diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 339b764..ad9f3b0 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -8,4 +8,4 @@ on:
       - '*'
 jobs:
   docs:
-    uses: tskit-dev/.github/.github/workflows/docs.yml@v13
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v14
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 5bfbe56..f7a8ffb 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -5,4 +5,4 @@ on:
 
 jobs:
   Lint:
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v12
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v14
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index b459381..c3cc093 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -10,14 +10,14 @@ jobs:
 
   packaging:
     name: Python packaging
-    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v12
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v14
     with:
      cli-test-cmd: tszip --help
 
 
   test:
     name: Python
-    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v12
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v14
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python }}
diff --git a/prek.toml b/prek.toml
index 24db4f0..d809628 100644
--- a/prek.toml
+++ b/prek.toml
@@ -7,8 +7,6 @@
 [[repos]]
 repo = "builtin"
 hooks = [
-    # { id = "trailing-whitespace" },
-    # { id = "end-of-file-fixer" },
     { id = "check-added-large-files" },
     { id = "check-merge-conflict" },
     { id = "mixed-line-ending" },
@@ -24,7 +22,7 @@ hooks = [
     id = "ruff-check",
     name = "ruff check",
     language = "system",
-    entry = "ruff check --fix --force-exclude",
+    entry = "uv run --only-group=lint ruff check --fix --force-exclude",
     types = ["python"],
   },
 ]
@@ -36,7 +34,7 @@ hooks = [
     id = "ruff-format",
     name = "ruff format",
     language = "system",
-    entry = "ruff format --force-exclude",
+    entry = "uv run --only-group=lint ruff format --force-exclude",
     types = ["python"],
   },
 ]