[pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v6.0.0](pre-commit/pre-commit-hooks@v4.4.0...v6.0.0)
- [github.com/PyCQA/isort: 5.10.1 → 7.0.0](PyCQA/isort@5.10.1...7.0.0)
- [github.com/codespell-project/codespell: v2.2.2 → v2.4.1](codespell-project/codespell@v2.2.2...v2.4.1)
- https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror
- [github.com/psf/black-pre-commit-mirror: 22.10.0 → 25.11.0](psf/black-pre-commit-mirror@22.10.0...25.11.0)
- [github.com/nbQA-dev/nbQA: 1.5.3 → 1.9.1](nbQA-dev/nbQA@1.5.3...1.9.1)
- [github.com/macisamuele/language-formatters-pre-commit-hooks: v2.4.0 → v2.15.0](macisamuele/language-formatters-pre-commit-hooks@v2.4.0...v2.15.0)
- [github.com/snakemake/snakefmt: v0.7.0 → v0.11.2](snakemake/snakefmt@v0.7.0...v0.11.2)
- [github.com/fsfe/reuse-tool: v1.0.0 → v6.2.0](fsfe/reuse-tool@v1.0.0...v6.2.0)

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ exclude: "^LICENSES"
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v6.0.0
   hooks:
   - id: check-merge-conflict
   - id: end-of-file-fixer
@@ -19,51 +19,51 @@ repos:
 
 # Sort package imports alphabetically
 - repo: https://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 7.0.0
   hooks:
   - id: isort
     args: ["--profile", "black", "--filter-files"]
 
 # Find common spelling mistakes in comments and docstrings
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.4.1
   hooks:
   - id: codespell
     args: ['--ignore-regex="\b[A-Z]+\b"'] # Ignore capital case words, e.g. country codes
     types_or: [python, rst, markdown]
     files: ^(actions|doc)/
 
 # Formatting with "black" coding style
-- repo: https://github.com/psf/black
-  rev: 22.10.0
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 25.11.0
   hooks:
   # Format Python files
   - id: black
   # Format Jupyter Python notebooks
   - id: black-jupyter
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.5.3
+  rev: 1.9.1
   hooks:
     # Apply isort to Jupyter Python notebooks
   - id: nbqa-isort
 
 # Do YAML formatting (before the linter checks it for misses)
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.4.0
+  rev: v2.15.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --indent, '2', --preserve-quotes]
 
 # Format Snakemake rule / workflow files
 - repo: https://github.com/snakemake/snakefmt
-  rev: v0.7.0
+  rev: v0.11.2
   hooks:
   - id: snakefmt
 
 # Check for FSFE REUSE compliance (licensing)
 - repo: https://github.com/fsfe/reuse-tool
-  rev: v1.0.0
+  rev: v6.2.0
   hooks:
   - id: reuse