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"""
For tests using dask
"""
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import pytest
from scipy import sparse
import anndata as ad
from anndata._core.anndata import AnnData
from anndata.compat import CupyArray, DaskArray
from anndata.experimental.merge import as_group
from anndata.tests.helpers import (
GEN_ADATA_DASK_ARGS,
as_dense_cupy_dask_array,
as_dense_dask_array,
as_sparse_dask_array,
assert_equal,
gen_adata,
)
if TYPE_CHECKING:
from pathlib import Path
from typing import Literal
pytest.importorskip("dask.array")
@pytest.fixture(
params=[
[(2000, 1000), (100, 100)],
[(200, 100), (100, 100)],
[(200, 100), (100, 100)],
[(20, 10), (1, 1)],
[(20, 10), (1, 1)],
]
)
def sizes(request):
return request.param
@pytest.fixture
def adata(sizes):
import dask.array as da
import numpy as np
(M, N), chunks = sizes
X = da.random.random((M, N), chunks=chunks)
obs = pd.DataFrame(
{"batch": np.random.choice(["a", "b"], M)},
index=[f"cell{i:03d}" for i in range(M)],
)
var = pd.DataFrame(index=[f"gene{i:03d}" for i in range(N)])
return AnnData(X, obs=obs, var=var)
def test_dask_X_view():
import dask.array as da
M, N = 50, 30
adata = ad.AnnData(
obs=pd.DataFrame(index=[f"cell{i:02}" for i in range(M)]),
var=pd.DataFrame(index=[f"gene{i:02}" for i in range(N)]),
)
adata.X = da.ones((M, N))
view = adata[:30]
view.copy()
def test_dask_write(adata, tmp_path, diskfmt):
import dask.array as da
import numpy as np
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)
M, N = adata.X.shape
adata.obsm["a"] = da.random.random((M, 10))
adata.obsm["b"] = da.random.random((M, 10))
adata.varm["a"] = da.random.random((N, 10))
orig = adata
write(orig, pth)
curr = read(pth)
with pytest.raises(AssertionError):
assert_equal(curr.obsm["a"], curr.obsm["b"])
assert_equal(curr.varm["a"], orig.varm["a"])
assert_equal(curr.obsm["a"], orig.obsm["a"])
assert isinstance(curr.X, np.ndarray)
assert isinstance(curr.obsm["a"], np.ndarray)
assert isinstance(curr.varm["a"], np.ndarray)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["a"], DaskArray)
assert isinstance(orig.varm["a"], DaskArray)
@pytest.mark.xdist_group("dask")
def test_dask_distributed_write(
adata: AnnData,
tmp_path: Path,
diskfmt: Literal["h5ad", "zarr"],
local_cluster_addr: str,
) -> None:
import dask.array as da
import dask.distributed as dd
import numpy as np
pth = tmp_path / f"test_write.{diskfmt}"
g = as_group(pth, mode="w")
with dd.Client(local_cluster_addr):
M, N = adata.X.shape
adata.obsm["a"] = da.random.random((M, 10))
adata.obsm["b"] = da.random.random((M, 10))
adata.varm["a"] = da.random.random((N, 10))
orig = adata
if diskfmt == "h5ad":
with pytest.raises(ValueError, match=r"Cannot write dask arrays to hdf5"):
ad.io.write_elem(g, "", orig)
return
ad.io.write_elem(g, "", orig)
# TODO: See https://github.com/zarr-developers/zarr-python/issues/2716
g = as_group(pth, mode="r")
curr = ad.io.read_elem(g)
with pytest.raises(AssertionError):
assert_equal(curr.obsm["a"], curr.obsm["b"])
assert_equal(curr.varm["a"], orig.varm["a"])
assert_equal(curr.obsm["a"], orig.obsm["a"])
assert isinstance(curr.X, np.ndarray)
assert isinstance(curr.obsm["a"], np.ndarray)
assert isinstance(curr.varm["a"], np.ndarray)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["a"], DaskArray)
assert isinstance(orig.varm["a"], DaskArray)
def test_dask_to_memory_check_array_types(adata, tmp_path, diskfmt):
import dask.array as da
import numpy as np
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)
M, N = adata.X.shape
adata.obsm["a"] = da.random.random((M, 10))
adata.obsm["b"] = da.random.random((M, 10))
adata.varm["a"] = da.random.random((N, 10))
orig = adata
write(orig, pth)
curr = read(pth)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["a"], DaskArray)
assert isinstance(orig.varm["a"], DaskArray)
mem = orig.to_memory()
with pytest.raises(AssertionError):
assert_equal(curr.obsm["a"], curr.obsm["b"])
assert_equal(curr.varm["a"], orig.varm["a"])
assert_equal(curr.obsm["a"], orig.obsm["a"])
assert_equal(mem.obsm["a"], orig.obsm["a"])
assert_equal(mem.varm["a"], orig.varm["a"])
assert isinstance(curr.X, np.ndarray)
assert isinstance(curr.obsm["a"], np.ndarray)
assert isinstance(curr.varm["a"], np.ndarray)
assert isinstance(mem.X, np.ndarray)
assert isinstance(mem.obsm["a"], np.ndarray)
assert isinstance(mem.varm["a"], np.ndarray)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["a"], DaskArray)
assert isinstance(orig.varm["a"], DaskArray)
def test_dask_to_memory_copy_check_array_types(adata, tmp_path, diskfmt):
import dask.array as da
import numpy as np
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)
M, N = adata.X.shape
adata.obsm["a"] = da.random.random((M, 10))
adata.obsm["b"] = da.random.random((M, 10))
adata.varm["a"] = da.random.random((N, 10))
orig = adata
write(orig, pth)
curr = read(pth)
mem = orig.to_memory(copy=True)
with pytest.raises(AssertionError):
assert_equal(curr.obsm["a"], curr.obsm["b"])
assert_equal(curr.varm["a"], orig.varm["a"])
assert_equal(curr.obsm["a"], orig.obsm["a"])
assert_equal(mem.obsm["a"], orig.obsm["a"])
assert_equal(mem.varm["a"], orig.varm["a"])
assert isinstance(curr.X, np.ndarray)
assert isinstance(curr.obsm["a"], np.ndarray)
assert isinstance(curr.varm["a"], np.ndarray)
assert isinstance(mem.X, np.ndarray)
assert isinstance(mem.obsm["a"], np.ndarray)
assert isinstance(mem.varm["a"], np.ndarray)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["a"], DaskArray)
assert isinstance(orig.varm["a"], DaskArray)
def test_dask_copy_check_array_types(adata):
import dask.array as da
M, N = adata.X.shape
adata.obsm["a"] = da.random.random((M, 10))
adata.obsm["b"] = da.random.random((M, 10))
adata.varm["a"] = da.random.random((N, 10))
orig = adata
curr = adata.copy()
with pytest.raises(AssertionError):
assert_equal(curr.obsm["a"], curr.obsm["b"])
assert_equal(curr.varm["a"], orig.varm["a"])
assert_equal(curr.obsm["a"], orig.obsm["a"])
assert isinstance(curr.X, DaskArray)
assert isinstance(curr.obsm["a"], DaskArray)
assert isinstance(curr.varm["a"], DaskArray)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["a"], DaskArray)
assert isinstance(orig.varm["a"], DaskArray)
def test_assign_X(adata):
"""Check if assignment works"""
import dask.array as da
import numpy as np
from anndata.compat import DaskArray
adata.X = da.ones(adata.X.shape)
prev_type = type(adata.X)
adata_copy = adata.copy()
adata.X = -1 * da.ones(adata.X.shape)
assert prev_type is DaskArray
