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from __future__ import annotations
from functools import partial
from itertools import product
from typing import TYPE_CHECKING, Literal, get_args
import h5py
import numpy as np
import pytest
import zarr
from scipy import sparse
import anndata as ad
from anndata._core.anndata import AnnData
from anndata._core.sparse_dataset import sparse_dataset
from anndata._io.specs.registry import read_elem_lazy
from anndata._io.zarr import open_write_group
from anndata.compat import (
CSArray,
CSMatrix,
DaskArray,
ZarrGroup,
is_zarr_v2,
)
from anndata.experimental import read_dispatched
from anndata.tests.helpers import AccessTrackingStore, assert_equal, subset_func
if TYPE_CHECKING:
from collections.abc import Callable, Generator, Sequence
from pathlib import Path
from types import EllipsisType
from _pytest.mark import ParameterSet
from numpy.typing import ArrayLike, NDArray
from pytest_mock import MockerFixture
from anndata.abc import CSCDataset, CSRDataset
Idx = slice | int | NDArray[np.integer] | NDArray[np.bool_]
subset_func2 = subset_func
M = 50
N = 50
@pytest.fixture
def zarr_metadata_key():
return ".zarray" if ad.settings.zarr_write_format == 2 else "zarr.json"
@pytest.fixture
def zarr_separator():
return "" if ad.settings.zarr_write_format == 2 else "/c"
@pytest.fixture
def ondisk_equivalent_adata(
tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]
) -> tuple[AnnData, AnnData, AnnData, AnnData]:
csr_path = tmp_path / f"csr.{diskfmt}"
csc_path = tmp_path / f"csc.{diskfmt}"
dense_path = tmp_path / f"dense.{diskfmt}"
write = lambda x, pth, **kwargs: getattr(x, f"write_{diskfmt}")(pth, **kwargs)
csr_mem = ad.AnnData(X=sparse.random(M, N, format="csr", density=0.1))
csc_mem = ad.AnnData(X=csr_mem.X.tocsc())
dense_mem = ad.AnnData(X=csr_mem.X.toarray())
write(csr_mem, csr_path)
write(csc_mem, csc_path)
# write(csr_mem, dense_path, as_dense="X")
write(dense_mem, dense_path)
if diskfmt == "h5ad":
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")
else:
def read_zarr_backed(path):
path = str(path)
f = zarr.open(path, mode="r")
# Read with handling for backwards compat
def callback(func, elem_name, elem, iospec):
if iospec.encoding_type == "anndata" or elem_name.endswith("/"):
return AnnData(
**{
k: read_dispatched(v, callback)
for k, v in dict(elem).items()
}
)
if iospec.encoding_type in {"csc_matrix", "csr_matrix"}:
return sparse_dataset(elem)
return func(elem)
adata = read_dispatched(f, callback=callback)
return adata
csr_disk = read_zarr_backed(csr_path)
csc_disk = read_zarr_backed(csc_path)
dense_disk = read_zarr_backed(dense_path)
return csr_mem, csr_disk, csc_disk, dense_disk
@pytest.mark.parametrize(
"empty_mask", [[], np.zeros(M, dtype=bool)], ids=["empty_list", "empty_bool_mask"]
)
def test_empty_backed_indexing(
ondisk_equivalent_adata: tuple[AnnData, AnnData, AnnData, AnnData],
empty_mask,
):
csr_mem, csr_disk, csc_disk, _ = ondisk_equivalent_adata
assert_equal(csr_mem.X[empty_mask], csr_disk.X[empty_mask])
assert_equal(csr_mem.X[:, empty_mask], csc_disk.X[:, empty_mask])
# The following do not work because of https://github.com/scipy/scipy/issues/19919
# Our implementation returns a (0,0) sized matrix but scipy does (1,0).
# assert_equal(csr_mem.X[empty_mask, empty_mask], csr_disk.X[empty_mask, empty_mask])
# assert_equal(csr_mem.X[empty_mask, empty_mask], csc_disk.X[empty_mask, empty_mask])
def test_backed_indexing(
ondisk_equivalent_adata: tuple[AnnData, AnnData, AnnData, AnnData],
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.X[...], csc_disk.X[...])
