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spatial_autocorr limit the numba threads as n_jobs temporarily #984

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spatial_autocorr limit the numba threads as n_jobs temporarily #984

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25 changes: 15 additions & 10 deletions src/squidpy/gr/_ppatterns.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
import numpy as np
import pandas as pd
from anndata import AnnData
from numba import njit
from numba import get_num_threads, njit, set_num_threads
from numpy.random import default_rng
from scanpy import logging as logg
from scanpy.get import _get_obs_rep
Expand Down Expand Up @@ -206,15 +206,20 @@ def extract_obsm(adata: AnnData, ixs: int | Sequence[int] | None) -> tuple[NDArr
_assert_positive(n_perms, name="n_perms")
perms = list(np.arange(n_perms))

score_perms = parallelize(
_score_helper,
collection=perms,
extractor=np.concatenate,
use_ixs=True,
n_jobs=n_jobs,
backend=backend,
show_progress_bar=show_progress_bar,
)(mode=mode, g=g, vals=vals, seed=seed)
old_n_jobs = get_num_threads()
set_num_threads(n_jobs)
try:
score_perms = parallelize(
_score_helper,
collection=perms,
extractor=np.concatenate,
use_ixs=True,
n_jobs=n_jobs,
backend=backend,
show_progress_bar=show_progress_bar,
)(mode=mode, g=g, vals=vals, seed=seed)
finally:
set_num_threads(old_n_jobs)
else:
score_perms = None

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