scverse · flying-sheep · Jul 23, 2025 · Jul 21, 2025 · Jul 21, 2025 · Jul 21, 2025
diff --git a/pyproject.toml b/pyproject.toml
@@ -181,6 +181,7 @@ filterwarnings = [
     'ignore:\n*.*scipy\.sparse array:DeprecationWarning:networkx',
     # we want to see and eventually fix these
     'default::numba.core.errors.NumbaPerformanceWarning',
+    'default:.*TSNE.*random.*to.*pca:FutureWarning',      # we should set init=obsm["X_pca"] or so
 ]
 
 [tool.coverage.run]

diff --git a/src/scanpy/tools/_tsne.py b/src/scanpy/tools/_tsne.py
@@ -3,8 +3,6 @@
 import warnings
 from typing import TYPE_CHECKING
 
-from packaging.version import Version
-
 from .. import logging as logg
 from .._compat import old_positionals
 from .._settings import settings
@@ -111,8 +109,6 @@ def tsne(  # noqa: PLR0913
         tSNE parameters.
 
     """
-    import sklearn
-
     start = logg.info("computing tSNE")
     adata = adata.copy() if copy else adata
     X = _choose_representation(adata, use_rep=use_rep, n_pcs=n_pcs)
@@ -129,8 +125,6 @@ def tsne(  # noqa: PLR0913
         metric=metric,
         n_components=n_components,
     )
-    if metric != "euclidean" and (Version(sklearn.__version__) < Version("1.3.0rc1")):
-        params_sklearn["square_distances"] = True
 
     # Backwards compat handling: Remove in scanpy 1.9.0
     if n_jobs != 1 and not use_fast_tsne: