pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "ribotricer"
version = "1.5.0"
description = "Python package to detect translating ORFs from Ribo-seq data"
readme = "README.md"
license = {text = "GPLv3"}
authors = [
    {name = "Saket Choudhary", email = "saketkc@gmail.com"},
    {name = "Wenzheng Li"},
]
maintainers = [
    {name = "Saket Choudhary", email = "saketkc@gmail.com"},
]
requires-python = ">=3.9"
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Natural Language :: English",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Utilities",
    "Typing :: Typed",
]
keywords = ["bioinformatics", "ribo-seq", "ribosome-profiling", "ORF", "translation"]
dependencies = [
    "click>=8.1.3",
    "click-help-colors>=0.9.1",
    "matplotlib>=3.5.3",
    "numpy>=1.21.1",
    "pandas>=1.3",
    "pyfaidx>=0.7.1",
    "pysam>=0.19.1",
    "quicksect>=0.2.2",
    "scipy>=1.7.0",
    "tqdm>=4.64.1",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "black>=23.0",
    "isort>=5.12",
    "ruff>=0.1.0",
    "mypy>=1.0",
    "pre-commit>=3.0",
    "build>=1.0",
    "twine>=4.0",
]
docs = [
    "sphinx>=6.0",
    "sphinx-rtd-theme>=1.0",
    "sphinx-click>=4.0",
]

[project.scripts]
ribotricer = "ribotricer.cli:cli"

[project.urls]
Homepage = "https://github.com/smithlabcode/ribotricer"
Documentation = "https://github.com/smithlabcode/ribotricer#readme"
Repository = "https://github.com/smithlabcode/ribotricer"
Issues = "https://github.com/smithlabcode/ribotricer/issues"
Changelog = "https://github.com/smithlabcode/ribotricer/blob/master/HISTORY.md"

[tool.setuptools.packages.find]
where = ["."]
include = ["ribotricer*"]

[tool.black]
line-length = 88
target-version = ["py39", "py310", "py311", "py312", "py313"]
include = '\.pyi?$'
exclude = '''
/(
    \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
  | docs
)/
'''

[tool.isort]
profile = "black"
line_length = 88
known_first_party = ["ribotricer"]
skip = [".git", ".venv", "build", "dist"]

[tool.ruff]
target-version = "py39"
line-length = 88
exclude = [
    ".git",
    ".mypy_cache",
    ".ruff_cache",
    ".venv",
    "build",
    "dist",
    "docs",
    "notebooks",
]

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # Pyflakes
    "I",      # isort
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "UP",     # pyupgrade
    "ARG",    # flake8-unused-arguments
    "SIM",    # flake8-simplify
]
ignore = [
    "E501",   # line too long (handled by black)
    "B008",   # do not perform function calls in argument defaults
    "B007",   # loop control variable not used within loop body
    "B028",   # no explicit stacklevel keyword argument found
    "B904",   # raise exceptions with raise ... from err
    "C901",   # too complex
    "ARG001", # unused function argument
    "ARG002", # unused method argument
    "SIM102", # use single if statement instead of nested if
    "SIM108", # use ternary operator
    "SIM113", # use enumerate for index variable
    "SIM117", # use single with statement with multiple contexts
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"tests/*" = ["ARG001", "ARG002"]

[tool.mypy]
python_version = "3.9"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true
exclude = [
    "build",
    "dist",
    "docs",
]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = [
    "-v",
    "--tb=short",
    "--strict-markers",
]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
]

[tool.coverage.run]
source = ["ribotricer"]
branch = true
omit = [
    "*/tests/*",
    "*/__init__.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
]
fail_under = 0
show_missing = true

[tool.bumpversion]
current_version = "1.5.0"
commit = true
tag = false
parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(\\-(?P<release>[a-z]+)(?P<build>\\d+))?"
serialize = [
    "{major}.{minor}.{patch}-{release}{build}",
    "{major}.{minor}.{patch}",
]

[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = 'version = "{current_version}"'
replace = 'version = "{new_version}"'

[[tool.bumpversion.files]]
filename = "ribotricer/__init__.py"
search = '__version__ = "{current_version}"'
replace = '__version__ = "{new_version}"'