diff --git a/.github/workflows/check_sphinx_links.yml b/.github/workflows/check_sphinx_links.yml
index cf0737f4e..fb96323b2 100644
--- a/.github/workflows/check_sphinx_links.yml
+++ b/.github/workflows/check_sphinx_links.yml
@@ -13,7 +13,7 @@ jobs:
       cancel-in-progress: true
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
index 9b61c3681..4d12bef46 100644
--- a/.github/workflows/codespell.yml
+++ b/.github/workflows/codespell.yml
@@ -9,6 +9,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
index b83be30a1..9e8a380e3 100644
--- a/.github/workflows/deploy_release.yml
+++ b/.github/workflows/deploy_release.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required for versioneer to determine the version
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
index 605b5f952..d5ac69c30 100644
--- a/.github/workflows/ruff.yml
+++ b/.github/workflows/ruff.yml
@@ -6,6 +6,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Run ruff
         uses: astral-sh/ruff-action@v3
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
index 0baed3fb9..576bee7ca 100644
--- a/.github/workflows/run_all_tests.yml
+++ b/.github/workflows/run_all_tests.yml
@@ -48,7 +48,7 @@ jobs:
           - { name: macos-python3.13-prerelease-optional   , test-tox-env: pytest-py313-prerelease-optional , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
@@ -106,7 +106,7 @@ jobs:
           - { name: macos-gallery-python3.12-prerelease-optional   , test-tox-env: gallery-py312-prerelease-optional , python-ver: "3.12", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
@@ -144,7 +144,7 @@ jobs:
           - { name: macos-python3.13-ros3   , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
index 6e269e767..20870bd09 100644
--- a/.github/workflows/run_coverage.yml
+++ b/.github/workflows/run_coverage.yml
@@ -34,7 +34,7 @@ jobs:
       PYTHON: '3.12'  # TODO: Update to 3.13 when linkml and its deps support 3.13
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
@@ -89,7 +89,7 @@ jobs:
           - { name: linux-python3.13-ros3  , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
diff --git a/.github/workflows/run_hdmf_zarr_tests.yml b/.github/workflows/run_hdmf_zarr_tests.yml
index 4a24a2d61..8cc90729f 100644
--- a/.github/workflows/run_hdmf_zarr_tests.yml
+++ b/.github/workflows/run_hdmf_zarr_tests.yml
@@ -13,7 +13,7 @@ jobs:
       cancel-in-progress: true
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
diff --git a/.github/workflows/run_nwb_extension_tests.yml b/.github/workflows/run_nwb_extension_tests.yml
index 6466736df..6a1bf5580 100644
--- a/.github/workflows/run_nwb_extension_tests.yml
+++ b/.github/workflows/run_nwb_extension_tests.yml
@@ -55,7 +55,7 @@ jobs:
       matrix: ${{ steps.generate-matrix.outputs.matrix }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up Python
         uses: actions/setup-python@v6
@@ -91,7 +91,7 @@ jobs:
       fail-fast: false  # Continue testing other extensions even if one fails
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
diff --git a/.github/workflows/run_pynwb_tests.yml b/.github/workflows/run_pynwb_tests.yml
index 259f8d054..19d306158 100644
--- a/.github/workflows/run_pynwb_tests.yml
+++ b/.github/workflows/run_pynwb_tests.yml
@@ -13,7 +13,7 @@ jobs:
       cancel-in-progress: true
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 17aff4c03..55336c872 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -32,7 +32,7 @@ jobs:
           - { name: macos-python3.13-upgraded-optional   , test-tox-env: pytest-py313-upgraded-optional , python-ver: "3.13", os: macos-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
@@ -92,7 +92,7 @@ jobs:
           - { name: windows-gallery-python3.12-upgraded-optional , test-tox-env: gallery-py312-upgraded-optional , python-ver: "3.12", os: windows-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
@@ -122,7 +122,7 @@ jobs:
       cancel-in-progress: true
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version
@@ -166,7 +166,7 @@ jobs:
           - { name: linux-python3.13-ros3  , python-ver: "3.13", os: ubuntu-latest }
     steps:
       - name: Checkout repo with submodules
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           submodules: 'recursive'
           fetch-depth: 0  # tags are required to determine the version