chore: bump shared workflows to v14 and use uv run in prek

Author: jeromekelleher

.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

.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

.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 }}

.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
 

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,
   },