pyproject.toml

[build-system]
requires = ["setuptools>=64", "setuptools_scm>=8", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "recfinder"
authors = [
    {name = "Elizabeth Robbins", email = "lizzie.robbins1@gmail.com"},
    {name = "Yi Liu", email = "caoxen7ys@yahoo.com"}
]
description = "recurrant evolution"
readme = "README.md"
version= "2.0.0"
requires-python = ">=3.8"
keywords = [
    "Reccurant Evolution",
    "Monte-Carlo",  
    "Phylogeneticrelationships"
]
license = { file = "License" }
classifiers = [
    # How mature is this project? Common values are
    #   3 - Alpha
    #   4 - Beta
    #   5 - Production/Stable
    'Development Status :: 4 - Beta',

    # Indicate who your project is intended for
    'Intended Audience :: Science/Research',
    'Topic :: Scientific/Engineering :: Bio-Informatics',

    # Pick your license as you wish (should match "license" above)
    'License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)',

    # Specify the Python versions you support here.
    'Programming Language :: Python :: 3.8', # 
    'Programming Language :: Python :: 3.9', # 
    "Programming Language :: Python :: 3.10", # base version
    "Programming Language :: Python :: 3.11", # 
    "Programming Language :: Python :: 3.12", # 
]
dependencies = [
    "numpy",
    "scipy",
    "pandas",
    "dendropy",
]

    [project.urls]
    repository = "https://github.com/ElizabethRobbins/RecFinder"

    [project.optional-dependencies]
    build = ["build", "twine"]
    dev = [
        "python-semantic-release",
        "mypy",
        "pytest",
        "pytest-cov",
        "tox",
        "seaborn",
        "delayed-assert",
        "flake8",
        "pylint",
        "black",
        "build",
        "wheel",
        "setuptools>=64",
        "setuptools_scm>=8"
    ]

    [project.scripts]
    recfinder = "recfinder.run.__main__:main"

[tool.semantic_release]
version_variable = "pyproject.toml:version"

[tool.setuptools.packages.find]
where = ["src"]
include = [
    "recfinder",
]

[tool.setuptools.package-data]
"recfinder.genetic_codes" = ["*"]
"ExampleData" = ["*"]

[tool.setuptools.exclude-package-data]
mypkg = ["tests"]

[tool.pytest.ini_options]
addopts = "--cov=recfinder"
testpaths = ["tests"]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "disabled: marks tests as disabled (deselect with '-m \"not disabled\"')",
    "regression: marks a test as a regression test",
]

[tool.mypy]
mypy_path = "src"
check_untyped_defs = true
disallow_any_generics = true
ignore_missing_imports = true
no_implicit_optional = true
show_error_codes = true
strict_equality = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
no_implicit_reexport = true

[tool.setuptools_scm]
version_file = "src/recfinder/_version.py"
version_scheme = "no-guess-dev"
root = "."  
tag_regex = "^(?P<prefix>v)?(?P<version>[^\\+]+)(?P<suffix>.*)?$"
fallback_version = "2.0.0"
local_scheme = "dirty"