From 8369414427e5c9829ad5fb463d7c2f36e3bf2c4f Mon Sep 17 00:00:00 2001
From: Philipp A <flying-sheep@web.de>
Date: Fri, 10 Nov 2023 10:35:58 +0100
Subject: [PATCH] XFail lobpcg with small test data (#2745)

---
 pyproject.toml           |  2 +-
 scanpy/tests/test_pca.py | 15 +++++++++++++--
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 46d3ee558..a782f9e62 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -107,7 +107,7 @@ test-full = [
 ]
 doc = [
     "sphinx>=5",
-    "sphinx-book-theme",
+    "sphinx-book-theme>=1.0.1",
     "scanpydoc>=0.9.5",
     "sphinx-autodoc-typehints",
     "myst-parser",
diff --git a/scanpy/tests/test_pca.py b/scanpy/tests/test_pca.py
index 50f7427bf..b95a5366c 100644
--- a/scanpy/tests/test_pca.py
+++ b/scanpy/tests/test_pca.py
@@ -1,3 +1,4 @@
+from typing import Literal
 import numpy as np
 import pytest
 import warnings
@@ -71,7 +72,9 @@ def zero_center(request: pytest.FixtureRequest):
 
 
 @pytest.fixture
-def pca_params(array_type, svd_solver_type, zero_center):
+def pca_params(
+    array_type, svd_solver_type: Literal[None, "valid", "invalid"], zero_center
+):
     all_svd_solvers = {"auto", "full", "arpack", "randomized", "tsqr", "lobpcg"}
 
     expected_warning = None
@@ -120,7 +123,9 @@ def test_pca_warnings(array_type, zero_center, pca_params):
     if expected_warning is not None:
         with pytest.warns(UserWarning, match=expected_warning):
             sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)
-    else:
+        return
+
+    try:
         with warnings.catch_warnings():
             warnings.simplefilter("error")
             warnings.filterwarnings(
@@ -129,6 +134,12 @@ def test_pca_warnings(array_type, zero_center, pca_params):
                 DeprecationWarning,
             )
             sc.pp.pca(adata, svd_solver=svd_solver, zero_center=zero_center)
+    except UserWarning:
+        # TODO: Fix this case, maybe by increasing test data size.
+        # https://github.com/scverse/scanpy/issues/2744
+        if svd_solver == "lobpcg":
+            pytest.xfail(reason="lobpcg doesn’t work with this small test data")
+        raise
 
 
 # This warning test is out of the fixture because it is a special case in the logic of the function