assert_equal(csr_mem[obs_idx, :].X, dense_disk[obs_idx, :].X)
assert_equal(csr_mem[obs_idx].X, csr_disk[obs_idx].X)
assert_equal(csr_mem[:, var_idx].X, dense_disk[:, var_idx].X)
def test_backed_ellipsis_indexing(
ondisk_equivalent_adata: tuple[AnnData, AnnData, AnnData, AnnData],
ellipsis_index: tuple[EllipsisType | slice, ...] | EllipsisType,
equivalent_ellipsis_index: tuple[slice, slice],
):
csr_mem, csr_disk, csc_disk, _ = ondisk_equivalent_adata
assert_equal(csr_mem.X[equivalent_ellipsis_index], csr_disk.X[ellipsis_index])
assert_equal(csr_mem.X[equivalent_ellipsis_index], csc_disk.X[ellipsis_index])
def make_randomized_mask(size: int) -> np.ndarray:
randomized_mask = np.zeros(size, dtype=bool)
inds = np.random.choice(size, 20, replace=False)
inds.sort()
for i in range(0, len(inds) - 1, 2):
randomized_mask[inds[i] : inds[i + 1]] = True
return randomized_mask
def make_alternating_mask(size: int, step: int) -> np.ndarray:
mask_alternating = np.ones(size, dtype=bool)
for i in range(0, size, step): # 5 is too low to trigger new behavior
mask_alternating[i] = False
return mask_alternating
# non-random indices, with alternating one false and n true
make_alternating_mask_5 = partial(make_alternating_mask, step=5)
make_alternating_mask_15 = partial(make_alternating_mask, step=15)
def make_one_group_mask(size: int) -> np.ndarray:
one_group_mask = np.zeros(size, dtype=bool)
one_group_mask[1 : size // 2] = True
return one_group_mask
def make_one_elem_mask(size: int) -> np.ndarray:
one_elem_mask = np.zeros(size, dtype=bool)
one_elem_mask[size // 4] = True
return one_elem_mask
# test behavior from https://github.com/scverse/anndata/pull/1233
@pytest.mark.parametrize(
("make_bool_mask", "should_trigger_optimization"),
[
(make_randomized_mask, None),
(make_alternating_mask_15, True),
(make_alternating_mask_5, False),
(make_one_group_mask, True),
(make_one_elem_mask, False),
],
ids=["randomized", "alternating_15", "alternating_5", "one_group", "one_elem"],
)
def test_consecutive_bool(
mocker: MockerFixture,
ondisk_equivalent_adata: tuple[AnnData, AnnData, AnnData, AnnData],
make_bool_mask: Callable[[int], np.ndarray],
should_trigger_optimization: bool | None,
):
"""Tests for optimization from https://github.com/scverse/anndata/pull/1233
Parameters
----------
mocker
Mocker object
ondisk_equivalent_adata
AnnData objects with sparse X for testing
make_bool_mask
Function for creating a boolean mask.
should_trigger_optimization
Whether or not a given mask should trigger the optimized behavior.
"""
_, csr_disk, csc_disk, _ = ondisk_equivalent_adata
mask = make_bool_mask(csr_disk.shape[0])
# indexing needs to be on `X` directly to trigger the optimization.
# `_normalize_indices`, which is used by `AnnData`, converts bools to ints with `np.where`
from anndata._core import sparse_dataset
spy = mocker.spy(sparse_dataset, "get_compressed_vectors_for_slices")
assert_equal(csr_disk.X[mask, :], csr_disk.X[np.where(mask)])
if should_trigger_optimization is not None:
assert (
spy.call_count == 1 if should_trigger_optimization else not spy.call_count
)
assert_equal(csc_disk.X[:, mask], csc_disk.X[:, np.where(mask)[0]])
if should_trigger_optimization is not None:
assert (
spy.call_count == 2 if should_trigger_optimization else not spy.call_count
)
assert_equal(csr_disk[mask, :], csr_disk[np.where(mask)])
if should_trigger_optimization is not None:
assert (
spy.call_count == 3 if should_trigger_optimization else not spy.call_count
)
subset = csc_disk[:, mask]
assert_equal(subset, csc_disk[:, np.where(mask)[0]])
if should_trigger_optimization is not None:
assert (
spy.call_count == 4 if should_trigger_optimization else not spy.call_count
)
if should_trigger_optimization is not None and not csc_disk.isbacked:
size = subset.shape[1]
if should_trigger_optimization:
subset_subset_mask = np.ones(size).astype("bool")
subset_subset_mask[size // 2] = False
else:
subset_subset_mask = make_one_elem_mask(size)
assert_equal(
subset[:, subset_subset_mask], subset[:, np.where(subset_subset_mask)[0]]
)
assert (
