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from __future__ import annotations
import numpy as np
import pytest
from scipy import sparse
from anndata.tests.helpers import (
as_dense_dask_array,
assert_equal,
gen_adata,
)
from anndata.utils import asarray
@pytest.fixture(
params=[
np.array,
sparse.csr_matrix,
sparse.csc_matrix,
sparse.csr_array,
sparse.csc_array,
as_dense_dask_array,
],
ids=[
"np_array",
"scipy_csr",
"scipy_csc",
"scipy_csr_array",
"scipy_csc_array",
"dask_array",
],
)
def matrix_type(request):
return request.param
def subset_dim(adata, *, obs=slice(None), var=slice(None)):
# Should probably get used for test_inplace_subset_var and test_inplace_subset_obs
from anndata._core.index import _subset
return _subset(adata, (obs, var))
# TODO: Test values of .uns
def test_inplace_subset_var(matrix_type, subset_func):
orig = gen_adata((30, 30), X_type=matrix_type)
subset_idx = subset_func(orig.var_names)
modified = orig.copy()
from_view = orig[:, subset_idx].copy()
modified._inplace_subset_var(subset_idx)
assert_equal(asarray(from_view.X), asarray(modified.X), exact=True)
assert_equal(from_view.obs, modified.obs, exact=True)
assert_equal(from_view.var, modified.var, exact=True)
for k in from_view.obsm:
assert_equal(from_view.obsm[k], modified.obsm[k], exact=True)
assert_equal(orig.obsm[k], modified.obsm[k], exact=True)
for k in from_view.varm:
assert_equal(from_view.varm[k], modified.varm[k], exact=True)
for k in from_view.layers:
assert_equal(from_view.layers[k], modified.layers[k], exact=True)
def test_inplace_subset_obs(matrix_type, subset_func):
orig = gen_adata((30, 30), X_type=matrix_type)
subset_idx = subset_func(orig.obs_names)
modified = orig.copy()
from_view = orig[subset_idx, :].copy()
modified._inplace_subset_obs(subset_idx)
assert_equal(asarray(from_view.X), asarray(modified.X), exact=True)
assert_equal(from_view.obs, modified.obs, exact=True)
assert_equal(from_view.var, modified.var, exact=True)
for k in from_view.obsm:
assert_equal(from_view.obsm[k], modified.obsm[k], exact=True)
for k in from_view.varm:
assert_equal(from_view.varm[k], modified.varm[k], exact=True)
assert_equal(orig.varm[k], modified.varm[k], exact=True)
for k in from_view.layers:
assert_equal(from_view.layers[k], modified.layers[k], exact=True)
@pytest.mark.parametrize("dim", ["obs", "var"])
def test_inplace_subset_no_X(subset_func, dim):
orig = gen_adata((30, 30))
del orig.X
subset_idx = subset_func(getattr(orig, f"{dim}_names"))
modified = orig.copy()
from_view = subset_dim(orig, **{dim: subset_idx}).copy()
getattr(modified, f"_inplace_subset_{dim}")(subset_idx)
assert_equal(modified, from_view, exact=True)
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