feat(update): Python

.github/workflows/black.yml

@@ -12,7 +12,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Set up Black
         uses: psf/black@stable

.github/workflows/build_dockerfile_on_push.yml

@@ -10,26 +10,26 @@ jobs:
     name: Create staging docker image
     steps:
      - name: Check out git repository
-       uses: actions/checkout@v4.1.1
+       uses: actions/checkout@v4
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
        shell: bash
        run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v3.0.0
+       uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
 
      - name: Set up Docker Buildx
        id: buildx
-       uses: docker/setup-buildx-action@v3.1.0
+       uses: docker/setup-buildx-action@v3
 
      - name: Build and push
        id: docker_build
-       uses: docker/build-push-action@v5.1.0
+       uses: docker/build-push-action@v6
        with:
          context: ./
          file: ./Dockerfile

.github/workflows/build_dockerfile_on_release.yml

@@ -12,26 +12,26 @@ jobs:
     name: Push production docker image to dockerhub
     steps:
       - name: Check out git repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Extract branch name and remove illegal chars
         id: get_branch_name
         shell: bash
         run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")"
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v3.0.0
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Set up Docker Buildx
         id: buildx
-        uses: docker/setup-buildx-action@v3.1.0
+        uses: docker/setup-buildx-action@v3
 
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v5.1.0
+        uses: docker/build-push-action@v6
         with:
           context: ./
           file: ./Dockerfile

.github/workflows/tests_coverage.yaml

@@ -12,20 +12,20 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4.1.1
+        uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install and configure Poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: false
 
       - name: Cache dependencies
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         id: cache
         with:
           path: ${{ env.pythonLocation }}
@@ -47,7 +47,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Coveralls Finished
-        uses: coverallsapp/github-action@v2.2.3
+        uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.github_token }}
           parallel-finished: true

Dockerfile

@@ -1,4 +1,4 @@
-FROM docker.io/library/python:3.11-slim-bullseye as base
+FROM docker.io/library/python:3.12-slim-bullseye as base
 
 LABEL about.home="https://github.com/Clinical-Genomics/genotype-api"
 LABEL about.tags="Genotype API"
@@ -24,7 +24,7 @@
 RUN poetry config virtualenvs.create false \
   && poetry install --no-interaction --no-ansi
 
 CMD gunicorn \
     --workers=$GUNICORN_WORKERS \
     --bind=$GUNICORN_BIND  \
     --threads=$GUNICORN_THREADS \

pyproject.toml

@@ -6,44 +6,42 @@ authors = ["Christian Oertlin <[email protected]>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-aiofiles = "^23.2.1"
-bcrypt = "^4.1.2"
-bump2version = "^1.0.1"
-click = "^8.1.7"
-coloredlogs = "^15.0.1"
-cryptography = "^42.0.8"
-email-validator = "^2.1.1"
-fastapi = ">=0.109.1"
-google-auth = "^2.29.0"
+aiofiles = "*"
+bcrypt = "*"
+bump2version = "*"
+click = "*"
+coloredlogs = "*"
+cryptography = "*"
+email-validator = "*"
+fastapi = "*"
+google-auth = "*"
 gunicorn = "*"
-httptools = "^0.6.1"
-numpy = "^1.26.4"
-openpyxl = "^3.1.2"
-passlib = "^1.7.4"
-pydantic = "^2.6.4"
-pydantic-settings = "^2.2.1"
-python = "^3.11"
-python-dotenv = "^1.0.1"
-python-jose = {extras = ["cryptography"], version = "^3.3.0"}
-python-multipart = "^0.0.9"
-pyyaml = "^6.0.1"
+httptools = "*"
+numpy = "*"
+openpyxl = "*"
+passlib = "*"
+pydantic = "*"
+pydantic-settings = "*"
+python = "^3.12"
+python-dotenv = "*"
+python-jose = {extras = ["cryptography"], version = "*"}
+python-multipart = "*"
+pyyaml = "*"
 requests = "*"
-sqlalchemy = {extras = ["asyncio"], version = "^2.0.35"}
-sqlalchemy-utils = "^0.41.2"
-starlette = "^0.37.2"
-uvicorn = "^0.29.0"
-uvloop = "^0.19.0"
-aiomysql = "^0.2.0"
-pytest-asyncio = "^0.24.0"
-tenacity = "^9.0.0"
+sqlalchemy = {extras = ["asyncio"], version = "*"}
+sqlalchemy-utils = "*"
+starlette = "*"
+uvicorn = "*"
+uvloop = "*"
+aiomysql = "*"
+pytest-asyncio = "*"
+tenacity = "*"
 
 [tool.poetry.group.dev.dependencies]
-bump2version = "^1.0.1"
-coveralls = "^3.3.1"
-pre-commit = "^3.7.0"
-pylint = "^3.1.0"
-pytest-cov = "^5.0.0"
-pytest = ">=5.2"
+coveralls = "*"
+pre-commit = "*"
+pytest-cov = "*"
+pytest = "*"
 
 [build-system]
 requires = ["poetry-core"]