pyproject.toml

[build-system]
requires = ["setuptools>=64"]
build-backend = "setuptools.build_meta"

[project]
name = "isovar"
requires-python = ">=3.9"
authors = [{name="Alex Rubinsteyn"}, {name="Arman Aksoy"}, {name="Julia Kodysh"}]
description = "Determine mutant protein sequences from RNA using assembly around variants"
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Operating System :: OS Independent",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
readme = "README.md"
dynamic = ["version", "dependencies"]

[tool.setuptools.dynamic]
version = {attr = "isovar.__version__"}
dependencies = {file = ["requirements.txt"]}

[tool.setuptools.packages.find]
include = ["isovar", "isovar.*"]

[tool.setuptools.package-data]
isovar = ["logging.conf"]

[project.urls]
"Homepage" = "https://github.com/openvax/isovar"
"Bug Tracker" = "https://github.com/openvax/isovar/issues"

[project.scripts]
isovar = "isovar.cli.isovar_main:run"
isovar-protein-sequences = "isovar.cli.isovar_protein_sequences:run"
isovar-translations = "isovar.cli.isovar_translations:run"
isovar-reference-contexts = "isovar.cli.isovar_reference_contexts:run"
isovar-allele-reads = "isovar.cli.isovar_allele_reads:run"
isovar-allele-counts = "isovar.cli.isovar_allele_counts:run"
isovar-variant-reads = "isovar.cli.isovar_variant_reads:run"
isovar-variant-sequences = "isovar.cli.isovar_variant_sequences:run"

[tool.ruff.lint]
select = ["E", "F"]
ignore = ["F821", "E501", "F841", "E731", "E741", "E722", "E721"]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"test*/*" = ["F401"]