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"""Tests for backing by just sticking zarr/h5py objects into AnnData."""
from __future__ import annotations
from typing import TYPE_CHECKING
import h5py
import numpy as np
import pytest
import zarr
from anndata import AnnData
from anndata._io.zarr import open_write_group
from anndata.io import write_elem
from anndata.tests.helpers import assert_equal
if TYPE_CHECKING:
from pathlib import Path
from typing import Literal
@pytest.fixture
def file(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]) -> h5py.File | zarr.Group:
path = tmp_path / f"test.{diskfmt}"
if diskfmt == "zarr":
return open_write_group(path, mode="a")
if diskfmt == "h5ad":
return h5py.File(path, "a")
pytest.fail(f"Unknown diskfmt: {diskfmt}")
@pytest.mark.parametrize("assign", ["init", "assign"])
@pytest.mark.parametrize("attr", ["X", "obsm", "varm", "layers"])
def test_create_delete(
diskfmt: Literal["h5ad", "zarr"],
file: h5py.File | zarr.Group,
assign: Literal["init", "assign"],
attr: Literal["X", "obsm", "varm", "layers"],
):
x = np.random.randn(10, 10)
write_elem(file, "a", x)
# initialize (and if applicable, assign)
if assign == "init":
kw = (
dict(X=file["a"])
if attr == "X"
else {attr: dict(a=file["a"]), "shape": x.shape}
)
adata = AnnData(**kw)
elif assign == "assign":
adata = AnnData(shape=x.shape)
if attr == "X":
adata.X = file["a"]
else:
getattr(adata, attr)["a"] = file["a"]
else:
pytest.fail(f"Unexpected assign: {assign}")
# check equality
if attr == "X":
# TODO: should that be inverted, e.g. when the Dataset’s path matches the backed mode path?
assert not adata.isbacked
backed_array = adata.X
else:
backed_array = getattr(adata, attr)["a"]
assert isinstance(backed_array, zarr.Array if diskfmt == "zarr" else h5py.Dataset)
assert_equal(backed_array, x)
# check that there’s no error deleting it either
if attr == "X":
del adata.X
else:
del getattr(adata, attr)["a"]
def test_assign_x_subset(file: h5py.File | zarr.Group):
x = np.ones((10, 10))
write_elem(file, "a", x)
adata = AnnData(file["a"])
view = adata[3:7, 6:8]
view.X = np.zeros((4, 2))
expected = x.copy()
expected[3:7, 6:8] = np.zeros((4, 2))
assert_equal(adata.X, expected)
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