spy.call_count == 5 if should_trigger_optimization else not spy.call_count
), f"Actual count: {spy.call_count}"
@pytest.mark.parametrize(
("sparse_format", "append_method"),
[
pytest.param(sparse.csr_matrix, sparse.vstack),
pytest.param(sparse.csc_matrix, sparse.hstack),
pytest.param(sparse.csr_array, sparse.vstack),
pytest.param(sparse.csc_array, sparse.hstack),
],
)
def test_dataset_append_memory(
tmp_path: Path,
sparse_format: Callable[[ArrayLike], CSMatrix],
append_method: Callable[[list[CSMatrix]], CSMatrix],
diskfmt: Literal["h5ad", "zarr"],
):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
a = sparse_format(sparse.random(100, 100))
b = sparse_format(sparse.random(100, 100))
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "mtx", a)
diskmtx = sparse_dataset(f["mtx"])
diskmtx.append(b)
fromdisk = diskmtx.to_memory()
frommem = append_method([a, b])
assert_equal(fromdisk, frommem)
def test_append_array_cache_bust(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
a = sparse.random(100, 100, format="csr")
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "mtx", a)
ad.io.write_elem(f, "mtx_2", a)
diskmtx = sparse_dataset(f["mtx"])
old_array_shapes = {}
array_names = ["indptr", "indices", "data"]
for name in array_names:
old_array_shapes[name] = getattr(diskmtx, f"_{name}").shape
diskmtx.append(sparse_dataset(f["mtx_2"]))
for name in array_names:
assert old_array_shapes[name] != getattr(diskmtx, f"_{name}").shape
@pytest.mark.parametrize("sparse_format", [sparse.csr_matrix, sparse.csc_matrix])
@pytest.mark.parametrize(
("subset_func", "subset_func2"),
product(
[
ad.tests.helpers.array_subset,
ad.tests.helpers.slice_subset,
ad.tests.helpers.array_int_subset,
ad.tests.helpers.array_bool_subset,
],
repeat=2,
),
)
def test_read_array(
tmp_path: Path,
sparse_format: Callable[[ArrayLike], CSMatrix],
diskfmt: Literal["h5ad", "zarr"],
subset_func,
subset_func2,
):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
a = sparse_format(sparse.random(100, 100))
obs_idx = subset_func(np.arange(100))
var_idx = subset_func2(np.arange(100))
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "mtx", a)
diskmtx = sparse_dataset(f["mtx"])
ad.settings.use_sparse_array_on_read = True
assert issubclass(type(diskmtx[obs_idx, var_idx]), CSArray)
ad.settings.use_sparse_array_on_read = False
assert issubclass(type(diskmtx[obs_idx, var_idx]), CSMatrix)
@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: Path,
sparse_format: Callable[[ArrayLike], CSMatrix],
append_method: Callable[[list[CSMatrix]], CSMatrix],
diskfmt: Literal["h5ad", "zarr"],
):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
a = sparse_format(sparse.random(10, 10))
b = sparse_format(sparse.random(10, 10))
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "a", a)
ad.io.write_elem(f, "b", b)
a_disk = sparse_dataset(f["a"])
b_disk = sparse_dataset(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", [sparse.csr_matrix, sparse.csc_matrix])
def test_lazy_array_cache(
tmp_path: Path, sparse_format: Callable[[ArrayLike], CSMatrix], zarr_metadata_key
):
elems = {"indptr", "indices", "data"}
path = tmp_path / "test.zarr"
a = sparse_format(sparse.random(10, 10))
f = open_write_group(path, mode="a")
ad.io.write_elem(f, "X", a)
store = AccessTrackingStore(path)
for elem in elems:
store.initialize_key_trackers([f"X/{elem}"])
f = open_write_group(store, mode="a")
a_disk = sparse_dataset(f["X"])
a_disk[:1]
a_disk[3:5]
a_disk[6:7]
a_disk[8:9]
# one each for .zarray and actual access
# see https://github.com/zarr-developers/zarr-python/discussions/2760 for why 4
assert store.get_access_count("X/indptr") == 2 if is_zarr_v2() else 4
for elem_not_indptr in elems - {"indptr"}:
assert (
sum(
zarr_metadata_key in key_accessed
for key_accessed in store.get_accessed_keys(f"X/{elem_not_indptr}")
)
== 1
)
Kind = Literal["slice", "int", "array", "mask"]
def mk_idx_kind(idx: Sequence[int], *, kind: Kind, l: int) -> Idx | None:
"""Convert sequence of consecutive integers (e.g. range with step=1) into different kinds of indexing."""
