pyproject.toml

[build-system]
requires = ["maturin>=1.5,<2.0"]
build-backend = "maturin"

[project]
name = "gramep"
version = "1.1.0"
requires-python = ">=3.12"
description = "GRAMEP - Genome vaRiation Analysis from the Maximum Entropy Principle"
authors = [
    { name="Matheus Pimenta", email="omatheuspimenta@outlook.com"},
    { name="Fabricio Lopes", email="fabricio@utfpr.edu.br"},
    ]
maintainers = [
    { name="Matheus Pimenta", email="omatheuspimenta@outlook.com"},
]
readme = "README.md"
license = {text = "MIT License"}
classifiers = [
    "Programming Language :: Rust",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Natural Language :: English",
    "Environment :: Console",
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3.12",
]

dependencies = [
    "rich >=13.7.1",
    "typer >=0.12.3",
    "biopython >=1.83",
    "pandas >=2.2.2",
    "gffpandas >=1.2.0",
    "joblib >=1.4.2",
    "joblib-progress >=1.0.5",
    "matplotlib >=3.9.0",
    "upsetplot >=0.9.0",
    "scikit-learn >=1.5.1",
    "seaborn >=0.13.2",
    "thefuzz >=0.22.1",
]


[project.urls]
"Code" = "https://github.com/omatheuspimenta/GRAMEP"
"Bug Tracker" = "https://github.com/omatheuspimenta/GRAMEP/issues"
"Documentation" = "https://gramep.readthedocs.io/en/latest/"

[tool.maturin]
python-source = "python"
module-name = "gramep.utilrs"
features = ["pyo3/extension-module"]


[project.scripts]
gramep = "gramep.cli:app"

[project.optional-dependencies]
dev = [
    "maturin >=1.5.1",
    "pytest >=8.3.2",
    "pytest-cov >=5.0.0",
    "taskipy >=1.13.0",
    "isort >=5.13.2",
    "blue >=0.9.1",
    ]

doc = [
    "mkdocstrings >=0.25.2",
    "mkdocstrings-python >=1.10.8",
    "mkdocs-macros-plugin >=1.0.5",
    "jinja2 >=3.1.4",
    "termynal >=0.12.1",
    "mkdocs-material >=9.5.32",
    ]

[tool.pytest.ini_options]
pythonpath = "python/"
addopts = "--doctest-modules"

[tool.isort]
profile = "black"
line_length = 79

[tool.taskipy.tasks]
codeck = "blue --check --diff python/ && isort --check --diff python/"
codecg = "blue python/ && isort python/"
docs = "mkdocs serve"
pre_test = "task codeck"
test = "pytest -s -x --cov=gramep -vv"
post_test = "coverage html"