assert type(adata_copy.X) is DaskArray
assert_equal(adata.X, -1 * np.ones(adata.X.shape))
assert_equal(adata_copy.X, np.ones(adata.X.shape))
# Test if dask arrays turn into numpy arrays after to_memory is called
@pytest.mark.parametrize(
("array_func", "mem_type"),
[
pytest.param(as_dense_dask_array, np.ndarray, id="dense_dask_array"),
pytest.param(as_sparse_dask_array, sparse.csr_matrix, id="sparse_dask_array"),
pytest.param(
as_dense_cupy_dask_array,
CupyArray,
id="cupy_dense_dask_array",
marks=pytest.mark.gpu,
),
],
)
def test_dask_to_memory_unbacked(array_func, mem_type):
orig = gen_adata((15, 10), X_type=array_func, **GEN_ADATA_DASK_ARGS)
orig.uns = {"da": {"da": array_func(np.ones((4, 12)))}}
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["da"], DaskArray)
assert isinstance(orig.layers["da"], DaskArray)
assert isinstance(orig.varm["da"], DaskArray)
assert isinstance(orig.uns["da"]["da"], DaskArray)
curr = orig.to_memory()
assert_equal(orig, curr)
assert isinstance(curr.X, mem_type)
assert isinstance(curr.obsm["da"], np.ndarray)
assert isinstance(curr.varm["da"], np.ndarray)
assert isinstance(curr.layers["da"], np.ndarray)
assert isinstance(curr.uns["da"]["da"], mem_type)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["da"], DaskArray)
assert isinstance(orig.layers["da"], DaskArray)
assert isinstance(orig.varm["da"], DaskArray)
assert isinstance(orig.uns["da"]["da"], DaskArray)
# Test if dask arrays turn into numpy arrays after to_memory is called
def test_dask_to_memory_copy_unbacked():
import numpy as np
orig = gen_adata((15, 10), X_type=as_dense_dask_array, **GEN_ADATA_DASK_ARGS)
orig.uns = {"da": {"da": as_dense_dask_array(np.ones(12))}}
curr = orig.to_memory(copy=True)
assert_equal(orig, curr)
assert isinstance(curr.X, np.ndarray)
assert isinstance(curr.obsm["da"], np.ndarray)
assert isinstance(curr.varm["da"], np.ndarray)
assert isinstance(curr.layers["da"], np.ndarray)
assert isinstance(curr.uns["da"]["da"], np.ndarray)
assert isinstance(orig.X, DaskArray)
assert isinstance(orig.obsm["da"], DaskArray)
assert isinstance(orig.layers["da"], DaskArray)
assert isinstance(orig.varm["da"], DaskArray)
assert isinstance(orig.uns["da"]["da"], DaskArray)
def test_to_memory_raw():
import dask.array as da
import numpy as np
orig = gen_adata((20, 10), **GEN_ADATA_DASK_ARGS)
orig.X = da.ones((20, 10))
with_raw = orig[:, ::2].copy()
with_raw.raw = orig.copy()
assert isinstance(with_raw.raw.X, DaskArray)
assert isinstance(with_raw.raw.varm["da"], DaskArray)
curr = with_raw.to_memory()
assert isinstance(with_raw.raw.X, DaskArray)
assert isinstance(with_raw.raw.varm["da"], DaskArray)
assert isinstance(curr.raw.X, np.ndarray)
assert isinstance(curr.raw.varm["da"], np.ndarray)
def test_to_memory_copy_raw():
import dask.array as da
import numpy as np
orig = gen_adata((20, 10), **GEN_ADATA_DASK_ARGS)
orig.X = da.ones((20, 10))
with_raw = orig[:, ::2].copy()
with_raw.raw = orig.copy()
assert isinstance(with_raw.raw.X, DaskArray)
assert isinstance(with_raw.raw.varm["da"], DaskArray)
curr = with_raw.to_memory(copy=True)
assert isinstance(with_raw.raw.X, DaskArray)
assert isinstance(with_raw.raw.varm["da"], DaskArray)
assert isinstance(curr.raw.X, np.ndarray)
assert isinstance(curr.raw.varm["da"], np.ndarray)
|
