immuneML/pyproject.toml at master · uio-bmi/immuneML · GitHub

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

[project]
name = "immuneML"
description = "immuneML is a software platform for machine learning analysis of immune receptor repertoires."
readme = "README.md"
authors = [
    { name = "immuneML Team", email = "milenpa@uio.no" }
]
dynamic = ["version"]
license = { text = "GNU Affero General Public License v3" }
requires-python = ">=3.7"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: GNU Affero General Public License v3",
]

dependencies = [
    'setuptools<70',
    "numpy<=1.26.4",
    "pandas>=2.1.0",
    "PyYAML>=5.3",
    "scikit-learn>=0.23",
    "matplotlib>=3.1",
    "editdistance",
    "regex",
    "tzlocal",
    "airr>=1.5.1",
    "pystache",
    "dill>=0.3",
    "plotly>=4",
    "matplotlib-venn>=0.11",
    "scipy<=1.12.0",
    "bionumpy>=1.0.12",
    "umap-learn",
    "olga>=1.2.4",
    "psutil",
    "kaleido",
    "logomaker",
    "python-glmnet"
]

[project.optional-dependencies]
word2vec = ["gensim>=4"]
fisher = ["fisher>=0.1.9", "fishersapi"]
TCRdist = ["tcrdist3>=0.1.6"]
gen_models = ["sonnia", "torch", 'transformers', 'datasets', 'tokenizers', 'tensorflow', 'accelerate>=0.26.0']
embeddings = ["transformers", "torch", "sentencepiece", "esm", 'httpx']
ligo = ["stitchr", "IMGTgeneDL"]
DL = ["torch", "keras", "tensorflow", "logomaker", "gensim"]
all = [
    "tcrdist3>=0.1.6",
    "sonnia",
    "torch",
    "stitchr",
    "IMGTgeneDL",
    "keras",
    "tensorflow",
    "fisher>=0.1.9",
    "logomaker",
    "fishersapi",
    "gensim>=4",
    "transformers",
    "sentencepiece",
    'httpx',
    'datasets',
    'tokenizers',
    'accelerate>=0.26.0'
]

[project.urls]
Homepage = "https://github.com/uio-bmi/immuneML"

[project.scripts]
immune-ml = "immuneML.app.ImmuneMLApp:main"
immune-ml-quickstart = "immuneML.workflows.instructions.quickstart:main"
ligo = "immuneML.app.LigoApp:main"

[tool.setuptools.packages.find]
exclude = ["test", "test.*"]

[tool.setuptools.package-data]
immuneML = [
    "IO/dataset_import/conversion/*.csv",
    "presentation/html/templates/*.html",
    "presentation/html/templates/css/*.css",
    "config/physicochemical_factors/*.tsv",
    "config/default_params/*/*.yaml"
]

[tool.setuptools.dynamic]
version = { attr = "immuneML.environment.Constants.VERSION" }