pyproject.toml

[project]
name = "FONtools"
authors = [{name = "Charles E. Vejnar"}]
description = "JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage"
readme = "README.md"
requires-python = ">=3.8"
license = {text = "Mozilla Public License 2.0 (MPL 2.0)"}
classifiers = [
    "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics"
]
dependencies = [
    "pyfaidx",
    "pyfnutils",
    "zstandard",
]
dynamic = ["version"]

[project.urls]
homepage = "https://git.sr.ht/~vejnar/FONtools"

[project.scripts]
ensembl2ucsc = "fontools_scripts.ensembl2ucsc:main"
fasta_format = "fontools_scripts.fasta_format:main"
fasta_seq_length = "fontools_scripts.fasta_seq_length:main"
fon_import = "fontools_scripts.fon_import:main"
fon_mask_fasta = "fontools_scripts.fon_mask_fasta:main"
fon_transform = "fontools_scripts.fon_transform:main"
import_ensembl = "fontools_scripts.import_ensembl:main"
merge_annot = "fontools_scripts.merge_annot:main"

[build-system]
requires = ["setuptools>=61", "setuptools_scm", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools_scm]

[tool.ruff]
line-length = 120
src = ["src", "tests"]

[tool.ruff.lint]
select = [
    # Pyflakes
    "F",
    # Pycodestyle
    "E",
    "W",
    # isort
    "I001",
    "I002",
    # flake8-bugbear
    "B",
    # pydocstyle
    "D"
]
ignore = ["D100", "D104", "D200" , "D202", "D205", "D212", "D415", "D416",
    "E501", "E731", "ANN101", "ANN102", "ANN401", "C408", "PT018"]

[tool.ruff.lint.per-file-ignores]
"**/{tests,docs}/*" = ["D101", "D102", "D103", "D105"]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.isort]
lines-after-imports = 2