add(poetry support)

.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 +20,10 @@ WORKDIR /home/worker/app
 COPY . /home/worker/app
 
 # Install app requirements
-RUN pip install -r requirements.txt
+RUN pip install poetry
+RUN poetry config virtualenvs.create false \
+  && poetry install
 
-# Install app
-RUN pip install -e .
 
 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
@@ -26,14 +27,14 @@ Go to `http://localhost:8000/docs` and test the API
 ## Authorization
 
 
-There is currently no working demo avalible. 
-To autorize you'l need to provide a valid ID-token.
+There is currently no working demo available. 
+To autorise you'll need to provide a valid ID-token.
 
 ## Description
 
 After sample prep a small part of the DNA is sent to MAF where they do SNP calling with a orthogonal method for a predefined set of SNPs. MAF also to gender prediction based on their result. The result from MAF is sent back as an excel sheet and this get uploaded to genotype via the `Upload Plate`-endpoint. 
 
-The same samples get sequenced and genotyped inhouse and the result of this is uploaded in the VCF format via the `Upload Sequence`-endpoint.
+The same samples get sequenced and genotyped in-house and the result of this is uploaded in the VCF format via the `Upload Sequence`-endpoint.
 
 The two analyses for each sample are then compared to check for anomalies.
 

pyproject.toml

@@ -0,0 +1,47 @@
+[tool.poetry]
+name = "genotype_api"
+version = "2.0.8"
+description = "Genotype is a tool to validate integrity and sex of samples."
+authors = ["Måns Magnusson","Maya Brandi"]
+license = "MIT License"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+sqlalchemy = ">=2.0.0"
+aiofiles = "^23.2.1"
+bcrypt = "^4.1.2"
+bump2version = "^1.0.1"
+click = "^8.1.7"
+coloredlogs = "^15.0.1"
+email-validator = "^2.1.1"
+fastapi = "0.75.0"
+google-auth = "^2.28.1"
+gunicorn = "^21.2.0"
+httptools = "^0.6.1"
+numpy = "^1.26.4"
+openpyxl = "^3.1.2"
+passlib = "^1.7.4"
+pydantic = "1.10.14"
+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"
+sqlmodel = "^0.0.16"
+uvicorn = "^0.27.1"
+uvloop = "^0.19.0"
+
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+coveralls = "^3.3.1"
+pre-commit = "^3.6.2"
+pylint = "^3.1.0"
+pytest-cov = "^4.1.0"
+pytest = ">=5.2"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

requirements-dev.txt

@@ -3,4 +3,4 @@ coveralls
 pre-commit
 pylint
 pytest-cov
-pytest>=5.2<
+pytest>=5.2

requirements.txt

@@ -1,4 +1,4 @@
-SQLAlchemy==1.4.30
+SQLAlchemy>=2.0.0
 aiofiles
 bcrypt
 bump2version