pyproject.toml

[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "specflow"
version = "0.1.0"
description = "Spectral-guided control-anchored flow matching for perturbation prediction"
readme = "README.md"
requires-python = ">=3.9"
dependencies = [
    "numpy>=1.23,<2",
    "scipy>=1.9",
    "torch>=2.0",
    "PyYAML>=6.0",
    "tqdm>=4.66",
]

[project.optional-dependencies]
data = ["anndata>=0.9,<0.11", "scanpy>=1.9,<1.11", "pandas>=2,<3"]
ode = ["torchdiffeq>=0.2.3"]
dev = ["pytest>=7.0", "anndata>=0.9,<0.11", "pandas>=2,<3"]

[project.scripts]
specflow-synthetic = "specflow.cli:run_synthetic"

[tool.setuptools.packages.find]
where = ["src"]

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src"]