pyproject.toml

[build-system]
requires = ["setuptools>=42", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "SPARCED"
version = "2.0"
description = "A simple and efficient pipeline for constructing, merging, expanding and simulating large-scale, single-cell mechanistic models."
authors = [
    { name = "Cemal Erdem", email = "Cemal.erdem@umu.se" },
    { name = "Aurore Amrit", email = "aurore.amrit@umu.se" },
    { name = "Jonah Huggins", email = "JonahRileyHuggins@gmail.com" },
    { name = "Arnab Mutsuddy", email = "Arnab.mutsuddy@gmail.com" },
    { name = "Marc Birtwistle", email = "marc.birtwistle@gmail.com" }
]
license = {text = "GPL-2.0"}
dependencies = [
    "h5py==3.11",
    "numpy==1.26.0",
    "scipy==1.12.0",
    "sympy==1.12",
    "pandas==2.2.1",
    "matplotlib==3.8.0",
    "python-libsbml==5.18.0",
    "swig==4.0.0",
    "amici==0.11.12",
    "antimony==2.12.0.1",
    "pyyaml==6.0.1",
    "mpi4py==3.1.6",
    "phrasedml==1.3.0",
    "lxml==5.3.0"
]
requires-python = ">=3.10"
keywords = ["mechanistic modeling", "single-cell models", "simulation", "systems biology"]

readme = {file = "README.md", content-type = "text/markdown"}

[project.urls]
Homepage = "https://github.com/JonahRileyHuggins/SPARCED/"
Repository = "https://github.com/JonahRileyHuggins/SPARCED"

[project.scripts]
sparced = "cli.cli:main"

[tool.setuptools]
# Specify the src directory as a package
packages = { find = { where = ["src"] } }

[tool.setuptools.package-data]
"src" = ["**/*.yaml", "**/*.json", "**/*.ini"]
[tool.setuptools.exclude-package-data]
"*" = ["*.tmp", "*.log"]