning: A NumPy version >=1.22.4 and <1.29.0 is required for this version of SciPy (detected version 2.0.2)
  import scipy.stats as stats
Traceback (most recent call last):
  File "/home/j/jidu/MetaXcan-0.8.1/software/Predict.py", line 16, in <module>
    from metax.genotype import Genotype
...
    from ._kdtree import *
  File "/scratch/tmp/jidu/predict/.pixi/envs/imlabtools/lib/python3.9/site-packages/scipy/spatial/_kdtree.py", line 4, in <module>
    from ._ckdtree import cKDTree, cKDTreeNode
  File "_ckdtree.pyx", line 1, in init scipy.spatial._ckdtree
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

The proposed change in the yaml file uses pip to install scipy and numpy so this incompatibility disappeared.

2. It takes forever to use bgen-reader to iterate a bgen file, so I switched to the bgen package. Now the speed of using bgen for prediction is really faster than using vcf.