pyproject.toml

[build-system]
requires = ["setuptools < 72.0"]
build-backend = "setuptools.build_meta"

[project]
name = "helixer"
version = "0.3.3"
description = "Deep Learning fun on gene structure data"
readme = "README.md"
requires-python = ">=3.8.5"
classifiers = [
    "Programming Language :: Python :: 3",
    "Operating System :: POSIX :: Linux",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
]
dependencies = [
    "geenuff @ git+https://github.com/weberlab-hhu/GeenuFF@v0.3.2",
    "sqlalchemy==1.3.22",
    "tensorflow>=2.6.2",
    "tensorflow-addons>=0.21.0",
    "nni",
    "seaborn",
    "Keras<3.0.0",
    "keras_layer_normalization",
    "terminaltables",
    "HTSeq",
    "intervaltree",
    "numpy",
    "h5py",
    "multiprocess",
    "numcodecs",
    "appdirs"
]

[project.urls]
"Homepage" = "https://github.com/weberlab-hhu/Helixer"
"Documentation" = "https://github.com/weberlab-hhu/Helixer"

[tool.setuptools]
packages = [
    "helixer",
    "helixer.core",
    "helixer.prediction",
    "helixer.evaluation",
    "helixer.tests",
    "helixer.export"
]
package-data = {helixer = ["testdata/*.fa", "testdata/*.gff"]}
script-files = ["Helixer.py", "fasta2h5.py", "geenuff2h5.py", "helixer/prediction/HybridModel.py", "scripts/fetch_helixer_models.py"]