pyproject.toml

[build-system]
requires = ["setuptools>=77.0.3"]
build-backend = "setuptools.build_meta"

[project]
name = "flashspread"
dynamic = ["version"]
description = "FlashSpread: GPU-accelerated Markovian and Non-Markovian Spreading Processes on Complex Networks"
readme = "README.md"
license = "MIT"
license-files = ["LICENSE"]
authors = [
    {name = "Heman Shakeri", email = "hs9hd@virginia.edu"}
]
keywords = [
    "epidemic simulation",
    "stochastic processes",
    "GPU computing",
    "network epidemiology",
    "Markovian",
    "non-Markovian",
    "renewal processes",
    "tau-leaping",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.10"

# A bare `import flashspread` is metadata-only. Torch and NumPy provide the
# simulation runtime; optional extras add Triton GPU kernels, NetworkX topology
# generators, and SciPy reverse Cuthill-McKee graph reordering independently.
dependencies = [
    "torch>=2.0",
    "numpy>=1.24",
]

[project.optional-dependencies]
# The tiled ensemble rate kernel uses `tl.range(..., loop_unroll_factor=)`, which
# Triton added in 3.2. On 3.1 that kernel fails to *compile*, so the declared
# `>=2.1` floor advertised a GPU feature that could not run. Verified on an A100:
# 3.1.0 raises CompilationError; 3.2.0, 3.3.1 and 3.6.0 all run.
gpu = ["triton>=3.2"]
graph = ["networkx>=3.0"]
reorder = ["scipy>=1.10"]
dev = [
    "pytest>=7.0",
    "pytest-cov",
    "ruff",
    "mypy",
    "networkx>=3.0",
    "scipy>=1.10",
]
docs = ["mkdocs-material", "mkdocstrings[python]"]
# All optional *runtime* capabilities. Development and documentation tooling
# remain explicit extras and are not pulled into a user's simulation install.
all = ["triton>=3.2", "networkx>=3.0", "scipy>=1.10"]

[project.urls]
Homepage = "https://github.com/Shakeri-Lab/FlashSpread"
Repository = "https://github.com/Shakeri-Lab/FlashSpread.git"

[tool.setuptools.dynamic]
version = {attr = "flashspread.__version__"}

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

[tool.pytest.ini_options]
markers = [
    "gpu: marks tests that require a CUDA device (deselect with -m 'not gpu')",
]

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
# Conservative default: pyflakes (F) + a subset of pycodestyle (E).
select = ["E", "F"]
ignore = ["E501"]  # line length is handled by the formatter, not enforced hard