if kind == "slice":
start = idx[0] if idx[0] > 0 else None
if len(idx) == 1:
return slice(start, idx[0] + 1)
if all(np.diff(idx) == 1):
stop = idx[-1] + 1 if idx[-1] < l - 1 else None
return slice(start, stop)
if kind == "int":
if len(idx) == 1:
return idx[0]
if kind == "array":
return np.asarray(idx)
if kind == "mask":
return np.isin(np.arange(l), idx)
return None
def idify(x: object) -> str:
if isinstance(x, slice):
start, stop = ("" if s is None else str(s) for s in (x.start, x.stop))
return f"{start}:{stop}" + (f":{x.step}" if x.step not in (1, None) else "")
return str(x)
def width_idx_kinds(
*idxs: tuple[Sequence[int], Idx, Sequence[str]], l: int
) -> Generator[ParameterSet, None, None]:
"""Convert major (first) index into various identical kinds of indexing."""
for (idx_maj_raw, idx_min, exp), maj_kind in product(idxs, get_args(Kind)):
if (idx_maj := mk_idx_kind(idx_maj_raw, kind=maj_kind, l=l)) is None:
continue
id_ = "-".join(map(idify, [idx_maj_raw, idx_min, maj_kind]))
yield pytest.param(idx_maj, idx_min, exp, id=id_)
@pytest.mark.parametrize("sparse_format", [sparse.csr_matrix, sparse.csc_matrix])
@pytest.mark.parametrize(
("idx_maj", "idx_min", "exp"),
width_idx_kinds(
(
[0],
slice(None, None),
["X/data/{zarr_metadata_key}", "X/data{zarr_separator}/0"],
),
(
[0],
slice(None, 3),
["X/data/{zarr_metadata_key}", "X/data{zarr_separator}/0"],
),
(
[3, 4, 5],
slice(None, None),
[
"X/data/{zarr_metadata_key}",
"X/data{zarr_separator}/3",
"X/data{zarr_separator}/4",
"X/data{zarr_separator}/5",
],
),
l=10,
),
)
@pytest.mark.parametrize(
"open_func",
[
sparse_dataset,
lambda x: read_elem_lazy(
x, chunks=(1, -1) if x.attrs["encoding-type"] == "csr_matrix" else (-1, 1)
),
],
ids=["sparse_dataset", "read_elem_lazy"],
)
def test_data_access(
tmp_path: Path,
sparse_format: Callable[[ArrayLike], CSMatrix],
idx_maj: Idx,
idx_min: Idx,
exp: list[str],
open_func: Callable[[ZarrGroup], CSRDataset | CSCDataset | DaskArray],
zarr_metadata_key,
zarr_separator,
):
exp = [
e.format(zarr_metadata_key=zarr_metadata_key, zarr_separator=zarr_separator)
for e in exp
]
path = tmp_path / "test.zarr"
a = sparse_format(np.eye(10, 10))
f = open_write_group(path, mode="a")
ad.io.write_elem(f, "X", a)
data = f["X/data"][...]
