pyproject.toml

[build-system]
requires = ["setuptools>=68.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "scienceflow"
version = "0.1.0"
description = "An end-to-end autoresearch agent framework for long-horizon ML research, scientific discovery, and beyond"
requires-python = ">=3.11"
# The default ``uv sync`` already includes: runtime dependencies + pytest + the workspace
# script stack + the ML packages needed by category_models (@pretrained), plus **mlebench**
# pinned to the official Git commit and the **2D detection** packages (dicomsdl, ensemble-boxes).
dependencies = [
    "python-dotenv>=1.0",
    "pydantic>=2.0",
    "omegaconf>=2.3",
    "pyyaml>=6.0",
    "psutil>=5.9",
    "aiofiles>=23.0",
    "rich>=13.0",
    "click>=8.1",
    "dataclasses-json>=0.6.0",
    "openai>=1.0",
    "deepcraft-core",
    "deepcraft-agent",
    "deepcraft-tool-ext",
    "pydicom>=2.4",
    # langchain→langsmith→requests→urllib3: the optional zstd in 2.12+ requires the full
    # backports.zstd (unrelated to installing dev only)
    "backports-zstd>=1.3",
    # tenacity loads tornadoweb when `import tornado` succeeds; a leftover empty tornado
    # namespace in site-packages would cause ImportError: gen
    "tornado>=6.4",
    # --- tests (formerly optional dev) ---
    "pytest>=7.0",
    "pytest-asyncio>=0.21",
    "pytest-cov>=4.0",
    # --- workspace scripts (formerly optional workspace) ---
    "openpyxl>=3.1",
    "matplotlib>=3.8",
    "seaborn>=0.13",
    "tabpfn>=7.0",
    # --- PyTorch stack + category / pretrained tests (formerly optional pretrained-test, merged and deduplicated) ---
    "torch>=2.11",
    "torchvision>=0.20",
    "pillow>=10.0",
    "torchaudio>=2.11.0,<2.12",
    "sentencepiece>=0.2",
    "timm>=1.0.3",
    "segmentation-models-pytorch>=0.3.4",
    "ultralytics>=8.0",
    "transformers>=4.40",
    "protobuf>=4.25",
    "tiktoken>=0.7",
    "librosa>=0.10",
    "muq",
    "catboost>=1.2",
    "xgboost>=2.0",
    "lightgbm>=4.0",
    "scipy>=1.12",
    "opencv-python-headless>=4.8",
    "scikit-learn>=1.3",
    "pandas>=2.2",
    "torchmetrics>=1.0",
    "termcolor>=2.0",
    # --- MLE-bench (pinned to the official Git commit; see ``[tool.uv.sources]``) ---
    "mlebench",
    # --- 2D detection skill (``skills/library/categories/detection_2d.md``) ---
    "dicomsdl>=0.107",
    "ensemble-boxes>=1.0",
]

# Local packages under ./deepcraft (paths resolved by uv; with pip, install the subpackages
# with -e first, in README order)
[tool.uv.sources]
deepcraft-core = { path = "deepcraft/core", editable = true }
deepcraft-agent = { path = "deepcraft/agent", editable = true }
deepcraft-tool-ext = { path = "deepcraft/tool_ext", editable = true }
mlebench = { git = "https://github.com/openai/mle-bench.git", rev = "507f92e1138bb6e40dac5c6ee7a6758e6424bf97" }
# PyTorch: the default PyPI build is +cu130, which needs a CUDA 13 driver; switch to cu128
# to match common 570/575 drivers (nvidia-smi shows CUDA 12.8)
torch = { index = "pytorch-cu128" }
torchvision = { index = "pytorch-cu128" }
torchaudio = { index = "pytorch-cu128" }

[[tool.uv.index]]
name = "pytorch-cu128"
url = "https://download.pytorch.org/whl/cu128"
explicit = true

[project.optional-dependencies]
# Merged into the main ``dependencies``; the empty extras are kept for compatibility with
# ``uv sync --extra mlebench`` / ``--extra detection-2d``.
mlebench = []
detection-2d = []
scientific-design = [
    "cloudpickle>=3.0",
    "sci-modeling-bench==0.10.0",
]

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

[tool.setuptools]
# Keep editable builds bounded to the Python package. Repo-local workspaces can
# contain dataset symlinks; automatic package-data discovery may otherwise walk
# into external MLE-bench data during `uv run`.
include-package-data = false
license-files = []

[tool.setuptools.packages.find]
where = ["."]
include = ["scienceflow*"]
exclude = [
    "workspace*",
    "deepcraft*",
    "doc*",
    "scripts*",
    "tests*",
    "parallel_logs*",
    "cache*",
]
namespaces = false

[tool.setuptools.package-data]
"scienceflow.core.agent.prompts" = [
    "*.md",
    "L0/*.md",
]
"scienceflow.solver.lnr.prompt_templates" = [
    "evaluation/*.md",
    "estra/*.md",
    "resources/*.md",
    "stage/*.md",
    "task/*/*.md",
]

[tool.pytest.ini_options]
asyncio_mode = "auto"
testpaths = ["tests"]
pythonpath = ["deepcraft/core", "deepcraft/agent", "deepcraft/tool_ext"]
addopts = [
    "--ignore=tests/test_llm_ask.py",
    "--ignore=tests/test_llm_tool_call.py",
    "--ignore=tests/test_openai_parallel_tool_calls.py",
]
filterwarnings = [
    # jieba still uses pkg_resources (setuptools); not actionable in this repo.
    "ignore:pkg_resources is deprecated as an API:UserWarning",
    # Third-party / extension noise during pretrained tests (not actionable here).
    "ignore:builtin type SwigPyPacked has no __module__ attribute:DeprecationWarning",
    "ignore:builtin type SwigPyObject has no __module__ attribute:DeprecationWarning",
    "ignore:builtin type swigvarlink has no __module__ attribute:DeprecationWarning",
    "ignore:`torch.jit.script` is deprecated. Please switch to `torch.compile` or `torch.export`.:DeprecationWarning",
    "ignore:`torch.nn.utils.weight_norm` is deprecated in favor of `torch.nn.utils.parametrizations.weight_norm`.:FutureWarning",
]
markers = [
    "pretrained: end-to-end tests that load pretrained weights and run forward (may download; prefer GPU)",
    "mlebench: official mlebench Git dependency (installed by default with uv sync)",
]