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"""\
This file contains tests for deprecated functions.
This includes correct behaviour as well as throwing warnings.
"""
import h5py
import numpy as np
import pytest
from scipy import sparse
import anndata as ad
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]]),
obs=dict(obs_names=["s1", "s2"], anno1=["c1", "c2"]),
var=dict(var_names=["a", "b", "c"]),
)
adata.raw = adata
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(DeprecationWarning):
adata._get_obs_array("a")
with pytest.warns(DeprecationWarning):
adata._get_var_array("s1")
# TODO: Why doesn’t this mark work?
# @pytest.mark.filterwarnings("ignore::DeprecationWarning")
def test_get_obsvar_array(adata):
with pytest.warns(DeprecationWarning): # Just to hide warnings
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 pytest.warns(None) as records:
adata.var_vector("s1", layer="X")
adata.obs_vector("a", layer="X")
for r in records:
# This time it shouldn’t throw a warning
if "anndata" in r.filename:
assert r.category is not FutureWarning
def test_force_dense_deprecated(tmp_path):
dense_pth = tmp_path / "dense.h5ad"
adata = AnnData(X=sparse.random(10, 10, format="csr"))
adata.raw = adata
with pytest.warns(FutureWarning):
adata.write_h5ad(dense_pth, force_dense=True)
with h5py.File(dense_pth, "r") as f:
assert isinstance(f["X"], h5py.Dataset)
assert isinstance(f["raw/X"], h5py.Dataset)
dense = ad.read_h5ad(dense_pth)
assert isinstance(dense.X, np.ndarray)
assert isinstance(dense.raw.X, np.ndarray)
assert_equal(adata, dense)
#######################################
# Dealing with uns adj matrices
#######################################
def test_get_uns_neighbors_deprecated(adata):
n = adata.shape[0]
mtx = sparse.random(n, n, density=0.3, format="csr")
adata.obsp["connectivities"] = mtx
adata.uns["neighbors"] = {}
with pytest.warns(FutureWarning):
from_uns = adata.uns["neighbors"]["connectivities"]
assert_equal(from_uns, mtx)
with pytest.warns(None) as rec:
v = adata[: n // 2]
assert not rec
with pytest.warns(FutureWarning):
from_uns_v = v.uns["neighbors"]["connectivities"]
assert_equal(from_uns_v, v.obsp["connectivities"])
def test_set_uns_neighbors_deprecated(adata):
n = adata.shape[0]
mtx = sparse.random(n, n, format="csr")
adata.uns["neighbors"] = {}
with pytest.warns(FutureWarning):
adata.uns["neighbors"]["connectivities"] = sparse.random(n, n, format="csr")
assert_equal(adata.obsp["connectivities"], mtx)
with pytest.warns(FutureWarning):
assert_equal(adata.uns["neighbors"]["connectivities"], mtx)
# Make sure that we can write to uns normally:
adata.uns["new_key"] = 100
assert adata.uns["new_key"] == 100
def test_slice_uns_sparse_deprecated():
adata = AnnData(sparse.csr_matrix((500, 10)))
n = adata.shape[0]
mtx = sparse.random(n, n, density=0.2, format="csr")
adata.uns["sparse_mtx"] = mtx
with pytest.warns(FutureWarning):
v = adata[: n // 2]
assert_equal(adata.uns["sparse_mtx"], mtx)
assert_equal(v.uns["sparse_mtx"], mtx[: n // 2, : n // 2])
@pytest.fixture
def adata_neighbors():
return ad.AnnData(
X=sparse.random(100, 200, format="csr"),
obsp=dict(
distances=sparse.random(100, 100, format="csr"),
connectivities=sparse.random(100, 100, format="csr"),
),
uns={"neighbors": {"params": {"method": "umap", "n_neighbors": 10}}},
)
def test_deprecated_neighbors_get_mtx(adata_neighbors):
"""Test getting neighbor matrices from adata.uns"""
adata = adata_neighbors
with pytest.warns(FutureWarning):
assert_equal(adata.obsp["distances"], adata.uns["neighbors"]["distances"])
with pytest.warns(FutureWarning):
assert_equal(
adata.obsp["connectivities"], adata.uns["neighbors"]["connectivities"]
)
def test_deprecated_neighbors_get_other(adata_neighbors):
"""Test getting other fields from adata.uns"""
adata = adata_neighbors
# This shouldn't throw a warning
with pytest.warns(None) as rec:
assert adata.uns["neighbors"]["params"] == {"method": "umap", "n_neighbors": 10}
assert not rec
def test_deprecated_neighbors_set_other(adata_neighbors):
adata = adata_neighbors
# This shouldn't throw a warning
with pytest.warns(None) as rec:
adata.uns["neighbors"]["new_key"] = 10
assert adata.uns["neighbors"]["new_key"] == 10
# Test nested
adata.uns["neighbors"]["params"]["new_param"] = 100
assert adata.uns["neighbors"]["params"]["new_param"] == 100
assert adata.uns["neighbors"]["params"] == {
"method": "umap",
"n_neighbors": 10,
"new_param": 100,
}
assert not rec
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