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107 lines (96 loc) · 2.74 KB
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[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"
[project]
name = "amulety"
version = "2.1.3"
description = "Python package to create embeddings of BCR amino acid sequences."
readme = {file = "README.md", content-type = "text/markdown"}
requires-python = ">=3.8, <4"
license = {text = "MIT"}
keywords = [
"immcantation",
"immunoinformatics",
"bioinformatics",
"embedding",
"antibody",
"BCR",
"Machine Learning",
"biology",
"NGS",
"next generation sequencing"
]
authors = [
{name = "Mamie Wang", email = "mamie.wang@yale.edu"},
{name = "Wengyao Jiang", email = "wengyao.jiang@yale.edu"},
{name = "Steven Kleinstein", email = "steven.kleinstein@yale.edu"},
{name = "Gisela Gabernet", email = "gisela.gabernet@yale.edu"}
]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
"numpy",
"pandas",
"torch",
"torchvision",
"transformers<4.52", #Antiberty fails on transformers 4.52+ due to a breaking change in the API
"typer",
"antiberty",
# ablang depends on numba which currently supports Python <3.14.
# Use an environment marker so installation on 3.14+ skips ablang instead of failing.
"ablang; python_version < '3.14'",
"rjieba",
"sentencepiece",
"anndata"
]
[project.urls]
Homepage = "https://github.com/immcantation/amulety"
Repository = "https://github.com/immcantation/amulety"
Issues = "https://github.com/immcantation/amulety/issues"
[project.scripts]
amulety = "amulety.amulety:main"
[tool.setuptools]
packages = ["amulety"]
[tool.pytest.ini_options]
markers = ["datafiles: load datafiles"]
testpaths = ["tests"]
norecursedirs = [
".*",
"build",
"dist",
"*.egg",
"data",
"__pycache__",
".github",
"src",
"docs",
]
python_files = ["test_*.py"]
[tool.mypy.overrides]
warn_unused_configs = true
ignore_missing_imports = true
[tool.ruff]
line-length = 120
target-version = "py38"
cache-dir = "~/.cache/ruff"
[tool.ruff.lint]
select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
[tool.ruff.lint.isort]
known-first-party = ["amulety"]
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["E402", "F401"]
"tests/*" = ["N802"]
"amulety.py" = ["N806"]
[tool.ruff.lint.pep8-naming]
extend-ignore-names = ["mocked_*", "*allOf", "*URI*"]