pyproject.toml

[project]
name = "scout-browser"
version = "4.94.1"
description = "Clinical DNA variant visualizer and browser"
authors = [{name="Chiara Rasi", email="chiara.rasi@scilifelab.se"}, {name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Robin Andeer", email="robin.andeer@gmail.com"}, {name="Mans Magnuson", email="monsunas@gmail.com"}]
license = {text = "MIT License"}
readme = "README.md"
include = [
  "README.md",
  "scout/**/*",
]
requires-python = ">=3.9"
keywords = ["vcf", "variants", "dna", "lrs", "wgs", "wes", "panel", "wts", "rna", "fusion",
	"snv", "sv", "str", "cnv", "outliers", "cancer", "sma", "ogm",
	"acmg", "clingen-cgc-vicc", "phenopacket", "clinvar", "coverage", "beacon", "matchmaker exchange","panelapp",
	"genome visualisation", "variant triage", "variant ranking",]
classifiers = [
	"Environment :: Web Environment",
	"Intended Audience :: Developers",
	"License :: OSI Approved :: MIT License",
 	"Operating System :: MacOS :: MacOS X",
 	"Operating System :: Unix",
	"Programming Language :: Python",
  	"Programming Language :: Python :: Implementation :: CPython",
	"Topic :: Internet :: WWW/HTTP :: Dynamic Content",
	"Programming Language :: Python :: 3.9",
	"Programming Language :: Python :: 3.10",
	"Programming Language :: Python :: 3.11",
	"Programming Language :: Python :: 3.12",
	"Programming Language :: Python :: 3.13",
  	"Development Status :: 5 - Production/Stable",
	"Intended Audience :: Science/Research",
  	"Topic :: Scientific/Engineering :: Bio-Informatics",
  	"Topic :: Scientific/Engineering :: Medical Science Apps.",
]
dependencies = [
	# Everything needed in production
	"werkzeug",
	"Flask>=2.0",
	"Flask-Bootstrap",
	"Flask-CORS",
"path.py", # this is deprecated
	"markdown",
	"WTForms",
	"Flask-WTF",
	"Flask-Mail",
	"coloredlogs",
	"query_phenomizer",
	"Flask-Babel>=3",
	"livereload>=2.7",
	"tornado >=6.4.1",
	"python-dateutil",
	"pymongo",
	"pathlib",
	"pdfkit",
	"phenopackets",
	"xlsxwriter",
	"click",
	"cryptography",
	"defusedxml",
	"svglib",
	"cairosvg",
	"importlib_resources",
	# webapp login
	"authlib",
	"flask_login",
	"flask-ldapconn",
	# Parsing
	"cyvcf2",
	"configobj",
	"ped_parser",
	"pydantic>=2",
	"PyYaml>=5.1",
	# extras
	"intervaltree==3.0.2",
	"anytree",
	# Required by scripts
	"tabulate",
]

[project.optional-dependencies]
coverage=[
            "chanjo-report",
            "pymysql",
			"python-dateutil",
        ]


[project.urls]
Repository = "https://github.com/Clinical-Genomics/scout"
Changelog = "https://github.com/Clinical-Genomics/scout/blob/main/CHANGELOG.md"
Documentation = "https://clinical-genomics.github.io/scout/"
"Bug Tracker" = "https://github.com/Clinical-Genomics/scout/issues"
Issues = "https://github.com/Clinical-Genomics/scout/issues"

[project.scripts]
scout = "scout.commands:cli"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
  packages = ["scout/"]
  include = [
    "scout/**/*",
  ]
  exclude = [
  	"tests/",
  	"scripts/",
  ]


[tool.pytest.ini_options]
looponfailroots = ["tests/", "scout/"]

[tool.black]
line-length = 100
target-version = ['py313']

[tool.ruff]
src = ["scout", "tests", "scripts"]
line-length = 100

[tool.isort]
profile = "black"

[dependency-groups]
dev = [
	"pytest-mock",
	"pytest>=5.2",
	"pytest-flask",
	"pytest-test-groups",
	"pytest-cov",
	"mongomock",
	"responses",
    "pytest-cov>=4.1.0",
    "pytest>=7.4.4",
	"invoke",
]
docs = [
	"mkdocs",
	"mkdocs-material",
	"markdown-include",
]
lint = [
    "black>=23.3.0",
    "isort>=5.11.5",
    "ruff>=0.8.0",
]