ResistanceProfiler/pyproject.toml at master · the-foxlab/ResistanceProfiler · GitHub

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[build-system]
requires = ['hatchling']
build-backend = 'hatchling.build'

[project]
name = 'respro'
version = '0.3.3'
description = 'Pathogen-agnostic framework for genotypic antiviral resistance profiling from SANGER or NGS-derived variants.'
readme = 'README.md'
license = {text = 'AGPL-3.0-only'}
requires-python = '>=3.11'
authors = [
    {name = 'Jonas Fuchs', email = 'jonas.fuchs@uniklinik-freiburg.de'},
]
classifiers = [
    'Intended Audience :: Science/Research',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
    'License :: OSI Approved :: GNU Affero General Public License v3',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3.11',
    'Programming Language :: Python :: 3.12',
    'Programming Language :: Python :: 3.13',
]
dependencies = [
    'click>=8.1',
    'typer>=0.12.4',
    'rich>=13.0',
    'numpy>=1.24',
    'biopython>=1.81',
    'pysam>=0.22',
    'mappy>=2.24',
    'jinja2>=3.1.5',
    'markupsafe>=2.1',
    'matplotlib>=3.7',
    'weasyprint>=62.3',
]

[project.optional-dependencies]
dev = ['pytest>=7.4', 'pytest-cov>=4.1', 'ruff>=0.1', 'httpx>=0.27', 'fakeredis>=2.0', 'mypy>=1.10']
docs = ['mkdocs>=1.6', 'mkdocs-material>=9.5', 'mkdocs-mermaid2-plugin>=1.1', 'mkdocs-glightbox>=0.4']

[project.scripts]
respro = 'respro.cli.main:app'

[tool.pytest.ini_options]
testpaths = ['tests']
addopts = '-v --tb=short'

[tool.ruff]
target-version = 'py311'
line-length = 100

[tool.ruff.lint]
select = ['E', 'F', 'W', 'I', 'N', 'UP']
extend-ignore = ['E501']  # line length enforced by editor convention, not CI

[tool.mypy]
python_version = '3.11'
files = ['respro']
pretty = true
show_error_codes = true
ignore_missing_imports = true
warn_unused_ignores = true
warn_return_any = true

[tool.hatch.build]
include = [
    'respro/**/*.py',
    'respro/config/*.toml',
    'respro/report/templates/*.j2',
    'respro/report/static/*.css',
    'respro/report/static/*.js',
    'respro/report/static/assets/*.svg',
]