Pin GitHub Actions to SHAs and fix zizmor findings

.github/workflows/ci.yml

@@ -6,14 +6,19 @@ on:
   pull_request:
     branches: [main, dev]
 
+permissions:
+  contents: read
+
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "3.11"
 
@@ -31,10 +36,12 @@ jobs:
   typecheck:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "3.11"
 
@@ -50,10 +57,12 @@ jobs:
   build-css:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Set up Node.js
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
         with:
           node-version: "20"
 
@@ -79,15 +88,17 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Set up Java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
         with:
           distribution: "temurin"
           java-version: "17"
@@ -101,7 +112,7 @@ jobs:
         run: pytest -v --cov=nf_docs --cov-report=xml
 
       - name: Upload coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@e79a6962e0d4c0c17b229090214935d2e33f8354 # v6.0.1
         if: matrix.python-version == '3.11'
         with:
           files: ./coverage.xml

.github/workflows/docs.yml

@@ -13,15 +13,17 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/configure-pages@v5
-      - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
+      - uses: actions/configure-pages@45bfe0192ca1faeb007ade9deae92b16b8254a0d # v6.0.0
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: 3.x
       - run: pip install zensical
       - run: zensical build --clean
-      - uses: actions/upload-pages-artifact@v4
+      - uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9 # v5.0.0
         with:
           path: site
-      - uses: actions/deploy-pages@v4
+      - uses: actions/deploy-pages@cd2ce8fcbc39b97be8ca5fce6e763baed58fa128 # v5.0.0
         id: deployment

.github/workflows/publish.yml

@@ -4,15 +4,20 @@ on:
   release:
     types: [published]
 
+permissions:
+  contents: read
+
 jobs:
   build:
     name: Build distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "3.x"
 
@@ -23,7 +28,7 @@ jobs:
         run: python -m build
 
       - name: Store the distribution packages
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: python-package-distributions
           path: dist/
@@ -41,10 +46,10 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
         with:
           name: python-package-distributions
           path: dist/
 
       - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0