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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "DAJIN2"
version = "0.5.5.1"
description = "One-step genotyping tools for targeted long-read sequencing"
authors = ["Akihiro Kuno <[email protected]>"]
readme = "README.md"
homepage = "https://github.com/akikuno/DAJIN2"
license = "MIT"
packages = [{ include = "DAJIN2", from = "src" }]
classifiers = [
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Operating System :: POSIX",
"Operating System :: MacOS",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
include = [
"src/DAJIN2/template_igvjs.html",
"src/DAJIN2/templates/**",
"src/DAJIN2/static/**",
"src/DAJIN2/utils/**",
]
[tool.poetry.dependencies]
python = "^3.8"
numpy = ">=1.24.0"
pandas = ">=1.3.0"
scipy = ">=1.10.0"
openpyxl = ">=3.1.0"
plotly = ">=5.19.0"
kaleido = ">=0.2.0"
# Machine learning
rapidfuzz = ">=3.6.0"
scikit-learn = ">=1.3.0"
ruptures = ">=1.1.8"
# BioConda
mappy = ">=2.24"
pysam = ">=0.21.0"
# GUI
Flask = ">=2.2.0"
waitress = ">=2.1.0"
Jinja2 = ">=3.1.0"
# Custom packages
cstag = ">=1.0.0"
midsv = ">=0.11.0"
wslPath = ">=0.4.1"
[tool.poetry.scripts]
DAJIN2 = "DAJIN2.main:execute"
[tool.ruff]
line-length = 119
[tool.ruff.lint]
select = [
"E", # pycodestyle errors
"W", # pycodestyle warnings
"F", # pyflakes
"I", # isort
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"UP", # pyupgrade
]
ignore = [
"E501", # line too long, handled by black
"B008", # do not perform function calls in argument defaults
"C901", # too complex
"W191", # indentation contains tabs
"B904", # ignore errors for raise ... from ... not being used
]
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
[tool.ruff.lint.isort]
combine-as-imports = true
known-first-party = ["musubi_restapi"]
section-order = [
"future",
"standard-library",
"third-party",
"first-party",
"local-folder",
]
split-on-trailing-comma = true
[tool.ruff.format]
quote-style = "double"
[tool.ruff.lint.pyupgrade]
keep-runtime-typing = true # Settings for Python 3.8 compatibility