diff --git a/.github/workflows/cd-python.yaml b/.github/workflows/cd-python.yaml
index bbcb3b0..b9620dc 100644
--- a/.github/workflows/cd-python.yaml
+++ b/.github/workflows/cd-python.yaml
@@ -37,7 +37,7 @@ jobs:
           - runner: ubuntu-latest
             target: ppc64le
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6
@@ -78,7 +78,7 @@ jobs:
           - runner: ubuntu-latest
             target: armv7
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6
@@ -115,7 +115,7 @@ jobs:
           - runner: windows-latest
             target: x86
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6
@@ -152,7 +152,7 @@ jobs:
           - runner: macos-14
             target: aarch64
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6
@@ -181,7 +181,7 @@ jobs:
     outputs:
       version: ${{ steps.determine-version.outputs.version }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6
diff --git a/.github/workflows/cd-r.yaml b/.github/workflows/cd-r.yaml
index 3181833..31b69d5 100644
--- a/.github/workflows/cd-r.yaml
+++ b/.github/workflows/cd-r.yaml
@@ -20,7 +20,7 @@ jobs:
   build-windows:
     runs-on: windows-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: Set up Python
@@ -73,7 +73,7 @@ jobs:
           - runner: macos-15-intel
             target: x86_64
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: Set up Python
@@ -116,7 +116,7 @@ jobs:
   build-linux:
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - name: Set up Python
diff --git a/.github/workflows/ci-R.yml b/.github/workflows/ci-R.yml
index d4e4173..d31e309 100644
--- a/.github/workflows/ci-R.yml
+++ b/.github/workflows/ci-R.yml
@@ -19,7 +19,7 @@ jobs:
     name: R project
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.9.6
         with:
           environments: ${{ env.R_ENV }}
diff --git a/.github/workflows/ci-python.yml b/.github/workflows/ci-python.yml
index 5cc20de..4aab8ba 100644
--- a/.github/workflows/ci-python.yml
+++ b/.github/workflows/ci-python.yml
@@ -22,7 +22,7 @@ jobs:
       matrix:
         python-environment: ['py310', 'py311', 'py312', 'py313']
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.9.6
         with:
           environments: ${{ matrix.python-environment }}
@@ -31,7 +31,7 @@ jobs:
     name: Python benchmarks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.9.6
         with:
           environments: py-phylo2vec
@@ -40,7 +40,7 @@ jobs:
     name: Test main demo notebook
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: prefix-dev/setup-pixi@v0.9.6
         with:
           environments: py-phylo2vec
diff --git a/.github/workflows/ci-rust.yaml b/.github/workflows/ci-rust.yaml
index 780c962..819b0d5 100644
--- a/.github/workflows/ci-rust.yaml
+++ b/.github/workflows/ci-rust.yaml
@@ -23,7 +23,7 @@ jobs:
           # - beta
           # - nightly
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - name: Setup Rust
         run: rustup update ${{ matrix.toolchain }} && rustup default ${{ matrix.toolchain }}
       - name: Install rustfmt
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
index d85d3b0..ee3b5ae 100644
--- a/.github/workflows/draft-pdf.yml
+++ b/.github/workflows/draft-pdf.yml
@@ -11,7 +11,7 @@ jobs:
     name: Paper Draft
     steps:
       - name: Checkout
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
       - name: Build draft PDF
         uses: openjournals/openjournals-draft-action@master
         with: