[pre-commit.ci] pre-commit autoupdate

.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]

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