From 3c285cdf88005e434f7dddbf7250f27c2056151f Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 4 Mar 2026 14:32:28 +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  | 8 ++++----
 .github/workflows/wheels.yml | 2 +-
 prek.toml                    | 6 +++---
 5 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 8c68874945..51b911ca57 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -12,7 +12,7 @@ env:
 
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs.yml@v12
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v14
     with:
       pyproject-directory: python
       additional-apt-packages: doxygen
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 4826bfc17b..82ff02f86a 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -5,6 +5,6 @@ on:
 
 jobs:
   Lint:
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v12
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v14
     with:
       pyproject-directory: python
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0846488b48..ae0398c7a9 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -13,21 +13,21 @@ 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:
       pyproject-directory: python
       cli-test-cmd: tskit --help
 
   test-c:
     name: C tests
-    uses: tskit-dev/.github/.github/workflows/c-tests.yml@v12
+    uses: tskit-dev/.github/.github/workflows/c-tests.yml@v14
     with:
       library-directory: c
     secrets: inherit
 
   test-python-c:
     name: Python-C tests
-    uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@v12
+    uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@v14
     with:
       tests: python/tests/test_python_c.py python/tests/test_dict_encoding.py
       pyproject-directory: python
@@ -36,7 +36,7 @@ jobs:
 
   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/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index c45863ef8a..d15b8e378e 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -8,7 +8,7 @@ on:
 
 jobs:
   build-wheels:
-    uses: tskit-dev/.github/.github/workflows/build-wheels.yml@v12
+    uses: tskit-dev/.github/.github/workflows/build-wheels.yml@v14
     with:
       pyproject-directory: python
 
diff --git a/prek.toml b/prek.toml
index 7c5c2aeeaf..fe2e9df3b0 100644
--- a/prek.toml
+++ b/prek.toml
@@ -35,7 +35,7 @@ hooks = [
     id = "ruff-check",
     name = "ruff check",
     language = "system",
-    entry = "ruff check --fix --force-exclude",
+    entry = "uv run --project=python --group=lint ruff check --fix --force-exclude",
     types = ["python"],
   },
 ]
@@ -47,7 +47,7 @@ hooks = [
     id = "ruff-format",
     name = "ruff format",
     language = "system",
-    entry = "ruff format --force-exclude",
+    entry = "uv run --project=python --group=lint ruff format --force-exclude",
     types = ["python"],
   },
 ]
@@ -59,7 +59,7 @@ hooks = [
     id = "clang-format",
     name = "clang-format",
     language = "system",
-    entry = "clang-format -i",
+    entry = "uv run --project=python --group=lint clang-format -i",
     types = ["c"],
     verbose = true,
   },

From 0ea62361e8053d4a6bcc23ba10c5308d27f070ec Mon Sep 17 00:00:00 2001
From: Jerome Kelleher <jk@well.ox.ac.uk>
Date: Wed, 4 Mar 2026 15:10:48 +0000
Subject: [PATCH 2/2] Update to use only-group

---
 prek.toml | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/prek.toml b/prek.toml
index fe2e9df3b0..94f1a73982 100644
--- a/prek.toml
+++ b/prek.toml
@@ -4,22 +4,11 @@
 # rules implementing lint workflows.  We do not use any remote
 # workflow repos.
 
-# files = { glob = [
-#     "tskit/**",
-#     "benchmark/**",
-#     "tests/**",
-#     "_tskitmodule.c",
-#     "*.toml",
-#     "docs/**",
-# ]}
-
 exclude = { glob = ["c/subprojects/**"]}
 
 [[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" },
@@ -35,7 +24,7 @@ hooks = [
     id = "ruff-check",
     name = "ruff check",
     language = "system",
-    entry = "uv run --project=python --group=lint ruff check --fix --force-exclude",
+    entry = "uv run --project=python --only-group=lint ruff check --fix --force-exclude",
     types = ["python"],
   },
 ]
@@ -47,7 +36,7 @@ hooks = [
     id = "ruff-format",
     name = "ruff format",
     language = "system",
-    entry = "uv run --project=python --group=lint ruff format --force-exclude",
+    entry = "uv run --project=python --only-group=lint ruff format --force-exclude",
     types = ["python"],
   },
 ]
@@ -59,7 +48,7 @@ hooks = [
     id = "clang-format",
     name = "clang-format",
     language = "system",
-    entry = "uv run --project=python --group=lint clang-format -i",
+    entry = "uv run --project=python --only-group=lint clang-format -i",
     types = ["c"],
     verbose = true,
   },