pyproject.toml

# Orion build configuration.
#
# See `setup.md` for the full installation flow (host conda env + VMware Fusion
# guest with CellProfiler / QuPath / napari). The short version on the host:
#
#     git clone <orion-repo>
#     cd Orion
#     pip install -e .            # runtime
#     pip install -e .[dev]       # add lint + tests
#     pip install -e .[baselines] # add LangChain / dataset deps for benchmark_adapters
#
# `requirements.txt` is kept alongside this file as a flat backup for the
# (rare) case where a consumer wants to pin everything explicitly without
# resolving the project metadata.

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


[project]
name = "orion"
dynamic = ["version"]
description = "Orion: Towards Lab Automation with Computer-Using Agents (CellProfiler, QuPath, LabBench, MicroVQA, JUMP Cell Painting discovery)."
readme = "README.md"
requires-python = ">=3.11"
license = { file = "LICENSE" }
keywords = [
    "biology",
    "cell-painting",
    "cellprofiler",
    "qupath",
    "microvqa",
    "labbench",
    "jump",
    "agent",
    "swe-agent",
    "vmware",
    "desktop-env",
]
authors = [
    { name = "Genentech, Inc." },
]
maintainers = [
    { name = "Genentech, Inc." },
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Image Processing",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]

# Runtime dependencies needed to launch any of the five `sweagent.run.run_orion_*`
# entry points end-to-end on the host. (The guest-side VM has its own python39
# conda env documented in setup.md — those packages are NOT listed here.)
dependencies = [
    # SWE-agent / SWE-rex core
    "swe-rex>=1.2.0",
    "simple-parsing>=0.1",
    "rich>=13.0",
    "rich-argparse",
    "ruamel.yaml",
    "tabulate",
    "textual>=1.0.0",
    "unidiff>=0.7",
    "bashlex>=0.18",
    "ghapi",

    # Agent + LLM clients
    "anthropic",
    "openai>=1.0",
    "litellm>=1.0",
    "google-generativeai",
    "groq",
    "dashscope",
    "tiktoken",
    "tokenizers",
    "huggingface-hub",
    "datasets>=4.0",

    # AWS Bedrock (used by Biomni / Claude-on-Bedrock paths)
    "boto3",

    # Prompt templating + config
    "jinja2",
    "pyyaml>=6.0",
    "pydantic>=2.0",
    "pydantic-settings",
    "python-dotenv>=1.0",

    # Desktop / VM operator stack
    "gymnasium",
    "pyautogui",
    "requests>=2.32",
    "aiohttp",
    "httpx",

    # Scientific stack used by orion runners, evaluators, and prompt builders
    "numpy>=1.25,<2.0",
    "scipy>=1.14",
    "pandas>=2.0",
    "scikit-learn>=1.5",
    "scikit-image>=0.25",
    "opencv-python>=4.8",
    "pillow>=10.0",
    "matplotlib>=3.8",
    "napari>=0.6",

    # Utilities
    "tqdm>=4.65",
    "click>=8.0",
    "typer",
    "tenacity>=9.0",
    "backoff>=2.0",
    "filelock>=3.13",
    "packaging",
    "GitPython>=3.1",
    "jsonschema>=4.20",

    # Lightweight web bits used by run_orion's helpers
    "flask>=3.0",
    "flask-cors",
    "flask-socketio",
]


[project.optional-dependencies]
# Lint / test / docs — needed only for development on Orion itself.
dev = [
    "pytest>=8.0",
    "pytest-asyncio>=1.0",
    "pytest-mock>=3.0",
    "ruff>=0.5",
    "black>=25.0",
    "mypy>=1.10",
    "pre-commit",
]

# Optional dependencies for the `baselines/` runners (microscopy + deep-research
# baseline comparisons). Not required to run the core Orion agent.
baselines = [
    "langchain>=0.3",
    "langchain-core>=0.3",
    "langchain-openai>=0.3",
    "langchain-text-splitters>=0.3",
    "langsmith",
    "easyocr>=1.7",
    "imageio>=2.30",
]

# Document-processing extras used by some evaluator getters under
# sweagent/operator/desktop_env/evaluators/. Install only if you need them.
docs = [
    "pypdf>=6.0",
    "pdfplumber>=0.11",
    "python-docx>=1.0",
    "python-pptx>=1.0",
    "openpyxl>=3.1",
]


[project.scripts]
# After `pip install -e .` this exposes the orion dispatcher as a CLI:
#     orion cellprofiler
#     orion jump-discovery
#     orion labbench
#     orion microvqa
#     orion qupath
orion = "sweagent.run.run:main"


[project.urls]
Homepage = "https://github.com/Genentech/Orion"
Issues   = "https://github.com/Genentech/Orion/issues"
Source   = "https://github.com/Genentech/Orion"


[tool.setuptools]
include-package-data = true

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

[tool.setuptools.packages.find]
where = ["."]
include = ["sweagent*"]
namespaces = false


# ---------------------------------------------------------------------------
# Tool configurations (inherited from the upstream SWE-agent project, edited
# down to the rules that still make sense for Orion).
# ---------------------------------------------------------------------------

[tool.pytest.ini_options]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
]
testpaths = ["tests"]
xfail_strict = true
asyncio_default_fixture_loop_scope = "function"

[tool.ruff]
exclude = [
    ".bzr", ".direnv", ".eggs", ".git", ".git-rewrite", ".hg",
    ".ipynb_checkpoints", ".mypy_cache", ".nox", ".pants.d", ".pyenv",
    ".pytest_cache", ".pytype", ".ruff_cache", ".svn", ".tox", ".venv",
    ".vscode", "__pypackages__", "_build", "buck-out", "build", "dist",
    "node_modules", "site-packages", "venv",
    "tests/test_data",
    "config/commands",
]
line-length = 120
indent-width = 4
target-version = "py311"

[tool.ruff.lint]
select = [
    "E", "PLE",
    "E711", "E713", "E714",
    "F401", "F541", "F632", "F821", "F822", "F841", "F901",
    "I001", "I002",
    "UP",
    "C401", "C402", "C403", "C404", "C405",
    "W605",
    "B006", "B007", "B009",
    "EM",
    "FA102",
    "RET",
    "RUF019",
    "PT",
    "SIM201",
    "PTH100", "PTH110", "PTH111", "PTH112", "PTH113", "PTH114", "PTH117",
    "PTH118", "PTH119", "PTH120", "PTH121", "PTH122", "PTH202", "PTH203",
    "PTH204", "PTH205",
]
ignore = [
    "RET505", "RET506", "RET507",
    "E402", "E501", "E722", "E741",
    "PT011", "PT018",
]
fixable = ["ALL"]
unfixable = []
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"