pyproject.toml

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

[project]
name = "Gens"
dynamic = ["version"]
description = 'Visualise copy number profiles from WGS data'
readme = "README.md"
requires-python = ">=3.8"
license = "MIT"
keywords = ["WGS", "scout", "CNV", "cancer", "rare disease", "variant", "NGS", "browser"]
authors = [
  { name = "Markus Johansson", email = "markus.h.johansson@skane.se" },
  { name = "Jakob Willforss", email = "jakob.willforss@skane.se" },
]
classifiers = [
  "Development Status :: 4 - Beta",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: Implementation :: CPython",
  "Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = [
  "Click",
  "Flask",
  "flask-caching",
  "flask_login",
  "authlib",
  "pymongo",
  "gtfparse",
  "pysam",
  "pyyaml",
  "connexion==2.14.2",
  "fastapi",
  "flask-compress",
  "tabulate",
  "pydantic",
  "pydantic-settings",
  "pydantic-extra-types",
]

[project.urls]
Documentation = "https://github.com/SMD-Bioinformatics-Lund/gens#readme"
Issues = "https://github.com/SMD-Bioinformatics-Lund/gens/issues"
Changelog = "https://github.com/SMD-Bioinformatics-Lund/gens/blob/master/CHANGELOG.md"

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

[tool.hatch.version]
path = "gens/__version__.py"

[tool.hatch.build]
include = [
  "gens/templates/*.html",
  "gens/static/**/*",
  "gens/static/**/*",
  "gens/blueprints/**/static/*",
  "gens/openapi/openapi.yaml",
]

[tool.hatch.build.targets.wheel]
packages = ["gens"]

[tool.hatch.envs.types]
extra-dependencies = [
  "mypy>=1.0.0",
]
[tool.hatch.envs.types.scripts]
check = "mypy --install-types --non-interactive {args:src/temporary tests}"

[tool.coverage.run]
source_pkgs = ["gens", "tests"]
branch = true
parallel = true
omit = [
  "gens/__version__.py",
]

[tool.coverage.paths]
gens = ["gens",]
tests = ["tests", "*/temporary/tests"]

[tool.coverage.report]
exclude_lines = [
  "no cov",
  "if __name__ == .__main__.:",
  "if TYPE_CHECKING:",
]

[tool.isort]
profile = "black"
src_paths = ["gens"]