DeepDriveSim/pyproject.toml at devel · radical-collaboration/DeepDriveSim · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "DDSim"
version = "0.2.0"
description = "Toolkit for Deep learning-driven Adaptive Simulations"
license = {text = "MIT"}
keywords = [
    "deep-learning",
    "adaptive-simulation",
    "hpc",
    "machine-learning",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
]
authors = [
    {name = "Mariya Goliyad", email = "mariya.goliyad@rutgers.edu"},
    {name = "RADICAL Lab"},
]
maintainers = [
    {name = "Mariya Goliyad", email = "mariya.goliyad@rutgers.edu"},
]
readme = "README.md"
requires-python = ">=3.9"

dependencies = ["rhapsody-py", "pyyaml", "radical.asyncflow>=0.3.0"]

[tool.setuptools.packages.find]
include = ["ddsim*", "workflows*"]

[project.urls]
Homepage = "https://github.com/radical-collaboration/DeepDriveSim"
Issues = "https://github.com/radical-collaboration/DeepDriveSim/issues"
Documentation = "https://radical-collaboration.github.io/DeepDriveSim/"

[project.optional-dependencies]
lint = ["ruff"]

# All test deps
dev = [
    "pytest",
    "pytest-asyncio",
    "pytest-timeout",
    "pytest-cov",
    "pydantic-settings",
    "numpy",
    "pyyaml",
    "ruff",
    "tox<5",
    "packaging>=23"
]

# Dragon/RADICAL support
dragon = [
    "dragonhpc",
    "nvidia-ml-py",
]

doc = [
    "mkdocs==1.5.3",
    "mkdocs-material==9.5.9",
    "mkdocstrings[python]>=0.26.1",
    "mkdocs-gen-files==0.5.0",
    "mkdocs-literate-nav==0.6.1",
    "mkdocs-section-index==0.3.8",
    "mkdocs-glightbox",
    "mkdocs-material-extensions",
    "mkdocs-minify-plugin"
]

[tool.ruff]
line-length = 88
target-version = "py39"
fix = true
exclude = [
    # Legacy ddmd subdirectories — not actively maintained
    "workflows/ddmd_workflow/MD-tools_fix",
    "workflows/ddmd_workflow/agents",
    "workflows/ddmd_workflow/aggregation",
    "workflows/ddmd_workflow/data",
    "workflows/ddmd_workflow/models",
    "workflows/ddmd_workflow/selection",
    "workflows/ddmd_workflow/sim",
    # Legacy plot/asyncflow variants
    "workflows/ddmd_workflow/plot_utilization.py",
    "workflows/miniapps_workflow/plot_utilization.py",
    "workflows/miniapps_workflow/miniapps_workflow_asyncflow.py",
    # Docs notebooks
    "docs",
]

[tool.ruff.lint]
select = ["E", "F", "W", "B", "I", "N", "UP"]
ignore = ["UP007", "UP045"]

[tool.ruff.lint.per-file-ignores]
# Pydantic V1 @validator uses `cls` as first arg — N805 is a false positive here
"workflows/ddmd_workflow/config.py" = ["N805"]
# Scientific code uses uppercase variable names (matrices, arrays)
"workflows/dummy_workflow/train.py" = ["N806"]
# Legacy utility functions with uppercase scientific naming conventions
"workflows/ddmd_workflow/utils.py" = ["N802", "N803", "N806"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

[tool.pytest.ini_options]
minversion = "6.0"

testpaths = ["tests"]
asyncio_mode = "auto"
timeout = 30
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "integration: marks tests as integration tests",
]

[tool.coverage.run]
source = ["ddsim", "workflows"]
omit = ["tests/*"]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
]

[tool.codespell]
skip = """
.git,
.github,
__pycache__,
build,
dist,
.*egg-info
"""