From de0dcd5f1fe21c9168b46d54ac44ce7a884173c4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Jan 2026 20:52:43 +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/executablebooks/mdformat: 0.7.22 → 1.0.0](https://github.com/executablebooks/mdformat/compare/0.7.22...1.0.0)
- [github.com/igorshubovych/markdownlint-cli: v0.45.0 → v0.47.0](https://github.com/igorshubovych/markdownlint-cli/compare/v0.45.0...v0.47.0)
- [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.3...v0.14.10)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ec42b17..3e85b24 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -20,7 +20,7 @@ repos:
         types: [yaml]
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.22
+    rev: 1.0.0
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -31,7 +31,7 @@ repos:
           )$
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.45.0
+    rev: v0.47.0
     hooks:
       - id: markdownlint-fix
         exclude: |
@@ -40,7 +40,7 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.3
+    rev: v0.14.10
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

From 7450550ec1c5c18fd39d6794dbb90357c063b02e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Jan 2026 20:53:02 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 DOCKER_README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DOCKER_README.md b/DOCKER_README.md
index ec5f842..fe87c83 100644
--- a/DOCKER_README.md
+++ b/DOCKER_README.md
@@ -105,7 +105,9 @@ docker-compose run --rm --entrypoint /bin/bash gsmap
 ## Tips for Reproducibility
 
 1. **Pin versions**: Consider updating the Dockerfile to use specific versions of dependencies
+
 1. **Document data**: Keep track of input data versions and sources
+
 1. **Tag images**: Use version tags for your Docker images
 
     ```bash