chore: SPEC0 2026 Q2 updates

pyproject.toml

@@ -57,17 +57,17 @@ dependencies = [
     "h5py>=3.11",
     "joblib",
     # skip 3.11.0rc1 for now: https://github.com/matplotlib/matplotlib/issues/31575
-    "matplotlib>=3.9,!=3.11.0rc1",
+    "matplotlib>=3.10,!=3.11.0rc1",
     "natsort",
-    "networkx>=2.8.8",
-    "numba>=0.60",
-    "numpy>=2",
+    "networkx>=3.4",
+    "numba>=0.61",
+    "numpy>=2.1",
     "packaging>=25",
     "pandas>=2.3",
     "patsy",
     "pynndescent>=0.5.13",
     "scikit-learn>=1.6",
-    "scipy>=1.13",
+    "scipy>=1.14",
     "scverse-misc[settings]>=0.0.5",
     "seaborn>=0.13.2",
     "session-info2",
@@ -95,7 +95,7 @@ magic = [ "magic-impute>=2.0.4" ]
 paga = [ "igraph" ]
 plotting = [ "colour-science" ]
 scanorama = [ "scanorama" ]
-scrublet = [ "scikit-image>=0.23.1" ]
+scrublet = [ "scikit-image>=0.25" ]
 # highly_variable_genes method 'seurat_v3'
 skmisc = [ "scikit-misc>=0.5.1" ]
 scanpy2 = [ "igraph>=0.10.8", "scikit-misc>=0.5.1" ]
@@ -116,7 +116,7 @@ test = [
     { include-group = "test-min" },
 ]
 doc = [
-    "ipython>=7.20",                        # for nbsphinx code highlighting
+    "ipython>=8.27",                        # for nbsphinx code highlighting
     "myst-nb>=1.4",
     "myst-parser>=2",
     "nbsphinx>=0.9",

src/scanpy/preprocessing/_normalization.py

@@ -203,7 +203,7 @@ def normalize_total(  # noqa: PLR0912
     >>> import scanpy as sc
     >>> sc.settings.verbosity = "info"
     >>> sc.settings.logfile = sys.stdout  # for doctests
-    >>> np.set_printoptions(precision=2)
+    >>> np.set_printoptions(precision=2) and None
     >>> adata = AnnData(
     ...     np.array(
     ...         [

src/scanpy/preprocessing/_pca/__init__.py

@@ -4,10 +4,9 @@
 
 import numpy as np
 from anndata import AnnData
-from packaging.version import Version
 
 from ... import logging as logg
-from ..._compat import CSBase, DaskArray, pkg_version, warn
+from ..._compat import CSBase, DaskArray, warn
 from ..._docs import doc_rng
 from ..._settings import Default, settings
 from ..._utils import _doc_params, get_literal_vals, is_backed_type
@@ -35,10 +34,7 @@
 type SvdSolvTruncatedSVDDaskML = Literal["tsqr", "randomized"]
 type SvdSolvDaskML = SvdSolvPCADaskML | SvdSolvTruncatedSVDDaskML
 
-if pkg_version("scikit-learn") >= Version("1.5") or TYPE_CHECKING:
-    type SvdSolvPCASparseSklearn = Literal["arpack", "covariance_eigh"]
-else:
-    type SvdSolvPCASparseSklearn = Literal["arpack"]
+type SvdSolvPCASparseSklearn = Literal["arpack", "covariance_eigh"]
 type SvdSolvPCADenseSklearn = (
     Literal["auto", "full", "randomized"] | SvdSolvPCASparseSklearn
 )