From d933e14bda992adae4d676a018637f588bfa34ee Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Jan 2026 22:25:07 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v6.0.0)
- [github.com/asottile/reorder-python-imports: v3.12.0 → v3.16.0](https://github.com/asottile/reorder-python-imports/compare/v3.12.0...v3.16.0)
- [github.com/asottile/add-trailing-comma: v3.1.0 → v4.0.0](https://github.com/asottile/add-trailing-comma/compare/v3.1.0...v4.0.0)
- [github.com/asottile/pyupgrade: v3.15.0 → v3.21.2](https://github.com/asottile/pyupgrade/compare/v3.15.0...v3.21.2)
- https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror
- [github.com/psf/black-pre-commit-mirror: 23.12.1 → 26.1.0](https://github.com/psf/black-pre-commit-mirror/compare/23.12.1...26.1.0)
---
 .pre-commit-config.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a46cafd0..1f3efaf7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,29 +1,29 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
         exclude: .bumpversion.cfg
       - id: end-of-file-fixer
 
   - repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
+    rev: v3.16.0
     hooks:
       - id: reorder-python-imports
         args: ["--py38-plus"]
 
   - repo: https://github.com/asottile/add-trailing-comma
-    rev: v3.1.0
+    rev: v4.0.0
     hooks:
       - id: add-trailing-comma
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
 
-  - repo: https://github.com/psf/black
-    rev: 23.12.1
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 26.1.0
     hooks:
       - id: black
         args: [--safe]

From 6da0ad6225174e3a7d7f545f1a8e4e9707407ffa Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 19 Jan 2026 22:25:29 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 setup.py                    | 1 +
 src/pecanpy/__init__.py     | 1 +
 src/pecanpy/cli.py          | 1 +
 src/pecanpy/experimental.py | 1 +
 src/pecanpy/graph.py        | 1 +
 src/pecanpy/pecanpy.py      | 1 +
 src/pecanpy/rw/__init__.py  | 1 +
 src/pecanpy/rw/dense_rw.py  | 7 ++++---
 src/pecanpy/rw/sparse_rw.py | 7 ++++---
 src/pecanpy/typing.py       | 1 +
 src/pecanpy/wrappers.py     | 1 +
 11 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/setup.py b/setup.py
index 3c71798d..da0ee517 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,5 @@
 """Setup module."""
+
 import setuptools
 
 if __name__ == "__main__":
diff --git a/src/pecanpy/__init__.py b/src/pecanpy/__init__.py
index 3b450189..65806358 100644
--- a/src/pecanpy/__init__.py
+++ b/src/pecanpy/__init__.py
@@ -1,4 +1,5 @@
 """PecanPy: parallelized, efficient, and accelerated node2vec."""
+
 from . import graph
 from . import pecanpy
 
diff --git a/src/pecanpy/cli.py b/src/pecanpy/cli.py
index 577e59a2..6d69bd83 100755
--- a/src/pecanpy/cli.py
+++ b/src/pecanpy/cli.py
@@ -12,6 +12,7 @@
         $ pecanpy --help
 
 """
+
 import argparse
 import warnings
 
diff --git a/src/pecanpy/experimental.py b/src/pecanpy/experimental.py
index 26c820a5..872504b1 100644
--- a/src/pecanpy/experimental.py
+++ b/src/pecanpy/experimental.py
@@ -1,4 +1,5 @@
 """Experimental features."""
+
 import numpy as np
 from numba import njit
 from pecanpy.pecanpy import Base
diff --git a/src/pecanpy/graph.py b/src/pecanpy/graph.py
index 5fd07282..bdfa39db 100644
--- a/src/pecanpy/graph.py
+++ b/src/pecanpy/graph.py
@@ -1,4 +1,5 @@
 """Lite graph objects used by pecanpy."""
+
 import warnings
 
 import numpy as np
diff --git a/src/pecanpy/pecanpy.py b/src/pecanpy/pecanpy.py
index b25a449a..c587dcff 100755
--- a/src/pecanpy/pecanpy.py
+++ b/src/pecanpy/pecanpy.py
@@ -1,4 +1,5 @@
 """Different strategies for generating node2vec walks."""
+
 import numpy as np
 from gensim.models import Word2Vec
 from numba import njit
diff --git a/src/pecanpy/rw/__init__.py b/src/pecanpy/rw/__init__.py
index a521a465..dafc0ad2 100644
--- a/src/pecanpy/rw/__init__.py
+++ b/src/pecanpy/rw/__init__.py
@@ -1,4 +1,5 @@
 """Graph objects equipped with random walk transition functions."""
+
 from .dense_rw import DenseRWGraph
 from .sparse_rw import SparseRWGraph
 
diff --git a/src/pecanpy/rw/dense_rw.py b/src/pecanpy/rw/dense_rw.py
index ba44916f..3c2e1481 100644
--- a/src/pecanpy/rw/dense_rw.py
+++ b/src/pecanpy/rw/dense_rw.py
@@ -1,4 +1,5 @@
 """Dense Graph object equipped with random walk computation."""
+
 import numpy as np
 from numba import njit
 
@@ -106,9 +107,9 @@ def get_extended_normalized_probs(
             alpha = 1 / q + (1 - 1 / q) * t
 
             # suppress noisy edges
-            alpha[
-                unnormalized_probs[out_ind] < noise_threshold_ary[cur_idx]
-            ] = np.minimum(1, 1 / q)
+            alpha[unnormalized_probs[out_ind] < noise_threshold_ary[cur_idx]] = (
+                np.minimum(1, 1 / q)
+            )
             unnormalized_probs[out_ind] *= alpha  # apply out biases
             unnormalized_probs[prev_idx] /= p  # apply the return bias
 
diff --git a/src/pecanpy/rw/sparse_rw.py b/src/pecanpy/rw/sparse_rw.py
index 0ea0fb80..3a1ea205 100644
--- a/src/pecanpy/rw/sparse_rw.py
+++ b/src/pecanpy/rw/sparse_rw.py
@@ -1,4 +1,5 @@
 """Sparse Graph equipped with random walk computation."""
+
 import numpy as np
 from numba import boolean
 from numba import njit
@@ -119,9 +120,9 @@ def get_extended_normalized_probs(
             alpha = 1 / q + (1 - 1 / q) * t[out_ind]
 
             # suppress noisy edges
-            alpha[
-                unnormalized_probs[out_ind] < noise_threshold_ary[cur_idx]
-            ] = np.minimum(1, 1 / q)
+            alpha[unnormalized_probs[out_ind] < noise_threshold_ary[cur_idx]] = (
+                np.minimum(1, 1 / q)
+            )
             unnormalized_probs[out_ind] *= alpha  # apply out biases
             unnormalized_probs[prev_ptr] /= p  # apply the return bias
 
diff --git a/src/pecanpy/typing.py b/src/pecanpy/typing.py
index 90641eff..ad34270c 100644
--- a/src/pecanpy/typing.py
+++ b/src/pecanpy/typing.py
@@ -1,4 +1,5 @@
 """Type annotations."""
+
 from typing import Any
 from typing import Callable
 from typing import Dict
diff --git a/src/pecanpy/wrappers.py b/src/pecanpy/wrappers.py
index 3a972bca..20224aaf 100644
--- a/src/pecanpy/wrappers.py
+++ b/src/pecanpy/wrappers.py
@@ -1,4 +1,5 @@
 """Wrappers used by pecanpy."""
+
 import time