add poetry

.bumpversion.cfg

@@ -5,6 +5,6 @@ tag = True
 tag_name = v{new_version}
 message = Bump version: {current_version} → {new_version} [skip ci]
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
 [bumpversion:file:genotype_api/__init__.py]

Dockerfile

@@ -20,10 +20,9 @@ WORKDIR /home/worker/app
 COPY . /home/worker/app
 
 # Install app requirements
-RUN pip install -r requirements.txt
-
-# Install app
-RUN pip install -e .
+RUN pip install poetry
+RUN poetry config virtualenvs.create false \
+  && poetry install
 
 CMD gunicorn \
     --workers=$GUNICORN_WORKERS \

README.md

@@ -11,7 +11,8 @@ install [poetry]
 ```
 git clone https://github.com/Clinical-Genomics/genotype-api
 cd genotype-api
-pip install -e . -r requirements.txt
+pip install poetry
+poetry install
 ```
 
 ## Usage

pyproject.toml

@@ -0,0 +1,48 @@
+[tool.poetry]
+name = "genotype-api"
+version = "2.0.24"
+description = "Genotype-api"
+authors = ["Christian Oertlin <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+sqlalchemy = "^2.0.29"
+aiofiles = "^23.2.1"
+bcrypt = "^4.1.2"
+bump2version = "^1.0.1"
+click = "^8.1.7"
+starlette = "^0.37.2"
+coloredlogs = "^15.0.1"
+email-validator = "^2.1.1"
+fastapi = ">=0.109.1"
+google-auth = "^2.29.0"
+gunicorn = "^21.2.0"
+httptools = "^0.6.1"
+numpy = "^1.26.4"
+openpyxl = "^3.1.2"
+passlib = "^1.7.4"
+pydantic = "^2.6.4"
+pymysql = "^1.1.0"
+python-dotenv = "^1.0.1"
+python-jose = {extras = ["cryptography"], version = "^3.3.0"}
+python-multipart = "^0.0.9"
+pyyaml = "^6.0.1"
+requests = "^2.31.0"
+uvicorn = "^0.29.0"
+uvloop = "^0.19.0"
+sqlalchemy-utils = "^0.41.2"
+pydantic-settings = "^2.2.1"
+
+
+[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"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"