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import numpy as np
import pytest
from sklearn.utils.testing import assert_array_equal
from scipy import sparse
from anndata.tests.helpers import gen_adata, subset_func
from anndata.utils import asarray
@pytest.fixture(
params=[np.array, sparse.csr_matrix, sparse.csc_matrix],
ids=["np_array", "scipy_csr", "scipy_csc"],
)
def matrix_type(request):
return request.param
# 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_array_equal(asarray(from_view.X), asarray(modified.X))
assert_array_equal(from_view.obs, modified.obs)
assert_array_equal(from_view.var, modified.var)
for k in from_view.obsm:
assert_array_equal(asarray(from_view.obsm[k]), asarray(modified.obsm[k]))
assert_array_equal(asarray(orig.obsm[k]), asarray(modified.obsm[k]))
for k in from_view.varm:
assert_array_equal(asarray(from_view.varm[k]), asarray(modified.varm[k]))
for k in from_view.layers:
assert_array_equal(asarray(from_view.layers[k]), asarray(modified.layers[k]))
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_array_equal(asarray(from_view.X), asarray(modified.X))
assert_array_equal(from_view.obs, modified.obs)
assert_array_equal(from_view.var, modified.var)
for k in from_view.obsm:
assert_array_equal(asarray(from_view.obsm[k]), asarray(modified.obsm[k]))
for k in from_view.varm:
assert_array_equal(asarray(from_view.varm[k]), asarray(modified.varm[k]))
assert_array_equal(asarray(orig.varm[k]), asarray(modified.varm[k]))
for k in from_view.layers:
assert_array_equal(asarray(from_view.layers[k]), asarray(modified.layers[k]))
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