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from __future__ import annotations
import re
import warnings
from importlib.util import find_spec
from pathlib import Path
import pytest
import anndata as ad
from anndata.tests.helpers import GEN_ADATA_NO_XARRAY_ARGS, gen_adata
@pytest.mark.skipif(not find_spec("scanpy"), reason="Scanpy is not installed")
def test_old_format_warning_thrown() -> None:
import scanpy as sc
def msg_re(entry: str) -> str:
return re.escape(
f"Moving element from .uns['neighbors'][{entry!r}] to .obsp[{entry!r}]."
)
pth = Path(sc.datasets.__file__).parent / "10x_pbmc68k_reduced.h5ad"
warnings.simplefilter("default", FutureWarning)
with (
pytest.warns(FutureWarning, match=msg_re("distances")),
pytest.warns(FutureWarning, match=msg_re("connectivities")),
pytest.warns(ad.OldFormatWarning),
):
ad.read_h5ad(pth)
def test_old_format_warning_not_thrown(tmp_path: Path) -> None:
pth = tmp_path / "current.h5ad"
adata = gen_adata((20, 10), **GEN_ADATA_NO_XARRAY_ARGS)
adata.write_h5ad(pth)
with warnings.catch_warnings(record=True) as record:
warnings.simplefilter("always", ad.OldFormatWarning)
ad.read_h5ad(pth)
if len(record) != 0:
msg_content = "\n".join([
f"\t{w.category.__name__}('{w.message}')" for w in record
])
pytest.fail(
f"Warnings were thrown when they shouldn't be. Got:\n\n{msg_content}"
)
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