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
|
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
import numpy as np
import pytest
from anndata import AnnData
from anndata.experimental.backed._io import read_lazy
if TYPE_CHECKING:
from pathlib import Path
from typing import Literal
pytestmark = pytest.mark.skipif(not find_spec("xarray"), reason="xarray not installed")
@pytest.mark.parametrize("fmt", ["zarr", "h5ad", "loom", "csvs"])
@pytest.mark.parametrize("key", ["obs", "var", "obsm", "varm"])
def test_write_error(
tmp_path: Path,
fmt: Literal["zarr", "h5ad", "loom", "csvs"],
key: Literal["obs", "var", "obsm", "varm"],
):
path = tmp_path / "adata.h5ad"
X = np.random.random((4, 4))
adata = AnnData(X=X)
if key.endswith("m"):
elem = {"df": getattr(adata, key[:-1])}
setattr(adata, key, elem)
adata.write_h5ad(path)
adata_lazy = read_lazy(path)
if key.endswith("m"):
adata_lazy.obs = adata_lazy.obs.to_memory()
adata_lazy.obs = adata_lazy.var.to_memory()
noop_path = tmp_path / f"adata_noop.{fmt}"
with pytest.raises(
NotImplementedError,
match=r"Writing AnnData objects with a Dataset2D not supported yet. Please use `ds.to_memory`",
):
getattr(adata_lazy, f"write_{fmt}")(noop_path)
assert not noop_path.exists(), (
"Found a directory at the path at which no data should have been written"
)
|
