From a6db559b5678b57de93868fb12099c2591accc46 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 4 Mar 2026 14:32:27 +0000
Subject: [PATCH 1/2] chore: bump shared workflows to v14 and use uv run in
 prek

---
 .github/workflows/docs.yml  | 2 +-
 .github/workflows/lint.yml  | 2 +-
 .github/workflows/tests.yml | 4 ++--
 prek.toml                   | 4 ++--
 4 files changed, 6 insertions(+), 6 deletions(-)

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..030c1bfa 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 --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 --group=lint ruff format --force-exclude",
     types = ["python"],
   },
 ]

From c1967fdb07624118fad4ea1f98e2d5dc39a7c064 Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 4 Mar 2026 15:09:05 +0000
Subject: [PATCH 2/2] Use only-group for prek.toml

---
 prek.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/prek.toml b/prek.toml
index 030c1bfa..d8096287 100644
--- a/prek.toml
+++ b/prek.toml
@@ -22,7 +22,7 @@ hooks = [
     id = "ruff-check",
     name = "ruff check",
     language = "system",
-    entry = "uv run --group=lint 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 = "uv run --group=lint ruff format --force-exclude",
+    entry = "uv run --only-group=lint ruff format --force-exclude",
     types = ["python"],
   },
 ]