diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
index 04f8eec141..a2ac4d506b 100644
--- a/.github/workflows/benchmark.yml
+++ b/.github/workflows/benchmark.yml
@@ -51,7 +51,7 @@ jobs:
         - 5672:5672
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml
index 07ff0d2359..2ede81f785 100644
--- a/.github/workflows/ci-code.yml
+++ b/.github/workflows/ci-code.yml
@@ -54,7 +54,7 @@ jobs:
         - 5001:22
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install system dependencies
       run: sudo apt update && sudo apt install postgresql graphviz
@@ -103,7 +103,7 @@ jobs:
         - 15672:15672
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install graphviz
       run: sudo apt update && sudo apt install graphviz
@@ -130,7 +130,7 @@ jobs:
     timeout-minutes: 20
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install graphviz
       run: sudo apt update && sudo apt install graphviz
@@ -155,7 +155,7 @@ jobs:
     timeout-minutes: 10
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
@@ -198,7 +198,7 @@ jobs:
         - 15672:15672
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
diff --git a/.github/workflows/docker-build-test.yml b/.github/workflows/docker-build-test.yml
index 64edd7bd56..bd87da3c53 100644
--- a/.github/workflows/docker-build-test.yml
+++ b/.github/workflows/docker-build-test.yml
@@ -35,13 +35,13 @@ jobs:
     steps:
 
     - name: Checkout Repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
 
     - name: Build images
-      uses: docker/bake-action@v5
+      uses: docker/bake-action@v6
       with:
         # Load to Docker engine for testing
         load: true
@@ -55,7 +55,7 @@ jobs:
           build.json
 
     - name: Set Up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.11'
         cache: pip
diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index 3d22c080d4..1580676eaf 100644
--- a/.github/workflows/docker-build.yml
+++ b/.github/workflows/docker-build.yml
@@ -36,7 +36,7 @@ jobs:
     steps:
 
     - name: Checkout Repo ⚡️
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up QEMU
       if: ${{ inputs.platforms != 'linux/amd64' }}
@@ -58,7 +58,7 @@ jobs:
 
     - name: Build and upload to ghcr.io 📤
       id: build
-      uses: docker/bake-action@v5
+      uses: docker/bake-action@v6
       with:
         push: true
         workdir: .docker/
diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
index 53969ae2d8..4ba4ce359b 100644
--- a/.github/workflows/docker-publish.yml
+++ b/.github/workflows/docker-publish.yml
@@ -36,7 +36,7 @@ jobs:
         working-directory: .docker
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Login to GitHub Container Registry 🔑
       uses: docker/login-action@v3
diff --git a/.github/workflows/docker-test.yml b/.github/workflows/docker-test.yml
index 652c459102..e5d119daed 100644
--- a/.github/workflows/docker-test.yml
+++ b/.github/workflows/docker-test.yml
@@ -28,7 +28,7 @@ jobs:
     steps:
 
     - name: Checkout Repo ⚡️
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Login to GitHub Container Registry 🔑
       uses: docker/login-action@v3
@@ -39,7 +39,7 @@ jobs:
 
     - name: Set Up Python 🐍
       if: ${{ startsWith(inputs.runsOn, 'ubuntu') }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.11'
         cache: pip
diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml
index 83cb638513..a5b21b28bb 100644
--- a/.github/workflows/docs-build.yml
+++ b/.github/workflows/docs-build.yml
@@ -18,7 +18,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core and docs deps
       uses: ./.github/actions/install-aiida-core
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index 18325540da..4e7e85b31a 100644
--- a/.github/workflows/nightly.yml
+++ b/.github/workflows/nightly.yml
@@ -54,7 +54,7 @@ jobs:
         - 5001:22
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install system dependencies
       run: sudo apt update && sudo apt install postgresql
@@ -122,7 +122,7 @@ jobs:
         - 15672:15672
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core
       id: install
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 25ab2be126..b3a3c9abbf 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -20,7 +20,7 @@ jobs:
     timeout-minutes: 15
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install python dependencies
       uses: ./.github/actions/install-aiida-core
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 7f42a77315..e0fda4da5f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -28,10 +28,10 @@ jobs:
 
     steps:
     - name: Checkout repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
 
@@ -45,7 +45,7 @@ jobs:
     timeout-minutes: 30
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core and pre-commit
       uses: ./.github/actions/install-aiida-core
@@ -71,7 +71,7 @@ jobs:
         - 15672:15672
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install aiida-core
       uses: ./.github/actions/install-aiida-core
@@ -90,9 +90,9 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: install flit
@@ -118,9 +118,9 @@ jobs:
 
     steps:
     - name: Checkout source
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
     - name: install flit
diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml
index 1de4da38ac..9c532218f9 100644
--- a/.github/workflows/test-install.yml
+++ b/.github/workflows/test-install.yml
@@ -30,15 +30,15 @@ jobs:
     timeout-minutes: 5
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Set up Python 3.11
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.11'
 
     - name: Set up uv
-      uses: astral-sh/setup-uv@v5.2.1
+      uses: astral-sh/setup-uv@v6.8.0
       with:
         version: latest
 
@@ -57,7 +57,7 @@ jobs:
     timeout-minutes: 5
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
@@ -82,10 +82,10 @@ jobs:
         extras: ['', '[atomic_tools,docs,notebook,rest,tests,tui]']
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Set up Python 3.9
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.9'
 
@@ -124,7 +124,7 @@ jobs:
           optional: false
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
@@ -189,7 +189,7 @@ jobs:
         - 5001:22
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
 
     - name: Install system dependencies
       run: sudo apt update && sudo apt install postgresql graphviz