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from __future__ import annotations
from contextlib import nullcontext
from itertools import combinations, product
from typing import TYPE_CHECKING
import numpy as np
import pytest
import anndata as ad
from anndata import AnnData
from anndata.tests.helpers import gen_vstr_recarray
if TYPE_CHECKING:
from typing import Literal
def assert_str_contents_equal(A, B):
lA = [
[str(el) if not isinstance(el, bytes) else el.decode("utf-8") for el in a]
for a in A
]
lB = [
[str(el) if not isinstance(el, bytes) else el.decode("utf-8") for el in b]
for b in B
]
assert lA == lB
def test_io(
tmp_path, diskfmt: Literal["zarr", "h5ad"], diskfmt2: Literal["zarr", "h5ad"]
):
read1 = lambda pth: getattr(ad, f"read_{diskfmt}")(pth)
write1 = lambda adata, pth: getattr(adata, f"write_{diskfmt}")(pth)
read2 = lambda pth: getattr(ad, f"read_{diskfmt2}")(pth)
write2 = lambda adata, pth: getattr(adata, f"write_{diskfmt2}")(pth)
filepth1 = tmp_path / f"test1.{diskfmt}"
filepth2 = tmp_path / f"test2.{diskfmt2}"
str_recarray = gen_vstr_recarray(3, 5)
u_recarray = str_recarray.astype([(n, "U10") for n in str_recarray.dtype.fields])
s_recarray = str_recarray.astype([(n, "S10") for n in str_recarray.dtype.fields])
initial = AnnData(np.zeros((3, 3)))
initial.uns = dict(str_rec=str_recarray, u_rec=u_recarray, s_rec=s_recarray)
with (
pytest.raises(
NotImplementedError, match=r"zarr v3 does not support structured dtypes"
)
if diskfmt == "zarr" and ad.settings.zarr_write_format == 3
else nullcontext()
):
write1(initial, filepth1)
disk_once = read1(filepth1)
write2(disk_once, filepth2)
disk_twice = read2(filepth2)
adatas = [initial, disk_once, disk_twice]
keys = [
"str_rec",
"u_rec",
# "s_rec"
]
for (ad1, key1), (ad2, key2) in combinations(product(adatas, keys), 2):
assert_str_contents_equal(ad1.uns[key1], ad2.uns[key2])
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