pyproject.toml

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

[project]
name = "FastOMA"
dynamic = ["version"]
description = "FastOMA - a package to infer orthology information among proteomes"
readme = "README.md"
license = "MIT"
requires-python = ">=3.8"
authors = [
    { name = "Sina Majidian", email = "sina.majidian@gmail.com" },
    { name = "Adrian Altenhoff", email = "adrian.altenhoff@inf.ethz.ch" }
]
dependencies = [
    "biopython ~=1.81",
    "DendroPy >=4.5,<=4.6.1",
    "ete3 ~=3.1",
    "lxml >=4.6,<6",
    "omamer ~=2.0",
    "pyham ~=1.1",
    "numpy <2",   # temporary fix as pytables does not yet work with numpy 2.0
    "pyparsing",
    "networkx",
]

[project.optional-dependencies]
nextflow = [
    "nextflow"
]
report = [
    "papermill",
    "jupyter",
    "matplotlib",
    "seaborn",
]


[project.scripts]
fastoma-batch-roothogs = "FastOMA.batch_roothogs:fastoma_batch_roothogs"
fastoma-check-input = "FastOMA.check_input:fastoma_check_input"
fastoma-collect-subhogs = "FastOMA.collect_subhogs:fastoma_collect_subhogs"
fastoma-infer-roothogs = "FastOMA.infer_roothogs:fastoma_infer_roothogs"
fastoma-infer-subhogs = "FastOMA.infer_subhogs:fastoma_infer_subhogs"
fastoma-helper = "FastOMA.helper_scripts:main"

[project.urls]
Homepage = "https://github.com/DessimozLab/FastOMA"

[tool.hatch.version]
path = "FastOMA/__init__.py"

[tool.hatch.build.targets.sdist]
include = [
    "/FastOMA",
]

[tool.hatch.envs.default]
features = [
    "report",
]