Add zizmor

.github/workflows/docs.yml

@@ -10,10 +10,12 @@ on:
 env:
   FORCE_COLOR: 1
 
+permissions:
+  contents: read
+
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs.yml@v17
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v20
     with:
       pyproject-directory: python
       additional-apt-packages: doxygen
-      pre-build-command: cd docs/doxygen && doxygen

.github/workflows/lint.yml

@@ -3,8 +3,11 @@ name: Lint
 on:
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   Lint:
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v17
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v19
     with:
       pyproject-directory: python

.github/workflows/release-c.yml

@@ -2,22 +2,30 @@ name: Publish C API release
 
 on: push
 
+permissions:
+  contents: read
+
 jobs:
   build:
     runs-on: ubuntu-24.04
+    permissions:
+      contents: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v4.2.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
+        with:
+          persist-credentials: false
 
       - name: Install system deps
         run: |
           sudo apt-get update
           sudo apt-get install -y ninja-build libcunit1-dev
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
         with:
           version: "0.10.0"
+          enable-cache: false
 
       - name: Install meson
         run: uv tool install meson==1.10.1
@@ -36,7 +44,9 @@ jobs:
           meson dist
 
       - name: Release
-        uses: softprops/action-gh-release@v2.2.1
+        # zizmor: ignore[superfluous-actions] this action handles draft
+        # releases and glob-based multi-file uploads beyond plain `gh release`.
+        uses: softprops/action-gh-release@718ea10b132b3b2eba29c1007bb80653f286566b  # v3.0.1
         if: startsWith(github.ref, 'refs/tags/') && contains(github.event.ref, 'C_')
         with:
           draft: True

.github/workflows/tests.yml

@@ -6,39 +6,45 @@ on:
     branches: [main, test]
   merge_group:
 
+permissions:
+  contents: read
+
 jobs:
 
   packaging:
     name: Python packaging
-    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v17
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v19
     with:
       pyproject-directory: python
       cli-test-cmd: kastore --help
 
   test-c:
     name: C tests
-    uses: tskit-dev/.github/.github/workflows/c-tests.yml@v17
+    uses: tskit-dev/.github/.github/workflows/c-tests.yml@v19
     with:
       library-directory: c
-    secrets: inherit
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   test-python-c:
     name: Python-C tests
-    uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@v17
+    uses: tskit-dev/.github/.github/workflows/python-c-tests.yml@v19
     with:
       tests: python/tests/test_python_c.py
       pyproject-directory: python
-    secrets: inherit
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   test:
     name: Python
-    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v17
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v19
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python }}
       pyproject-directory: python
       coverage-directory: python/kastore
-    secrets: inherit
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     strategy:
       matrix:
         python: [ 3.11, 3.14 ]

.github/workflows/wheels.yml

@@ -6,10 +6,13 @@ on:
   release:
     types: [published]
 
+permissions:
+  contents: read
+
 jobs:
   build-wheels:
     if: "!startsWith(github.ref, 'refs/tags/C_')"
-    uses: tskit-dev/.github/.github/workflows/build-wheels.yml@v17
+    uses: tskit-dev/.github/.github/workflows/build-wheels.yml@v19
     with:
       pyproject-directory: python
 
@@ -21,7 +24,7 @@ jobs:
       id-token: write
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v7.0.0
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c  # v8.0.1
         with:
           pattern: build-*
           path: dist
@@ -32,11 +35,11 @@ jobs:
 
       - name: Publish distribution to Test PyPI
         if: github.event_name == 'push' && github.ref_name == 'test-publish'
-        uses: pypa/gh-action-pypi-publish@v1.13.0
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b  # v1.14.0
         with:
           repository-url: https://test.pypi.org/legacy/
           verbose: true
 
       - name: Publish distribution to Production PyPI
         if: github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@v1.13.0
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b  # v1.14.0

.github/zizmor.yml

@@ -0,0 +1,9 @@
+# zizmor configuration for tskit-dev repos.
+# Third-party actions must be hash-pinned; first-party tskit-dev reusable
+# workflows are trusted and may stay pinned to a version tag (e.g. @v17).
+rules:
+  unpinned-uses:
+    config:
+      policies:
+        tskit-dev/*: ref-pin
+        "*": hash-pin

prek.toml

@@ -52,3 +52,16 @@ hooks = [
     verbose = true,
   },
 ]
+
+[[repos]]
+repo = "local"
+hooks = [
+  {
+    id = "zizmor",
+    name = "zizmor",
+    language = "system",
+    entry = "uv run --project=python --only-group=lint zizmor",
+    files = "^\\.github/workflows/.*\\.ya?ml$",
+    pass_filenames = true,
+  },
+]

python/pyproject.toml

@@ -45,6 +45,7 @@ lint = [
     "clang-format==21.1.8",
     "ruff==0.15.1",
     "prek==0.3.3",
+    "zizmor==1.26.1",
 ]
 
 packaging = [