From e2c055591b4d3cad6922e8d8f267f25cffc8eef9 Mon Sep 17 00:00:00 2001
From: selmanozleyen <syozleyen@gmail.com>
Date: Wed, 21 May 2025 10:01:54 +0200
Subject: [PATCH 1/4] fixes numba warning

---
 src/squidpy/gr/_ligrec.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/squidpy/gr/_ligrec.py b/src/squidpy/gr/_ligrec.py
index d54ce91f..defdeac6 100644
--- a/src/squidpy/gr/_ligrec.py
+++ b/src/squidpy/gr/_ligrec.py
@@ -93,6 +93,9 @@ def _create_template(n_cls: int, return_means: bool = False, parallel: bool = Tr
     g{i} = np.zeros((data.shape[1],), dtype=np.float64); s{i} = 0"""
         for i in rng
     )
+    init += """
+    error = False
+    """
 
     loop_body = """
         if cl == 0:
@@ -110,7 +113,7 @@ def _create_template(n_cls: int, return_means: bool = False, parallel: bool = Tr
         cl = clustering[row]
         {loop_body}
         else:
-            assert False, "Unhandled case."
+            error = True
     """
     finalize = ", ".join(f"g{i} / s{i}" for i in rng)
     finalize = f"groups = np.stack(({finalize}))"
@@ -841,8 +844,16 @@ def _analysis_helper(
 
     for _ in perms:
         rs.shuffle(clustering)
-        test(interactions, interaction_clusters, data, clustering, mean, mask, res=res)
-
+        error = test(interactions, interaction_clusters, data, clustering, mean, mask, res=res)
+        if error:
+            raise ValueError(
+                "In the execution of the numba function, "
+                "an unhandled case was encountered. "
+            )
+            # This is mainly to avoid a numba warning
+            # Otherwise, the numba function wouldn't be
+            # executed in parallel
+            # See: https://github.com/scverse/squidpy/issues/994
         if queue is not None:
             queue.put(Signal.UPDATE)
 

From 40d8d5e3ad62f742c873d92d547d6e670a64b5f1 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 21 May 2025 08:05:23 +0000
Subject: [PATCH 2/4] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/squidpy/gr/_ligrec.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/squidpy/gr/_ligrec.py b/src/squidpy/gr/_ligrec.py
index defdeac6..2ddbd10f 100644
--- a/src/squidpy/gr/_ligrec.py
+++ b/src/squidpy/gr/_ligrec.py
@@ -846,10 +846,7 @@ def _analysis_helper(
         rs.shuffle(clustering)
         error = test(interactions, interaction_clusters, data, clustering, mean, mask, res=res)
         if error:
-            raise ValueError(
-                "In the execution of the numba function, "
-                "an unhandled case was encountered. "
-            )
+            raise ValueError("In the execution of the numba function, an unhandled case was encountered. ")
             # This is mainly to avoid a numba warning
             # Otherwise, the numba function wouldn't be
             # executed in parallel

From daf87bb6804f8980d6e859c038f314090ca14c6e Mon Sep 17 00:00:00 2001
From: selmanozleyen <syozleyen@gmail.com>
Date: Wed, 21 May 2025 13:06:33 +0200
Subject: [PATCH 3/4] add filterwarnings to pyproject

---
 pyproject.toml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 1143cab9..05433048 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -226,3 +226,8 @@ required-imports = ["from __future__ import annotations"]
 [tool.ruff.lint.flake8-tidy-imports]
 # Disallow all relative imports.
 ban-relative-imports = "all"
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "error:NumbaPerformanceWarning"
+]
\ No newline at end of file

From d02fddee46a0b04f35bfe105b42c50faf1664ab9 Mon Sep 17 00:00:00 2001
From: Ilan Gold <ilanbassgold@gmail.com>
Date: Wed, 28 May 2025 11:29:35 +0200
Subject: [PATCH 4/4] Update pyproject.toml

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 05433048..ee90805b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -229,5 +229,5 @@ ban-relative-imports = "all"
 
 [tool.pytest.ini_options]
 filterwarnings = [
-    "error:NumbaPerformanceWarning"
-]
\ No newline at end of file
+    "error::NumbaPerformanceWarning"
+]