Merge branch 'main' into renovate/numpy-2.x

Author: SevLG

.github/workflows/publish_container_image.yml

@@ -12,7 +12,7 @@ jobs:
       packages: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v6
+        uses: actions/checkout@v7
       - name: Run docker/setup-qemu-action
         uses: docker/setup-qemu-action@v4
       - name: Run docker/setup-buildx-action

.github/workflows/run_test.yml

@@ -10,7 +10,7 @@ jobs:
         python-version: ["3.14"]
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
         with:

.github/workflows/trivy-scan.yml

@@ -18,7 +18,7 @@
         runs-on: ubuntu-latest
         steps:
           - name: Checkout code
-            uses: actions/checkout@v6
+            uses: actions/checkout@v7
 
           - name: Run Trivy vulnerability scanner
             uses: aquasecurity/trivy-action@master

requirements-top.txt

@@ -9,6 +9,6 @@ flask-smorest==0.47.0
 Werkzeug==3.1.8
 gunicorn==26.0.0
 biopython==1.87
-pytest==9.1.0
+pytest==9.1.1
 pytest-env==1.6.0
-pyzipper==0.3.6
+pyzipper==0.4.0

requirements.txt

@@ -2,7 +2,7 @@ alembic==1.18.5
 apispec==6.10.0
 biopython==1.87
 blinker==1.9.0
-click==8.3.3
+click==8.4.2
 Flask==3.1.3
 flask-cors==6.0.5
 Flask-Migrate==4.1.0
@@ -20,11 +20,11 @@ packaging==26.2
 pluggy==1.6.0
 pycryptodomex==3.23.0
 Pygments==2.20.0
-pytest==9.1.0
+pytest==9.1.1
 pytest-env==1.6.0
 python-dotenv==1.2.2
-pyzipper==0.3.6
+pyzipper==0.4.0
 SQLAlchemy==2.0.51
-typing_extensions==4.15.0
+typing_extensions==4.16.0
 webargs==8.7.1
 Werkzeug==3.1.8