update typing

src/rapids_singlecell/_compat.py

@@ -2,29 +2,7 @@
 
 import cupy as cp
 from cupyx.scipy.sparse import csr_matrix
-
-try:
-    from dask.array import Array as DaskArray
-except ImportError:
-
-    class DaskArray:
-        pass
-
-
-try:
-    from dask.distributed import Client as DaskClient
-except ImportError:
-
-    class DaskClient:
-        pass
-
-
-def _get_dask_client(client=None):
-    from dask.distributed import default_client
-
-    if client is None or not isinstance(client, DaskClient):
-        return default_client()
-    return client
+from dask.array import Array as DaskArray  # noqa: F401
 
 
 def _meta_dense(dtype):

src/rapids_singlecell/_utils/__init__.py

@@ -2,6 +2,13 @@
 
 from typing import TYPE_CHECKING, Union
 
+import cupy as cp
 import numpy as np
+from cupyx.scipy.sparse import csc_matrix, csr_matrix
+from dask.array import Array as DaskArray
 
 AnyRandom = Union[int, np.random.RandomState, None]  # noqa: UP007
+
+
+ArrayTypes = Union[cp.ndarray, csc_matrix, csr_matrix]  # noqa: UP007
+ArrayTypesDask = Union[cp.ndarray, csc_matrix, csr_matrix, DaskArray]  # noqa: UP007

src/rapids_singlecell/preprocessing/_qc.py

@@ -15,6 +15,8 @@
 if TYPE_CHECKING:
     from anndata import AnnData
 
+    from rapids_singlecell._utils import ArrayTypesDask
+
 
 def calculate_qc_metrics(
     adata: AnnData,
@@ -110,7 +112,9 @@ def calculate_qc_metrics(
                 )
 
 
-def _first_pass_qc(X):
+def _first_pass_qc(
+    X: ArrayTypesDask,
+) -> tuple[cp.ndarray, cp.ndarray, cp.ndarray, cp.ndarray]:
     if isinstance(X, DaskArray):
         return _first_pass_qc_dask(X)
 
@@ -181,7 +185,9 @@ def _first_pass_qc(X):
 
 
 @with_cupy_rmm
-def _first_pass_qc_dask(X):
+def _first_pass_qc_dask(
+    X: DaskArray,
+) -> tuple[cp.ndarray, cp.ndarray, cp.ndarray, cp.ndarray]:
     import dask
     import dask.array as da
 
@@ -337,7 +343,7 @@ def __qc_calc_2(X_part):
     )
 
 
-def _second_pass_qc(X, mask):
+def _second_pass_qc(X: ArrayTypesDask, mask: cp.ndarray) -> cp.ndarray:
     if isinstance(X, DaskArray):
         return _second_pass_qc_dask(X, mask)
     sums_cells_sub = cp.zeros(X.shape[0], dtype=X.dtype)
@@ -381,7 +387,7 @@ def _second_pass_qc(X, mask):
 
 
 @with_cupy_rmm
-def _second_pass_qc_dask(X, mask):
+def _second_pass_qc_dask(X: DaskArray, mask: cp.ndarray) -> cp.ndarray:
     if isinstance(X._meta, sparse.csr_matrix):
         from ._kernels._qc_kernels import _sparse_qc_csr_sub