Add zizmor and harden GitHub Actions workflows

.github/workflows/docs.yml

@@ -6,8 +6,12 @@ on:
     tags:
       - '*'
   merge_group:
+
+permissions:
+  contents: read
+
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs.yml@v17
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v18
     with:
       additional-apt-packages: libgsl-dev

.github/workflows/lint.yml

@@ -4,6 +4,9 @@ on:
   pull_request:
   merge_group:
 
+permissions:
+  contents: read
+
 jobs:
   Lint:
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v17
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v18

.github/workflows/tests.yml

@@ -6,29 +6,36 @@ 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@v18
     with:
       additional-apt-packages: libgsl-dev
       cli-test-cmd: msp --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@v18
     with:
       additional-apt-packages: libgsl-dev
       library-directory: lib
-    secrets: inherit
+    # Trusted first-party tskit-dev reusable workflow; needs secrets (e.g.
+    # CODECOV_TOKEN) passed through.
+    secrets: inherit  # zizmor: ignore[secrets-inherit]
 
   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@v18
     with:
       additional-apt-packages: libgsl-dev
-    secrets: inherit
+    # Trusted first-party tskit-dev reusable workflow; needs secrets (e.g.
+    # CODECOV_TOKEN) passed through.
+    secrets: inherit  # zizmor: ignore[secrets-inherit]
 
   test-python:
     name: Python
@@ -44,14 +51,15 @@ jobs:
 
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.13.0
+        uses: styfle/cancel-workflow-action@d07a454dad7609a92316b57b23c9ccfd4f59af66  # 0.13.1
         with:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v6.0.2
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
         with:
           submodules: true
+          persist-credentials: false
 
       - name: Fix windows symlinks
         # This is horrible, but the "git config core.symlinks true" didn't work.
@@ -81,7 +89,7 @@ jobs:
         run: sudo apt-get update && sudo apt-get install -y libgsl-dev
 
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39  # v8.2.0
         with:
           python-version: ${{ matrix.python }}
           version: "0.10.0"
@@ -102,7 +110,7 @@ jobs:
             --cov-report=xml --cov-branch -n2
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v7.0.0
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f  # v7.0.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false

.github/workflows/wheels.yml

@@ -6,9 +6,12 @@ on:
   release:
     types: [published]
 
+permissions:
+  contents: read
+
 jobs:
   build-wheels:
-    uses: tskit-dev/.github/.github/workflows/build-wheels.yml@v17
+    uses: tskit-dev/.github/.github/workflows/build-wheels.yml@v18
     # To override os-list:
     # with:
     #   python-version: "3.12"
@@ -22,7 +25,7 @@ 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
@@ -33,11 +36,11 @@ 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

@@ -12,6 +12,7 @@ files = { glob = [
     "docs/**",
     "lib/*.[c,h]",
     "lib/tests/*.[c,h]",
+    ".github/workflows/**",
 ]}
 
 exclude = { glob = ["lib/avl.*", "lib/subprojects/**"]}
@@ -65,3 +66,16 @@ hooks = [
     verbose = true,
   },
 ]
+
+[[repos]]
+repo = "local"
+hooks = [
+  {
+    id = "zizmor",
+    name = "zizmor",
+    language = "system",
+    entry = "uv run --only-group=lint zizmor",
+    files = "^\\.github/workflows/.*\\.ya?ml$",
+    pass_filenames = true,
+  },
+]

pyproject.toml

@@ -104,6 +104,7 @@ lint = [
     "clang-format==21.1.8",
     "ruff==0.15.1",
     "prek==0.3.3",
+    "zizmor==1.26.1",
 ]
 
 wheels = [