pyproject.toml

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

[tool.poetry]
name = "core"
version = "0.0.0"
description = "The Gymrek Lab's core python library"
authors = ["Gymrek Lab"]
license = "MIT"
repository = "https://github.com/gymrek-lab/core"
homepage = "https://github.com/gymrek-lab/core"
documentation = "https://core.readthedocs.io"
readme = "README.md"

[tool.poetry.dependencies]
python = ">=3.7,<4.0"
numpy = ">=1.20.0"
click = ">=8.0.3"
pysam = ">=0.19.0"
cyvcf2 = ">=0.30.14"
matplotlib = ">=3.5.1"
Pgenlib = ">=0.90.1"

[tool.poetry.group.docs.dependencies]
Sphinx = ">=4.3.2"
sphinx-autodoc-typehints = ">=1.12.0"
sphinx-rtd-theme = ">=1.0.0"
numpydoc = ">=1.1.0"
sphinx-click = ">=3.0.2"

[tool.poetry.group.tests.dependencies]
pytest = ">=7.4.3"
pytest-cov = ">=3.0.0"
black = ">=23.3.0"
ipython = ">=7.34.0"
coverage = {extras = ["toml"], version = ">=7.2.7"}
filprofiler = ">=2023.3.1"

[tool.poetry.scripts]
core = 'core.__main__:main'

[tool.black]
line-length = 88
preview = true

[tool.pytest.ini_options]
log_cli_level = "DEBUG"
log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"
addopts = """
--ignore noxfile.py
"""

[tool.coverage.run]
omit = [
    ".nox/*",
    "noxfile.py",
    "core/__init__.py",
    "core/tr_harmonizer.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
]