del f["X/data"]
# chunk one at a time to count properly
zarr.array(
data,
store=path / "X" / "data",
chunks=(1,),
zarr_format=ad.settings.zarr_write_format,
)
store = AccessTrackingStore(path)
store.initialize_key_trackers(["X/data"])
f = zarr.open_group(store)
a_disk = AnnData(X=open_func(f["X"]))
if a.format == "csr":
subset = a_disk[idx_maj, idx_min]
else:
subset = a_disk[idx_min, idx_maj]
if isinstance(subset.X, DaskArray):
subset.X.compute(scheduler="single-threaded")
# zarr v2 fetches all and not just metadata for that node in 3.X.X python package
# TODO: https://github.com/zarr-developers/zarr-python/discussions/2760
if ad.settings.zarr_write_format == 2 and not is_zarr_v2():
exp = exp + ["X/data/.zgroup", "X/data/.zattrs"]
assert store.get_access_count("X/data") == len(exp), store.get_accessed_keys(
"X/data"
)
# dask access order is not guaranteed so need to sort
assert sorted(store.get_accessed_keys("X/data")) == sorted(exp)
@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: Path,
sparse_format: Literal["csr", "csc"],
a_shape: tuple[int, int],
b_shape: tuple[int, int],
diskfmt: Literal["h5ad", "zarr"],
):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
a_mem = sparse.random(*a_shape, format=sparse_format)
b_mem = sparse.random(*b_shape, format=sparse_format)
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "a", a_mem)
ad.io.write_elem(f, "b", b_mem)
a_disk = sparse_dataset(f["a"])
b_disk = sparse_dataset(f["b"])
with pytest.raises(AssertionError):
a_disk.append(b_disk)
def test_reset_group(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]):
path = tmp_path / "test.zarr"
base = sparse.random(100, 100, format="csr")
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "base", base)
disk_mtx = sparse_dataset(f["base"])
with pytest.raises(AttributeError):
disk_mtx.group = f
def test_wrong_formats(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
base = sparse.random(100, 100, format="csr")
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "base", base)
disk_mtx = sparse_dataset(f["base"])
pre_checks = disk_mtx.to_memory()
with pytest.raises(ValueError, match="must have same format"):
disk_mtx.append(sparse.random(100, 100, format="csc"))
with pytest.raises(ValueError, match="must have same format"):
disk_mtx.append(sparse.random(100, 100, format="coo"))
with pytest.raises(NotImplementedError):
disk_mtx.append(np.random.random((100, 100)))
if isinstance(f, ZarrGroup) and not is_zarr_v2():
data = np.random.random((100, 100))
disk_dense = f.create_array("dense", shape=(100, 100), dtype=data.dtype)
disk_dense[...] = data
else:
disk_dense = f.create_dataset(
"dense", data=np.random.random((100, 100)), shape=(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())
def test_anndata_sparse_compat(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]):
path = tmp_path / f"test.{diskfmt.replace('ad', '')}"
base = sparse.random(100, 100, format="csr")
if diskfmt == "zarr":
f = open_write_group(path, mode="a")
else:
f = h5py.File(path, "a")
ad.io.write_elem(f, "/", base)
adata = ad.AnnData(sparse_dataset(f["/"]))
assert_equal(adata.X, base)
def test_backed_sizeof(
ondisk_equivalent_adata: tuple[AnnData, AnnData, AnnData, AnnData],
):
csr_mem, csr_disk, csc_disk, _ = ondisk_equivalent_adata
assert csr_mem.__sizeof__() == csr_disk.__sizeof__(with_disk=True)
assert csr_mem.__sizeof__() == csc_disk.__sizeof__(with_disk=True)
assert csr_disk.__sizeof__(with_disk=True) == csc_disk.__sizeof__(with_disk=True)
assert csr_mem.__sizeof__() > csr_disk.__sizeof__()
assert csr_mem.__sizeof__() > csc_disk.__sizeof__()
@pytest.mark.parametrize(
"group_fn",
[
pytest.param(lambda _: zarr.group(), id="zarr"),
pytest.param(lambda p: h5py.File(p / "test.h5", mode="a"), id="h5py"),
],
)
@pytest.mark.parametrize(
"sparse_class",
[
sparse.csr_matrix,
pytest.param(
sparse.csr_array,
marks=[pytest.mark.skip(reason="scipy bug causes view to be allocated")],
),
],
)
def test_append_overflow_check(group_fn, sparse_class, tmp_path):
group = group_fn(tmp_path)
typemax_int32 = np.iinfo(np.int32).max
orig_mtx = sparse_class(np.ones((1, 1), dtype=bool))
# Minimally allocating new matrix
new_mtx = sparse_class(
(
np.broadcast_to(True, typemax_int32 - 1), # noqa: FBT003
np.broadcast_to(np.int32(1), typemax_int32 - 1),
[0, typemax_int32 - 1],
),
shape=(1, 2),
)
ad.io.write_elem(group, "mtx", orig_mtx)
backed = sparse_dataset(group["mtx"])
# Checking for correct caching behaviour
backed._indptr
with pytest.raises(
OverflowError,
match=r"This array was written with a 32 bit intptr, but is now large.*",
):
backed.append(new_mtx)
# Check for any modification
assert_equal(backed, orig_mtx)
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