0.10.6 (#215)

* updates release note

* updates for scanpy-1.10.2

* adds release note

docs/release-notes/0.10.6.md

@@ -1,14 +1,9 @@
-### 0.10.6 {small}`the future`
-
-```{rubric} Features
-```
-
-```{rubric} Performance
-```
+### 0.10.6 {small}`2024-06-25`
 
 ```{rubric} Bug fixes
 ```
  * removes `.A` to be compatible with scipy 1.14.0 {pr}`214` {smaller}`S Dicks`
 
 ```{rubric} Misc
 ```
+* updates tests to work without `scanpy.testing` {pr}`215` {smaller}`S Dicks`

tests/_helpers/__init__.py

@@ -0,0 +1,41 @@
+"""Like fixtures, but more flexible"""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+import pytest
+from anndata.tests.helpers import asarray
+from scipy import sparse
+
+
+if TYPE_CHECKING:
+    from collections.abc import Iterable
+    from typing import Literal
+
+    from _pytest.mark.structures import ParameterSet
+
+
+def param_with(
+    at: ParameterSet,
+    *,
+    marks: Iterable[pytest.Mark | pytest.MarkDecorator] = (),
+    id: str | None = None,
+) -> ParameterSet:
+    return pytest.param(*at.values, marks=[*at.marks, *marks], id=id or at.id)
+
+
+MAP_ARRAY_TYPES: dict[
+    tuple[Literal["mem", "dask"], Literal["dense", "sparse"]],
+    tuple[ParameterSet, ...],
+] = {
+    ("mem", "dense"): (pytest.param(asarray, id="numpy_ndarray"),),
+    ("mem", "sparse"): (
+        pytest.param(sparse.csr_matrix, id="scipy_csr"),
+        pytest.param(sparse.csc_matrix, id="scipy_csc"),
+    ),
+}
+
+ARRAY_TYPES_MEM = tuple(
+    at for (strg, _), ats in MAP_ARRAY_TYPES.items() if strg == "mem" for at in ats
+)

tests/test_aggregated.py

@@ -10,9 +10,9 @@
 
 import scanpy as sc
 from scanpy._utils import _resolve_axis
-from scanpy.testing._helpers import assert_equal
-from scanpy.testing._helpers.data import pbmc3k_processed
-from scanpy.testing._pytest.params import ARRAY_TYPES_MEM
+from anndata.tests.helpers import assert_equal
+from scanpy.datasets import pbmc3k_processed
+from _helpers import ARRAY_TYPES_MEM
 
 import rapids_singlecell as rsc
 

tests/test_pca.py

@@ -4,10 +4,9 @@
 import pytest
 import rapids_singlecell as rsc
 from anndata import AnnData
-from scanpy.datasets import pbmc3k_processed
+from scanpy.datasets import pbmc3k_processed, pbmc3k
 from scipy import sparse
 import scanpy as sc
-from scanpy.testing._helpers.data import pbmc3k_normalized
 
 A_list = [
     [0, 0, 7, 0, 0],
@@ -41,6 +40,15 @@
 )
 
 
+def _pbmc3k_normalized() -> AnnData:
+    pbmc = pbmc3k()
+    pbmc.X = pbmc.X.astype("float64")  # For better accuracy
+    sc.pp.filter_genes(pbmc, min_counts=1)
+    sc.pp.log1p(pbmc)
+    sc.pp.normalize_total(pbmc)
+    sc.pp.highly_variable_genes(pbmc)
+    return pbmc
+
 def test_pca_transform():
     A = np.array(A_list).astype("float32")
     A_pca_abs = np.abs(A_pca)
@@ -211,7 +219,7 @@ def test_pca_layer():
     """
     Tests that layers works the same way as .X
     """
-    X_adata = pbmc3k_normalized()
+    X_adata = _pbmc3k_normalized()
     X_adata.X = X_adata.X.astype(np.float64)
 
     layer_adata = X_adata.copy()

tests/test_scrublet.py

@@ -19,15 +19,13 @@
 
 
 def pbmc200() -> AnnData:
-    from scanpy.testing._helpers.data import _pbmc3k
-
-    return _pbmc3k()[200:400].copy()
+    from scanpy.datasets import pbmc3k
+    return pbmc3k()[200:400].copy()
 
 
 def paul500() -> AnnData:
-    from scanpy.testing._helpers.data import _paul15
-
-    return _paul15()[:500].copy()
+    from scanpy.datasets import paul15
+    return paul15()[:500].copy()
 
 
 @pytest.mark.parametrize(