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"""\
This file contains tests for deprecated functions.
This includes correct behaviour as well as throwing warnings.
"""
from __future__ import annotations
import warnings
import h5py
import numpy as np
import pytest
from scipy import sparse
import anndata.experimental
from anndata import AnnData
from anndata.tests.helpers import assert_equal
@pytest.fixture
def adata():
adata = AnnData(
X=sparse.csr_matrix([[0, 2, 3], [0, 5, 6]], dtype=np.float32),
obs=dict(obs_names=["s1", "s2"], anno1=["c1", "c2"]),
var=dict(var_names=["a", "b", "c"]),
)
adata.raw = adata.copy()
adata.layers["x2"] = adata.X * 2
adata.var["anno2"] = ["p1", "p2", "p3"]
adata.X = adata.X / 2
return adata
def test_get_obsvar_array_warn(adata):
with pytest.warns(FutureWarning):
adata._get_obs_array("a")
with pytest.warns(FutureWarning):
adata._get_var_array("s1")
@pytest.mark.filterwarnings("ignore::FutureWarning")
def test_get_obsvar_array(adata):
assert np.allclose(adata._get_obs_array("a"), adata.obs_vector("a"))
assert np.allclose(
adata._get_obs_array("a", layer="x2"),
adata.obs_vector("a", layer="x2"),
)
assert np.allclose(
adata._get_obs_array("a", use_raw=True), adata.raw.obs_vector("a")
)
assert np.allclose(adata._get_var_array("s1"), adata.var_vector("s1"))
assert np.allclose(
adata._get_var_array("s1", layer="x2"),
adata.var_vector("s1", layer="x2"),
)
assert np.allclose(
adata._get_var_array("s1", use_raw=True), adata.raw.var_vector("s1")
)
def test_obsvar_vector_Xlayer(adata):
with pytest.warns(FutureWarning):
adata.var_vector("s1", layer="X")
with pytest.warns(FutureWarning):
adata.obs_vector("a", layer="X")
adata = adata.copy()
adata.layers["X"] = adata.X * 3
with warnings.catch_warnings():
warnings.simplefilter("error")
adata.var_vector("s1", layer="X")
adata.obs_vector("a", layer="X")
# This should break in 0.9
def test_dtype_warning():
# Tests a warning is thrown
with pytest.warns(FutureWarning):
a = AnnData(np.ones((3, 3)), dtype=np.float32)
assert a.X.dtype == np.float32
# This shouldn't warn, shouldn't copy
with warnings.catch_warnings(record=True) as record:
b_X = np.ones((3, 3), dtype=np.float64)
b = AnnData(b_X)
assert not record
assert b_X is b.X
assert b.X.dtype == np.float64
# Should warn, should copy
with pytest.warns(FutureWarning):
c_X = np.ones((3, 3), dtype=np.float32)
c = AnnData(c_X, dtype=np.float64)
assert not record
assert c_X is not c.X
assert c.X.dtype == np.float64
def test_deprecated_write_attribute(tmp_path):
pth = tmp_path / "file.h5"
A = np.random.randn(20, 10)
from anndata._io.utils import read_attribute, write_attribute
from anndata.io import read_elem
with h5py.File(pth, "w") as f:
with pytest.warns(FutureWarning, match=r"write_elem"):
write_attribute(f, "written_attribute", A)
with h5py.File(pth, "r") as f:
elem_A = read_elem(f["written_attribute"])
with pytest.warns(FutureWarning, match=r"read_elem"):
attribute_A = read_attribute(f["written_attribute"])
assert_equal(elem_A, attribute_A)
assert_equal(A, attribute_A)
@pytest.mark.parametrize(
("old_name", "new_name", "module"),
(
(old_name, new_name, module)
for module in [anndata, anndata.experimental]
for (old_name, new_name) in module._DEPRECATED.items()
),
)
def test_warn_on_import_with_redirect(old_name: str, new_name: str, module):
with pytest.warns(FutureWarning, match=rf"Importing {old_name}.*is deprecated"):
getattr(module, old_name)
def test_warn_on_deprecated__io_module():
with pytest.warns(
FutureWarning, match=r"Importing read_h5ad from `anndata._io` is deprecated"
):
from anndata._io import read_h5ad # noqa
|
