Merge branch 'master' into revert_DEA_cost

Author: millingermarkus

.github/workflows/ci.yaml

@@ -25,7 +25,7 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Setup micromamba
       uses: mamba-org/setup-micromamba@v2

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: check-merge-conflict
   - id: check-added-large-files
@@ -17,7 +17,7 @@ repos:
 # Run ruff to lint and format
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.12.2
+  rev: v0.13.3
   hooks:
     # Run the linter.
   - id: ruff
@@ -44,6 +44,6 @@ repos:
 
   # Format Snakemake rule / workflow files
 - repo: https://github.com/snakemake/snakefmt
-  rev: v0.11.0
+  rev: v0.11.2
   hooks:
   - id: snakefmt