diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 6cca7d4d7..539a9809c 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -17,13 +17,13 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
       - name: Build package
         run: uv build
       - name: Check package
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
index aa98d6db1..933350d1b 100644
--- a/.github/workflows/release.yaml
+++ b/.github/workflows/release.yaml
@@ -18,16 +18,16 @@ jobs:
       contents: read
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: false
       - name: Build package
         run: uv build
       - name: Publish package distributions to PyPI
-        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
diff --git a/.github/workflows/test-notebooks.yaml b/.github/workflows/test-notebooks.yaml
index 528543925..99e5d93dd 100644
--- a/.github/workflows/test-notebooks.yaml
+++ b/.github/workflows/test-notebooks.yaml
@@ -21,21 +21,21 @@ jobs:
   ensure-data-is-cached:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: false
           python-version: "3.14"
 
       - name: Restore data cache
         id: data-cache
-        uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes
           key: data-${{ hashFiles('**/download_data.py') }}
@@ -58,16 +58,16 @@ jobs:
         python: ["3.12"]
 
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           submodules: recursive
           persist-credentials: false
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: ${{ matrix.python }}
 
-      - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+      - uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
           python-version: ${{ matrix.python }}
@@ -75,7 +75,7 @@ jobs:
 
       - name: Restore data cache
         id: data-cache
-        uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes
           key: data-${{ hashFiles('**/download_data.py') }}
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index ffacbe3da..48024f261 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -32,21 +32,21 @@ jobs:
   ensure-data-is-cached:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: false
           python-version: "3.14"
 
       - name: Restore data cache
         id: data-cache
-        uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes
           key: data-${{ hashFiles('**/download_data.py') }}
@@ -68,14 +68,14 @@ jobs:
     outputs:
       envs: ${{ steps.get-envs.outputs.envs }}
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           enable-cache: true
           cache-dependency-glob: pyproject.toml
@@ -113,14 +113,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ contains(matrix.env.name, 'pre') }}
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           python-version: ${{ matrix.env.python }}
           cache-dependency-glob: pyproject.toml
@@ -130,7 +130,7 @@ jobs:
 
       - name: Restore data cache
         id: data-cache
-        uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes
           key: data-${{ hashFiles('**/download_data.py') }}
@@ -163,7 +163,7 @@ jobs:
 
       - name: Archive figures generated during testing
         if: always()
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: visual_test_results_${{ runner.os }}_${{ matrix.env.name }}
           path: ${{ github.workspace }}/tests/figures/*
@@ -176,14 +176,14 @@ jobs:
       id-token: write # for codecov OIDC
       contents: read
     steps:
-      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           filter: blob:none
           fetch-depth: 0
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
         with:
           python-version: "3.14"
           cache-dependency-glob: pyproject.toml
@@ -193,7 +193,7 @@ jobs:
 
       - name: Restore data cache
         id: coverage-data-cache
-        uses: actions/cache@0057852bfaa89a56745cba8c7296529d2fc39830 # v4.3.0
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes
           key: data-${{ hashFiles('**/download_data.py') }}