pyproject.toml

[project]
name = "combined_gene_caller"
readme = "README.md"
authors = [
  {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"},
]
license = {text = "Apache Software License 2.0"}
keywords = ["bioinformatics", "gene", "metagenomics"]
dynamic = ["version"]
description = "Combined gene caller for MGnify pipeline, to combine predictions from FragGeneScan and Prodigal"
requires-python = ">=3.9"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
]

dependencies = [
    "biopython==1.81",
]

[project.optional-dependencies]
dev = [
    "pre-commit==3.3.3",
    "black==23.7.0",
    "isort==5.12.0",
    "bump-my-version==0.9.2",
]
test = [
    "pytest-workflow==2.0.1",
]

[build-system]
requires = ["setuptools>=61.0.0"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
packages = ["combined_gene_caller"]

[tool.setuptools.dynamic]
version = {attr = "combined_gene_caller.__version__"}

[project.scripts]
combined_gene_caller = "combined_gene_caller.cli:combine_main"

[tool.ruff.per-file-ignores]
"ci/*" = ["S"]

[tool.ruff]
extend-exclude = ["static", "ci/templates"]
ignore = [
    "RUF001", # ruff-specific rules ambiguous-unicode-character-string
    "S101", # flake8-bandit assert
    "S308", # flake8-bandit suspicious-mark-safe-usage
    "E501", # pycodestyle line-too-long
]
line-length = 140
src = ["src", "tests"]
target-version = "py39"

[tool.ruff.flake8-pytest-style]
fixture-parentheses = false
mark-parentheses = false

[tool.ruff.isort]
forced-separate = ["conftest"]
force-single-line = true

[tool.black]
line-length = 140
target-version = ["py39"]

[tool.isort]
profile = "black"

[tool.bumpversion]
current_version = "1.0.4"

[[tool.bumpversion.files]]
filename = "combined_gene_caller/__init__.py"