From fb198083a02234f30a043e10bc0b8bc94213cd0d Mon Sep 17 00:00:00 2001 From: Christian Oertlin Date: Thu, 7 Mar 2024 14:27:44 +0100 Subject: [PATCH 1/3] add poetry --- Dockerfile | 6 +- poetry.lock | 1607 ++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 47 ++ requirements-dev.txt | 2 +- requirements.txt | 2 +- 5 files changed, 1659 insertions(+), 5 deletions(-) create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/Dockerfile b/Dockerfile index ddef77c..d5561e7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,10 +21,10 @@ 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 . 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-0,0 +1,47 @@ +[tool.poetry] +name = "genotype-api" +version = "2.0.7" +description = "Genotype is a tool to validate integrity and sex of samples." +authors = ["Your Name "] +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" diff --git a/requirements-dev.txt b/requirements-dev.txt index 8c2cca8..261bbf2 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -3,4 +3,4 @@ coveralls pre-commit pylint pytest-cov -pytest>=5.2< \ No newline at end of file +pytest>=5.2 \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index c32a2ea..7256551 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -SQLAlchemy==1.4.30 +SQLAlchemy>=2.0.0 aiofiles bcrypt bump2version From 08d5663b55df3a58038a119433c942d5ff3c84dc Mon Sep 17 00:00:00 2001 From: Christian Oertlin Date: Fri, 8 Mar 2024 11:02:27 +0100 Subject: [PATCH 2/3] remove setup fix bump version --- .bumpversion.cfg | 2 +- pyproject.toml | 2 +- setup.py | 33 --------------------------------- 3 files changed, 2 insertions(+), 35 deletions(-) delete mode 100644 setup.py diff --git a/.bumpversion.cfg b/.bumpversion.cfg index c72a7ce..34450a1 100644 --- a/.bumpversion.cfg +++ b/.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] diff --git a/pyproject.toml b/pyproject.toml index 1651e0e..ddcfb6b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "genotype-api" -version = "2.0.7" +version = "2.0.8" description = "Genotype is a tool to validate integrity and sex of samples." authors = ["Your Name "] license = "MIT License" diff --git a/setup.py b/setup.py deleted file mode 100644 index d659f15..0000000 --- a/setup.py +++ /dev/null @@ -1,33 +0,0 @@ -from setuptools import find_packages, setup - - -try: - with open("requirements.txt", "r") as f: - install_requires = [x.strip() for x in f.readlines()] -except IOError: - install_requires = [] - - -with open("README.md", "r") as fh: - long_description = fh.read() - -setup( - name="genotype_api", - version="2.0.8", - description="", - long_description=long_description, - long_description_content_type="text/markdown", - url="https://github.com/Clinical-Genomics/genotype-api", - author="Måns Magnusson, Maya Brandi", - author_email="maya.brandi@scilifelab.se", - install_requires=install_requires, - packages=find_packages(), - include_package_data=True, - zip_safe=False, - classifiers=[ - "Programming Language :: Python :: 3", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", - ], - python_requires=">=3.11", -) From 4421a312acfc9e03419a62774b5108a7ec962a48 Mon Sep 17 00:00:00 2001 From: Christian Oertlin Date: Fri, 8 Mar 2024 11:30:41 +0100 Subject: [PATCH 3/3] fix pyproj --- README.md | 9 +++++---- pyproject.toml | 4 ++-- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 49226f0..4f5b98f 100644 --- a/README.md +++ b/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. diff --git a/pyproject.toml b/pyproject.toml index ddcfb6b..14febaa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,8 @@ [tool.poetry] -name = "genotype-api" +name = "genotype_api" version = "2.0.8" description = "Genotype is a tool to validate integrity and sex of samples." -authors = ["Your Name "] +authors = ["Måns Magnusson","Maya Brandi"] license = "MIT License" readme = "README.md"