pyproject.toml

[build-system]
requires = ["setuptools>=64", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "yeastgem"
version = "0.0.1.dev0"
description = "Python interface to the yeast-GEM consensus genome-scale metabolic model"
readme = "README.md"
requires-python = ">=3.11"
license = { text = "CC-BY-4.0" }
authors = [{ name = "SysBioChalmers", email = "info@sysbiochalmers.se" }]
keywords = ["systems biology", "metabolic model", "yeast", "Saccharomyces cerevisiae", "cobra"]

# Generic, organism-agnostic helpers live upstream in raven-toolbox; the\r
# local yeastgem package is just the yeast-specific repo orchestration on\r
# top. This mirrors the MATLAB side, where code/ is a thin layer over the\r
# RAVEN toolbox.\r
dependencies = [
    "raven-toolbox>=0.4.0",
    "cobra>=0.29",
    "pandas>=2.0",
    "pyyaml>=6.0",
    "matplotlib>=3.7",
    "numpy>=1.24",
    "python-dotenv>=1.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "ruff>=0.4",
]
# Optional. cobrapy solves with whatever optlang resolves; without this it
# is GLPK, which cobra pulls in via swiglpk. Installing gurobipy makes
# cobrapy pick Gurobi, matching the solver RAVEN uses on the MATLAB side.
# Needs a licence: the one bundled with the PyPI wheel is capped at 2000
# variables and 2000 constraints, well below yeast-GEM's ~4100 reactions
# and ~2750 metabolites.
gurobi = [
    "gurobipy>=11",
]

[project.urls]
"Source" = "https://github.com/SysBioChalmers/yeast-GEM"
"Issues" = "https://github.com/SysBioChalmers/yeast-GEM/issues"

[tool.setuptools.packages.find]
where = ["."]
include = ["yeastgem*"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "B", "RUF"]