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from __future__ import annotations
import numpy as np
import pytest
import anndata as ad
from anndata import ImplicitModificationWarning
from anndata.tests.helpers import GEN_ADATA_DASK_ARGS, assert_equal, gen_adata
# -------------------------------------------------------------------------------
# Some test data
# -------------------------------------------------------------------------------
data = [
[1, 2, 3],
[4, 5, 6],
[7, 8, 9],
] # data matrix of shape n_obs × n_vars
obs_dict = dict( # annotation of observations / rows
row_names=["name1", "name2", "name3"], # row annotation
oanno1=["cat1", "cat2", "cat2"], # categorical annotation
oanno2=["o1", "o2", "o3"], # string annotation
oanno3=[2.1, 2.2, 2.3], # float annotation
)
var_dict = dict( # annotation of variables / columns
col_names=["var1", "var2", "var3"], vanno1=[3.1, 3.2, 3.3]
)
uns_dict = dict( # unstructured annotation
oanno1_colors=["#000000", "#FFFFFF"], uns2=["some annotation"]
)
@pytest.fixture
def adata_raw() -> ad.AnnData:
adata = ad.AnnData(
np.array(data, dtype="int32"), obs=obs_dict, var=var_dict, uns=uns_dict
)
adata.raw = adata.copy()
# Make them different shapes
adata = adata[:, [0, 1]].copy()
return adata
# -------------------------------------------------------------------------------
# The test functions
# -------------------------------------------------------------------------------
def test_raw_init(adata_raw: ad.AnnData):
assert adata_raw.var_names.tolist() == ["var1", "var2"]
assert adata_raw.raw.var_names.tolist() == ["var1", "var2", "var3"]
assert adata_raw.raw[:, 0].X.tolist() == [[1], [4], [7]]
def test_raw_del(adata_raw: ad.AnnData):
del adata_raw.raw
assert adata_raw.raw is None
def test_raw_set_as_none(adata_raw: ad.AnnData):
# Test for scverse/anndata#445
a = adata_raw
b = adata_raw.copy()
del a.raw
b.raw = None
assert_equal(a, b)
def test_raw_of_view(adata_raw: ad.AnnData):
adata_view = adata_raw[adata_raw.obs["oanno1"] == "cat2"]
assert adata_view.raw.X.tolist() == [
[4, 5, 6],
[7, 8, 9],
]
def test_raw_rw(adata_raw: ad.AnnData, backing_h5ad):
adata_raw.write(backing_h5ad)
adata_read = ad.read_h5ad(backing_h5ad)
assert_equal(adata_read, adata_raw, exact=True)
assert adata_raw.var_names.tolist() == ["var1", "var2"]
assert adata_raw.raw.var_names.tolist() == ["var1", "var2", "var3"]
assert adata_raw.raw[:, 0].X.tolist() == [[1], [4], [7]]
def test_raw_view_rw(adata_raw: ad.AnnData, backing_h5ad):
# Make sure it still writes correctly if the object is a view
adata_raw_view = adata_raw[:, adata_raw.var_names]
assert_equal(adata_raw_view, adata_raw)
with pytest.warns(
ImplicitModificationWarning, match=r"initializing view as actual"
):
adata_raw_view.write(backing_h5ad)
adata_read = ad.read_h5ad(backing_h5ad)
assert_equal(adata_read, adata_raw_view, exact=True)
assert adata_raw.var_names.tolist() == ["var1", "var2"]
assert adata_raw.raw.var_names.tolist() == ["var1", "var2", "var3"]
assert adata_raw.raw[:, 0].X.tolist() == [[1], [4], [7]]
def test_raw_backed(adata_raw: ad.AnnData, backing_h5ad):
adata_raw.filename = backing_h5ad
assert adata_raw.var_names.tolist() == ["var1", "var2"]
assert adata_raw.raw.var_names.tolist() == ["var1", "var2", "var3"]
if adata_raw.raw[:, 0].X.shape[1] != 1:
pytest.xfail("Raw is broken for backed slices")
assert adata_raw.raw[:, 0].X[:].tolist() == [[1], [4], [7]]
def test_raw_view_backed(adata_raw: ad.AnnData, backing_h5ad):
adata_raw.filename = backing_h5ad
assert adata_raw.var_names.tolist() == ["var1", "var2"]
assert adata_raw.raw.var_names.tolist() == ["var1", "var2", "var3"]
if adata_raw.raw[:, 0].X.shape[1] != 1:
pytest.xfail("Raw is broken for backed slices")
assert adata_raw.raw[:, 0].X[:].tolist() == [[1], [4], [7]]
def test_raw_as_parent_view():
# https://github.com/scverse/anndata/issues/288
a = ad.AnnData(np.ones((4, 3)))
a.varm["PCs"] = np.ones((3, 3))
a.raw = a.copy()
# create a Raw containing views. This used to trigger #288.
b = a.raw[:, "0"]
# actualize
b.varm["PCs"] = np.array([[1, 2, 3]])
def test_to_adata():
# https://github.com/scverse/anndata/pull/404
adata = gen_adata((20, 10), **GEN_ADATA_DASK_ARGS)
with_raw = adata[:, ::2].copy()
with_raw.raw = adata.copy()
# Raw doesn't do layers or varp currently
# Deleting after creation so we know to rewrite the test if they are supported
del adata.layers, adata.varp
assert_equal(adata, with_raw.raw.to_adata())
def test_to_adata_populates_obs():
adata = gen_adata((20, 10), **GEN_ADATA_DASK_ARGS)
del adata.layers, adata.uns, adata.varp
adata_w_raw = adata.copy()
raw = adata.copy()
del raw.obs, raw.obsm, raw.obsp, raw.uns
adata_w_raw.raw = raw
from_raw = adata_w_raw.raw.to_adata()
assert_equal(adata, from_raw)
def test_no_copy():
adata = gen_adata((20, 10), X_type=np.asarray)
adata.raw = adata # no .copy() herer
np.log1p(adata.X, out=adata.X)
assert adata.X is adata.raw.X
|
