Update GitHub Actions (major)

.github/workflows/biosimdb_interface_project-ci.yaml

@@ -18,10 +18,10 @@ jobs:
         python-version: ["3.12", "3.13", "3.14"]
     steps:
       - name: Checkout repo
-        uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -82,9 +82,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - name: Set up Python 3.14
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: 3.14.7
       - name: Install python dependencies
@@ -98,9 +98,9 @@ jobs:
     runs-on: ubuntu-24.04
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - name: Set up Python 3.14
-        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+        uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
         with:
           python-version: 3.14.7
       - name: Install python dependencies

.github/workflows/docker-publish.yaml

@@ -18,13 +18,13 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262 # v4.4.0
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@c7c53464625b32c7a7e944ae62b3e17d2b600130 # v3.7.0
+        uses: docker/setup-qemu-action@1f40c72289eff860ee54a304f1438e3cff362e0a # v4.3.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@8d2750c68a42422c14e847fe6c8ac0403b4cbd6f # v3.12.0
+        uses: docker/setup-buildx-action@37fe631027851001ddb9b187196cc803df7f5f0e # v4.3.0
 
       - name: Fetch interface, schema and extractor versions and build date
         id: vars
@@ -38,15 +38,15 @@ jobs:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Log in to the Container registry
-        uses: docker/login-action@c94ce9fb468520275223c153574b00df6fe4bcc9 # v3.7.0
+        uses: docker/login-action@dbcb813823bdd20940b903addbd779551569679f # v4.6.0
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.repository_owner }}
           password: ${{ secrets.BUILD_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@c299e40c65443455700f0fdfc63efafe5b349051 # v5.10.0
+        uses: docker/metadata-action@dc802804100637a589fabce1cb79ff13a1411302 # v6.2.0
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |
@@ -60,7 +60,7 @@ jobs:
             biosim.extractor.version=${{ steps.vars.outputs.extractor }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@10e90e3645eae34f1e60eeb005ba3a3d33f178e8 # v6.19.2
+        uses: docker/build-push-action@c3c9e263c25d99ce0380d002d59b67737d91b0dc # v7.4.0
         with:
           context: .
           file: ./docker/Dockerfile

.github/workflows/release.yaml

@@ -18,15 +18,15 @@ jobs:
     steps:
     - name: Checkout repository
       id: repo
-      uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
     - name: Set up Python
-      uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
       with:
         python-version: 3.14.7
 
     - name: Checkout repository (full history and tags)
-      uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       with:
         fetch-depth: 0
 
@@ -62,7 +62,7 @@ jobs:
     steps:
 
       - name: checkout
-        uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
 
       - name: Change version in repo (init) and CITATION.cff
         run: |
@@ -117,7 +117,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout repository
-        uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           ref: main
 

.github/workflows/update-copyright-years-in-license-file.yaml

@@ -9,7 +9,7 @@ jobs:
     update-license-year:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@d23441a48e516b6c34aea4fa41551a30e30af803 # v6.1.0
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
               with:
                   fetch-depth: 0
             - uses: FantasticFiasco/action-update-license-year@f180e962fa988db222d8f03ef4636750312d1b3d # v3.0.4