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import h5py
import numpy as np
import pytest
from scipy import sparse
import anndata as ad
from anndata._core.sparse_dataset import SparseDataset
from anndata.tests.helpers import assert_equal, subset_func
subset_func2 = subset_func
@pytest.fixture(scope="function")
def ondisk_equivalent_adata(tmp_path):
csr_path = tmp_path / "csr.h5ad"
csc_path = tmp_path / "csc.h5ad"
dense_path = tmp_path / "dense.h5ad"
csr_mem = ad.AnnData(X=sparse.random(50, 50, format="csr", density=0.1))
csc_mem = ad.AnnData(X=csr_mem.X.tocsc())
csr_mem.write_h5ad(csr_path)
csc_mem.write_h5ad(csc_path)
csr_mem.write_h5ad(dense_path, as_dense="X")
csr_disk = ad.read_h5ad(csr_path, backed="r")
csc_disk = ad.read_h5ad(csc_path, backed="r")
dense_disk = ad.read_h5ad(dense_path, backed="r")
return csr_mem, csr_disk, csc_disk, dense_disk
def test_backed_indexing(ondisk_equivalent_adata, subset_func, subset_func2):
csr_mem, csr_disk, csc_disk, dense_disk = ondisk_equivalent_adata
obs_idx = subset_func(csr_mem.obs_names)
var_idx = subset_func2(csr_mem.var_names)
assert_equal(csr_mem[obs_idx, var_idx].X, csr_disk[obs_idx, var_idx].X)
assert_equal(csr_mem[obs_idx, var_idx].X, csc_disk[obs_idx, var_idx].X)
assert_equal(csr_mem[obs_idx, :].X, dense_disk[obs_idx, :].X)
assert_equal(csr_mem[:, var_idx].X, dense_disk[:, var_idx].X)
@pytest.mark.parametrize(
["sparse_format", "append_method"],
[
pytest.param(sparse.csr_matrix, sparse.vstack),
pytest.param(sparse.csc_matrix, sparse.hstack),
],
)
def test_dataset_append_memory(tmp_path, sparse_format, append_method):
h5_path = tmp_path / "test.h5"
a = sparse_format(sparse.random(100, 100))
b = sparse_format(sparse.random(100, 100))
with h5py.File(h5_path, "a") as f:
ad._io.h5ad.write_attribute(f, "mtx", a)
diskmtx = SparseDataset(f["mtx"])
diskmtx.append(b)
fromdisk = diskmtx.to_memory()
frommem = append_method([a, b])
assert_equal(fromdisk, frommem)
@pytest.mark.parametrize(
["sparse_format", "append_method"],
[
pytest.param(sparse.csr_matrix, sparse.vstack),
pytest.param(sparse.csc_matrix, sparse.hstack),
],
)
def test_dataset_append_disk(tmp_path, sparse_format, append_method):
h5_path = tmp_path / "test.h5"
a = sparse_format(sparse.random(10, 10))
b = sparse_format(sparse.random(10, 10))
with h5py.File(h5_path, "a") as f:
ad._io.h5ad.write_attribute(f, "a", a)
ad._io.h5ad.write_attribute(f, "b", b)
a_disk = SparseDataset(f["a"])
b_disk = SparseDataset(f["b"])
a_disk.append(b_disk)
fromdisk = a_disk.to_memory()
frommem = append_method([a, b])
assert_equal(fromdisk, frommem)
@pytest.mark.parametrize(
["sparse_format", "a_shape", "b_shape"],
[
pytest.param("csr", (100, 100), (100, 200)),
pytest.param("csc", (100, 100), (200, 100)),
],
)
def test_wrong_shape(tmp_path, sparse_format, a_shape, b_shape):
h5_path = tmp_path / "base.h5"
a_mem = sparse.random(*a_shape, format=sparse_format)
b_mem = sparse.random(*b_shape, format=sparse_format)
with h5py.File(h5_path, "a") as f:
ad._io.h5ad.write_attribute(f, "a", a_mem)
ad._io.h5ad.write_attribute(f, "b", b_mem)
a_disk = SparseDataset(f["a"])
b_disk = SparseDataset(f["b"])
with pytest.raises(AssertionError):
a_disk.append(b_disk)
def test_wrong_formats(tmp_path):
h5_path = tmp_path / "base.h5"
base = sparse.random(100, 100, format="csr")
with h5py.File(h5_path, "a") as f:
ad._io.h5ad.write_attribute(f, "base", base)
disk_mtx = SparseDataset(f["base"])
pre_checks = disk_mtx.to_memory()
with pytest.raises(ValueError):
disk_mtx.append(sparse.random(100, 100, format="csc"))
with pytest.raises(ValueError):
disk_mtx.append(sparse.random(100, 100, format="coo"))
with pytest.raises(NotImplementedError):
disk_mtx.append(np.random.random((100, 100)))
disk_dense = f.create_dataset("dense", data=np.random.random((100, 100)))
with pytest.raises(NotImplementedError):
disk_mtx.append(disk_dense)
post_checks = disk_mtx.to_memory()
# Check nothing changed
assert not np.any((pre_checks != post_checks).toarray())
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