pyproject.toml

[build-system]
requires = ["setuptools>=70.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "PyNCBI"
version = "0.2.0"
description = "Simple API for Python Integration with NCBI GEO Database"
readme = "README.md"
requires-python = ">=3.11"
license = { text = "MIT" }
authors = [{ name = "Thomas Konstantinovsky", email = "thomaskon90@gmail.com" }]
keywords = [
    "api",
    "database",
    "analytics",
    "biology",
    "methylation",
    "epigenetics",
    "ncbi",
    "geo",
    "bioinformatics",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Typing :: Typed",
]
dependencies = [
    "methylprep>=1.7.0",
    "wget>=3.2",
    "tqdm>=4.66.0",
    "pandas>=2.0.0",
    "numpy>=1.26.0,<3.0.0",
    "requests>=2.31.0",
    "termcolor>=2.4.0",
]

[project.urls]
Homepage = "https://github.com/MuteJester/PyNCBI"
Documentation = "https://pyncbi.readthedocs.io/"
Repository = "https://github.com/MuteJester/PyNCBI"
Issues = "https://github.com/MuteJester/PyNCBI/issues"
Changelog = "https://github.com/MuteJester/PyNCBI/releases"

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0",
    "pytest-cov>=4.1.0",
    "ruff>=0.4.0",
    "mypy>=1.10.0",
    "pandas-stubs>=2.0.0",
    "types-requests>=2.31.0",
    "types-tqdm>=4.66.0",
]
docs = [
    "sphinx>=7.0.0",
    "sphinx-rtd-theme>=2.0.0",
    "sphinx-autodoc-typehints>=2.0.0",
]

[tool.setuptools]
package-dir = { "" = "src" }
include-package-data = true

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
"*" = ["py.typed"]

# Ruff configuration (replaces flake8, isort, black)
[tool.ruff]
target-version = "py311"
line-length = 100
src = ["src", "tests"]

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # Pyflakes
    "I",      # isort
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "UP",     # pyupgrade
    "SIM",    # flake8-simplify
    "TCH",    # flake8-type-checking
    "PTH",    # flake8-use-pathlib
]
ignore = [
    "E501",   # line too long (handled by formatter)
    "B008",   # do not perform function calls in argument defaults
]

[tool.ruff.lint.isort]
known-first-party = ["PyNCBI"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false

# Mypy configuration
[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = true
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "methylprep.*"
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "wget.*"
ignore_missing_imports = true

# Pytest configuration
[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src"]
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests requiring network access",
]

# Coverage configuration
[tool.coverage.run]
source = ["src/PyNCBI"]
branch = true

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",
    "if __name__ == .__main__.:",
]