From 439e3b60af860d5d68b4969f32e094a65fe696a5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Oct 2026 16:36:15 +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/astral-sh/ruff-pre-commit: v0.16.2 → v0.16.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.16.2...v0.16.10)
- [github.com/PyCQA/bandit: 1.7.9 → 1.9.4](https://github.com/PyCQA/bandit/compare/1.7.9...1.9.4)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af3eb03..93daa98 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.16.2
+  rev: v0.16.10
   hooks:
     # Run the linter.
     - id: ruff-check
@@ -55,7 +55,7 @@ repos:
 #   - id: codespell
 
 - repo: https://github.com/PyCQA/bandit
-  rev: 1.7.9
+  rev: 1.9.4
   hooks:
     - id: bandit
       args: ["-c", "pyproject.toml"]

From 9b028648ea629e43b455efb6c1636299248e20cf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Oct 2026 16:38:16 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 README.md | 50 ++++++++++++++++++++++++++------------------------
 1 file changed, 26 insertions(+), 24 deletions(-)

diff --git a/README.md b/README.md
index ffc3143..81a7582 100644
--- a/README.md
+++ b/README.md
@@ -51,36 +51,38 @@ ncols = 500  # Number of spots/cells
 counts = np.random.rand(nrows, ncols)
 
 # Create feature annotations
-row_data = BiocFrame({
-    "gene_ids": [f"gene_{i}" for i in range(nrows)],
-    "gene_names": [f"Gene_{i}" for i in range(nrows)]
-})
+row_data = BiocFrame(
+    {"gene_ids": [f"gene_{i}" for i in range(nrows)], "gene_names": [f"Gene_{i}" for i in range(nrows)]}
+)
 
 # Create spot/cell annotations
-col_data = BiocFrame({
-    "n_genes": [50, 200] * int(ncols / 2),
-    "condition": ["healthy", "tumor"] * int(ncols / 2),
-    "cell_id": [f"spot_{i}" for i in range(ncols)],
-    "sample_id": ["sample_1"] * int(ncols / 2) + ["sample_2"] * int(ncols / 2),
-})
+col_data = BiocFrame(
+    {
+        "n_genes": [50, 200] * int(ncols / 2),
+        "condition": ["healthy", "tumor"] * int(ncols / 2),
+        "cell_id": [f"spot_{i}" for i in range(ncols)],
+        "sample_id": ["sample_1"] * int(ncols / 2) + ["sample_2"] * int(ncols / 2),
+    }
+)
 
 # Generate spatial coordinates
-spatial_coords = BiocFrame({
-    "x": np.random.uniform(low=0.0, high=100.0, size=ncols),
-    "y": np.random.uniform(low=0.0, high=100.0, size=ncols)
-})
+spatial_coords = BiocFrame(
+    {"x": np.random.uniform(low=0.0, high=100.0, size=ncols), "y": np.random.uniform(low=0.0, high=100.0, size=ncols)}
+)
 
 # Create image data
-img_data = BiocFrame({
-    "sample_id": ["sample_1", "sample_1", "sample_2"],
-    "image_id": ["aurora", "dice", "desert"],
-    "data": [
-        construct_spatial_image_class("tests/images/sample_image1.jpg"),
-        construct_spatial_image_class("tests/images/sample_image2.png"),
-        construct_spatial_image_class("tests/images/sample_image3.jpg"),
-    ],
-    "scale_factor": [1, 1, 1],
-})
+img_data = BiocFrame(
+    {
+        "sample_id": ["sample_1", "sample_1", "sample_2"],
+        "image_id": ["aurora", "dice", "desert"],
+        "data": [
+            construct_spatial_image_class("tests/images/sample_image1.jpg"),
+            construct_spatial_image_class("tests/images/sample_image2.png"),
+            construct_spatial_image_class("tests/images/sample_image3.jpg"),
+        ],
+        "scale_factor": [1, 1, 1],
+    }
+)
 
 # Create SpatialExperiment object
 spe = SpatialExperiment(