From 3443cff79519a0a1d936fa4659596540e5b53e0a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 13 Jul 2026 21:37:14 +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/rhysd/actionlint: v1.7.9 → v1.7.12](https://github.com/rhysd/actionlint/compare/v1.7.9...v1.7.12)
- [github.com/codespell-project/codespell: v2.4.1 → v2.4.2](https://github.com/codespell-project/codespell/compare/v2.4.1...v2.4.2)
- [github.com/DavidAnson/markdownlint-cli2: v0.20.0 → v0.23.0](https://github.com/DavidAnson/markdownlint-cli2/compare/v0.20.0...v0.23.0)
- [github.com/kynan/nbstripout: 0.8.2 → 0.9.1](https://github.com/kynan/nbstripout/compare/0.8.2...0.9.1)
- [github.com/psf/black-pre-commit-mirror: 25.12.0 → 26.5.1](https://github.com/psf/black-pre-commit-mirror/compare/25.12.0...26.5.1)
- [github.com/pycqa/isort: 7.0.0 → 9.0.0b1](https://github.com/pycqa/isort/compare/7.0.0...9.0.0b1)
---
 .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 61bfbfc9..343e0086 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -26,29 +26,29 @@ repos:
     hooks:
       - id: shellcheck
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.9
+    rev: v1.7.12
     hooks:
       - id: actionlint
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.20.0
+    rev: v0.23.0
     hooks:
       - id: markdownlint-cli2
   # Formatters should be run late so that they can re-format any prior changes.
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.2
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.5.1
     hooks:
       - id: black-jupyter
         args: ["--line-length", "120", "--target-version", "py310"]
   - repo: https://github.com/pycqa/isort
-    rev: 7.0.0
+    rev: 9.0.0b1
     hooks:
       - id: isort
         args: ["--profile", "black", "--py", "310"]

From 7cd3e8e81aadb623ea96e3c9062d89a501628450 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 13 Jul 2026 21:37:26 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 test/scripts/result_file_to_parquet.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/test/scripts/result_file_to_parquet.py b/test/scripts/result_file_to_parquet.py
index ce544b26..c5656949 100755
--- a/test/scripts/result_file_to_parquet.py
+++ b/test/scripts/result_file_to_parquet.py
@@ -159,8 +159,7 @@ def write_readme(result_file: pathlib.Path, output_prefix: pathlib.Path, chroms:
             chrom2 = "abc"
 
         f.write(
-            textwrap.dedent(
-                f"""
+            textwrap.dedent(f"""
         # README.md
 
         This folder contains the tables and metadata extracted from file \"{result_file.name}\".
@@ -207,8 +206,7 @@ def write_readme(result_file: pathlib.Path, output_prefix: pathlib.Path, chroms:
            - `attributes.json`: JSON file with the attributes for the current chromosome.
            - `xxx_where.parquet`: PARQUET file with the data from table "xxx" for location "where" from the current chromosome.
            - `xxx_where.missing`: text file with the exception message raised when trying to access tables without data.
-        """
-            ).lstrip("\n"),
+        """).lstrip("\n"),
         )