diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 25126d4c..48551f08 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -10,4 +10,4 @@ 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 5bfbe56e..f7a8ffb2 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 a95b24f1..dfc567d6 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -9,13 +9,13 @@ on:
 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: tsdate --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 3a258356..d8096287 100644
--- a/prek.toml
+++ b/prek.toml
@@ -22,7 +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"],
   },
 ]
@@ -34,7 +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"],
   },
 ]