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from importlib.util import find_spec
import pytest
import numpy as np
import pandas as pd
from anndata import AnnData, read_loom, read_h5ad
from anndata.tests.helpers import gen_typed_df_t2_size
X = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
L = np.array([[10, 11, 12], [13, 14, 15], [16, 17, 18]])
def test_creation():
adata = AnnData(X=X, layers=dict(L=L.copy()))
assert list(adata.layers.keys()) == ["L"]
assert "L" in adata.layers
assert "X" not in adata.layers
assert "some_other_thing" not in adata.layers
assert (adata.layers["L"] == L).all()
def test_views():
adata = AnnData(X=X, layers=dict(L=L.copy()))
adata_view = adata[1:, 1:]
assert adata_view.layers.is_view
assert adata_view.layers.parent_mapping == adata.layers
assert adata_view.layers.keys() == adata.layers.keys()
assert (adata_view.layers["L"] == adata.layers["L"][1:, 1:]).all()
adata.layers["S"] = X
assert adata_view.layers.keys() == adata.layers.keys()
assert (adata_view.layers["S"] == adata.layers["S"][1:, 1:]).all()
adata_view.layers["T"] = X[1:, 1:]
assert not adata_view.layers.is_view
assert not adata_view.is_view
@pytest.mark.parametrize(
"df,homogenous,dtype",
[
(lambda: gen_typed_df_t2_size(*X.shape), True, np.object_),
(lambda: pd.DataFrame(X ** 2), False, np.int_),
],
)
def test_set_dataframe(homogenous, df, dtype):
adata = AnnData(X)
if homogenous:
with pytest.warns(UserWarning, match=r"Layer 'df'.*dtype object"):
adata.layers["df"] = df()
else:
with pytest.warns(None) as warnings:
adata.layers["df"] = df()
assert not len(warnings)
assert isinstance(adata.layers["df"], np.ndarray)
def test_readwrite(backing_h5ad):
adata = AnnData(X=X, layers=dict(L=L.copy()))
adata.write(backing_h5ad)
adata_read = read_h5ad(backing_h5ad)
assert adata.layers.keys() == adata_read.layers.keys()
assert (adata.layers["L"] == adata_read.layers["L"]).all()
@pytest.mark.skipif(find_spec("loompy") is None, reason="loompy not installed")
def test_readwrite_loom(tmp_path):
loom_path = tmp_path / "test.loom"
adata = AnnData(X=X, layers=dict(L=L.copy()))
adata.write_loom(loom_path)
adata_read = read_loom(loom_path, X_name="")
assert adata.layers.keys() == adata_read.layers.keys()
assert (adata.layers["L"] == adata_read.layers["L"]).all()
def test_backed():
# backed mode for layers isn’t implemented, layers stay in memory
pass
def test_copy():
adata = AnnData(X=X, layers=dict(L=L.copy()))
bdata = adata.copy()
adata.layers["L"] += 10
assert np.all(adata.layers["L"] != bdata.layers["L"]) # 201
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