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from __future__ import annotations
from pathlib import Path
from subprocess import run
from typing import TYPE_CHECKING
import pandas as pd
import pytest
import zarr
import zarr.storage
from scipy import sparse
import anndata as ad
from anndata.compat import is_zarr_v2
from anndata.tests.helpers import assert_equal
if TYPE_CHECKING:
from typing import Literal
ARCHIVE_PTH = Path(__file__).parent / "data/archives"
@pytest.fixture(params=list(ARCHIVE_PTH.glob("v*")), ids=lambda x: x.name)
def archive_dir(request: pytest.FixtureRequest) -> Path:
return request.param
def read_archive(
archive_dir: Path, format: Literal["h5ad", "zarr"]
) -> tuple[ad.AnnData, Path]:
if format == "h5ad":
path = archive_dir / "adata.h5ad"
return ad.read_h5ad(path), path
if format == "zarr":
path = archive_dir / "adata.zarr.zip"
store = path if is_zarr_v2() else zarr.storage.ZipStore(path)
return ad.read_zarr(store), path
pytest.fail(f"Unknown format: {format}")
@pytest.mark.filterwarnings("ignore::anndata.OldFormatWarning")
def test_backwards_compat_files(archive_dir: Path) -> None:
from_h5ad, _ = read_archive(archive_dir, "h5ad")
from_zarr, _ = read_archive(archive_dir, "zarr")
assert_equal(from_h5ad, from_zarr, exact=True)
def test_no_diff(tmp_path: Path, archive_dir: Path) -> None:
if archive_dir.name in {"v0.7.8", "v0.7.0"}:
pytest.skip("DataFrame encoding changed between 0.7 and now")
adata, in_path = read_archive(archive_dir, "h5ad")
adata.write_h5ad(out_path := tmp_path / "adata.h5ad")
diff_proc = run(["h5diff", in_path, out_path], check=False)
assert diff_proc.returncode == 0
def test_clean_uns_backwards_compat(tmp_path, diskfmt):
pth = tmp_path / f"test_write.{diskfmt}"
write = lambda x, y: getattr(x, f"write_{diskfmt}")(y)
read = lambda x: getattr(ad, f"read_{diskfmt}")(x)
orig = ad.AnnData(
sparse.csr_matrix((3, 5), dtype="float32"),
obs=pd.DataFrame(
{"a": pd.Categorical(list("aab")), "b": [1, 2, 3]},
index=[f"cell_{i}" for i in range(3)],
),
uns={
"a_categories": "some string",
"b_categories": "another string",
},
)
write(orig, pth)
from_disk = read(pth)
assert_equal(orig, from_disk)
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