pyproject.toml

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[project]
name = "cg"
version = "67.0.9"
description = "Clinical Genomics command center"
readme = {file = "README.md", content-type = "text/markdown"}
homepage = "https://github.com/Clinical-Genomics/cg"
repository = "https://github.com/Clinical-Genomics/cg"
classifiers = [
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: Implementation :: CPython",
]
include = [
  "README.md",
  "cg/**/*",
  "tests/**/*"
]
requires-python = ">=3.9,<3.13"
dependencies = [
"alembic",
"SQLAlchemy",
"PyMySQL",
"click",
"blinker",
"CacheControl",
"Flask-Admin",
"Flask-CORS",
"Flask-Dance",
"Flask",
"Flask-WTF",
"WTForms == 3.0.0",
"google-auth",
"gunicorn",
"requests",
"werkzeug",
"cachetools",
"cryptography",
"coloredlogs",
"Jinja2",
"lxml",
"marshmallow",
"MarkupSafe",
"openpyxl",
"packaging",
"pandas",
"paramiko",
"petname",
"psutil",
"pydantic == 2.7.4",
"python-dateutil",
"PyYAML",
"tabulate",
"typing_extensions",
"urllib3",
"genologics",
"housekeeper>=4.11.3",
"pydantic-settings>=2.3.3",
"email-validator>=2.2.0",
"rich-click>=1.8.4",
  ]
[project.optional-dependencies]
coveralls = ["coveralls"]
mock = ["mock"]
pre-commit = ["pre-commit"]
pytest-cov = ["pytest-cov"]
pytest-mock = ["pytest-mock"]
pytest = ["pytest"]
ruff = ["ruff"]
pytest-xdist = ["pytest-xdist"]



[project.scripts]
cg = "cg.cli.base:base"


# Configurations

[tool.black]
line-length = 100

[tool.isort]
profile = "black"
include_trailing_comma = "true"
line_length=100
multi_line_output=3
ensure_newline_before_comments = "true"

[tool.ruff]
line-length = 100
target-version = "py311"
exclude = ["alembic"]
ignore = ["E501"]