1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
|
from __future__ import annotations
import numpy as np
import pytest
from scipy import sparse
import anndata as ad
from anndata.tests.helpers import assert_equal, gen_adata, shares_memory
def test_transpose_orig():
"""
Original test for transpose, should be covered by more thorough tests below, but
keeping around just in case.
"""
adata = gen_adata((5, 3))
adata.varp = {f"varp_{k}": v for k, v in adata.varp.items()}
adata1 = adata.T
adata1.uns["test123"] = 1
assert "test123" in adata.uns
assert_equal(adata1.X.shape, (3, 5))
assert_equal(adata1.obsp.keys(), adata.varp.keys())
def _add_raw(adata, *, var_subset=slice(None)):
new = adata[:, var_subset].copy()
new.raw = adata.copy()
return new
# TODO: Cases to add:
# * Views
# * X is None should have the xfail marker removed
# * Backed
@pytest.fixture(
params=[
pytest.param(gen_adata((50, 20)), id="csr_X"),
pytest.param(gen_adata((50, 20), sparse.csc_matrix), id="csc_X"),
pytest.param(_add_raw(gen_adata((50, 20))), id="with_raw"),
pytest.param(gen_adata((20, 10), X_type=None), id="None_X"),
]
)
def adata(request):
return request.param
def test_transpose_doesnt_copy():
adata = ad.AnnData(
sparse.random(50, 20, format="csr"),
layers={
"sparse": sparse.random(50, 20, format="csc"),
"dense": np.random.rand(50, 20),
},
obsm={
"sparse": sparse.random(50, 10, format="csc"),
"dense": np.random.rand(50, 10),
},
obsp={
"sparse": sparse.random(50, 50, format="csc"),
"dense": np.random.rand(50, 50),
},
)
t = adata.T
assert shares_memory(adata.X, t.X)
for k in adata.obsm:
assert shares_memory(adata.obsm[k], t.varm[k])
for k in adata.obsp:
assert shares_memory(adata.obsp[k], t.varp[k])
for k in adata.layers:
assert shares_memory(adata.layers[k], t.layers[k])
def test_transpose_removes_raw(adata):
"""
Since Raw must have the same `obs_names` as AnnData, but does not have the same
`var_names`, transpose doesn't really make sense for Raw. So it should just get
deleted.
"""
assert adata.T.raw is None
def test_transposed_contents(adata):
t = adata.T
if adata.X is not None:
assert_equal(adata.X.T, t.X)
else:
assert adata.X is t.X is None
assert_equal(
{k: v.T for k, v in adata.layers.items()}, {k: v for k, v in t.layers.items()}
)
assert_equal(adata.obs, t.var)
assert_equal(adata.var, t.obs)
assert_equal(dict(adata.obsm), dict(t.varm))
assert_equal(dict(adata.varm), dict(t.obsm))
assert_equal(dict(adata.obsp), dict(t.varp))
assert_equal(dict(adata.varp), dict(t.obsp))
assert_equal(adata.uns, t.uns)
def test_transpose_roundtrip(adata):
del adata.raw
assert_equal(adata, adata.T.T)
|
