pyproject.toml

# Specifies the build system requirements and backend
[build-system]
requires = [
    "hatchling",  # Build backend
    "hatch-vcs",  # Version control system plugin for dynamic versioning
    "setuptools", # Setuptools for compiling C extensions
    "wheel",      # Wheel for packaging
    "cython",     # Cython for compiling C extensions
    "numpy",      # NumPy for numerical operations and C extension includes
]
build-backend = "hatchling.build"


# Project metadata and configuration
[project]
name = "jcvi"
description = "Python utility libraries on genome assembly, annotation and comparative genomics"
readme = "README.md"
requires-python = ">=3.8"
license = { text = "BSD" }
authors = [
    { name = "Haibao Tang", email = "tanghaibao@gmail.com" },
    { name = "Vivek Krishnakumar" },
    { name = "Adam Taranto" },
]

classifiers = [
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

dependencies = [
    "biopython",
    "boto3",
    "brewer2mpl",
    "CrossMap",
    "cython",
    "deap",
    "ete3",
    "ftpretty",
    "genomepy",
    "gffutils",
    "goatools",
    "graphviz",
    "jinja2",
    "matplotlib",
    "more-itertools",
    "natsort",
    "networkx",
    "numpy<2",
    "ortools",
    "pybedtools",
    "pyefd",
    "pypdf",
    "pytesseract",
    "rich",
    "scikit-image",
    "scipy",
    "seaborn",
    "Wand",
    "webcolors",
]

dynamic = ["version"]

[project.optional-dependencies]
tests = ["mock", "pytest-benchmark", "pytest-cov", "pytest", "PyYAML"]

[project.urls]
homepage = "http://github.com/tanghaibao/jcvi"

# Command-line script entry point
[project.scripts]
jcvi = "jcvi.cli:main"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build]
packages = ["src"]

[tool.hatch.build.hooks.custom]
path = "build.py"

[tool.hatch.build.hooks.vcs]
version-file = "src/jcvi/_version.py"

[tool.hatch.version]
source = "vcs"

[tool.hatch.version.vcs]
tag-pattern = "v*"
fallback-version = "0.0.0"

[tool.hatch.build.targets.sdist]
include = ["src/**/*.py", "src/**/*.pyx", "README.md"]
force-include = { "build.py" = "build.py", "setup.py" = "setup.py" }
exclude = ["src/jcvi/**/*.so", "src/jcvi/**/*.pyd", "src/jcvi/**/*.c"]

[tool.hatch.build.targets.wheel]
packages = ["src/jcvi"]
artifacts = [
    "src/jcvi/**/*.so",  # Linux/Mac shared objects
    "src/jcvi/**/*.pyd", # Windows shared objects
    "src/jcvi/**/*.c",   # Generated C files
]