pyproject.toml

[build-system]
requires = ["poetry-core>=1.9.0"]
build-backend = "poetry.core.masonry.api"

[project]
name = "vertebrae"
version = "1.0.0"
description = "A framework for Benchmarking feature extractors and transfer-learning backbones."
authors = [{ name = "Niklas Melton", email = "niklasmelton@gmail.com" }]
readme = "README.md"
requires-python = ">=3.9,<3.15"
dynamic = ["dependencies", "optional-dependencies"]
keywords = [
    "embeddings",
    "feature-extraction",
    "model-evaluation",
    "transfer-learning",
    "overlapindex",
    "separatix"
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
    "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",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Information Analysis",
]

[project.urls]
Homepage = "https://github.com/NiklasMelton/vertebrae"
Repository = "https://github.com/NiklasMelton/vertebrae"
Documentation = "https://vertebrae.readthedocs.io/"

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

[tool.poetry]
license = "AGPL-3.0-or-later"
packages = [{ include = "vertebrae", from = "src" }]
include = [
    { path = "tests", format = "sdist" },
    { path = "docs", format = "sdist" },
    { path = "examples", format = "sdist" },
    { path = "img", format = "sdist" },
    { path = "src/vertebrae/py.typed", format = ["sdist", "wheel"] },
]
exclude = ["**/.DS_Store"]

[tool.poetry.dependencies]
python = ">=3.9,<3.15"
numpy = ">=2.0,<3.0"
scipy = ">=1.13,<2.0"
scikit-learn = "^1.5"
pandas = "^2.2"
joblib = "^1.3"
pydantic = "^2.0"
overlapindex = ">=0.1.4,<0.2.0"
separatix = ">=0.1.1"
psutil = "^5.9"
transformers = { version = "^4.0", optional = true }
datasets = { version = "^2.0", optional = true }
torch = { version = ">=2.1", optional = true }
timm = { version = "^1.0", optional = true }
torchvision = { version = ">=0.16", optional = true }
matplotlib = { version = ">=3.9,<4", optional = true }
sentence-transformers = { version = "^3.0", optional = true }
soundfile = { version = "^0.13", optional = true }
av = { version = ">=12,<16", optional = true }
pytorchvideo = { version = "^0.1.5", optional = true }
open-clip-torch = { version = "^2.24", optional = true }
pillow = [
    { version = ">=11.3,<12", python = ">=3.9,<3.10" },
    { version = ">=12,<13", python = ">=3.10,<3.15" },
]
onnxruntime = { version = "^1.18", optional = true }
keras = { version = ">=3.0", optional = true }
tensorflow = { version = ">=2.16", optional = true }
tensorflow-hub = { version = "^0.16", optional = true }
jax = { version = ">=0.4", optional = true }
flax = { version = ">=0.8", optional = true }
xgboost = { version = ">=2.0", optional = true }
lightgbm = { version = ">=4.0", optional = true }
catboost = { version = ">=1.2", optional = true }
torch-geometric = { version = ">=2.5", optional = true }
dgl = { version = ">=2.0", optional = true }
ray = { version = "^2.30", optional = true }
distributed = { version = "^2024.5", optional = true }
boto3 = { version = "^1.34", optional = true }
google-cloud-storage = { version = "^2.16", optional = true }

[tool.poetry.extras]
hf = ["transformers", "datasets", "torch", "sentence-transformers", "soundfile", "av", "pytorchvideo"]
audio = ["transformers", "torch", "soundfile"]
timeseries = ["transformers", "torch"]
video = ["transformers", "torch", "av", "pytorchvideo"]
torch = ["torch"]
timm = ["torch", "timm"]
torchvision = ["torch", "torchvision"]
visuals = ["torch", "torchvision", "matplotlib"]
text-visuals = ["torch", "matplotlib"]
backbone-selection = [
    "torch",
    "torchvision",
    "transformers",
    "timm",
    "open-clip-torch",
    "matplotlib",
]
openclip = ["torch", "open-clip-torch"]
mlp = ["torch"]
keras = ["keras"]
tensorflow = ["tensorflow"]
tensorflow-hub = ["tensorflow", "tensorflow-hub"]
jax = ["jax", "flax"]
trees = ["xgboost", "lightgbm", "catboost"]
graph = ["torch", "torch-geometric", "dgl"]
onnx = ["onnxruntime"]
ray = ["ray"]
dask = ["distributed"]
distributed = ["ray", "distributed"]
s3 = ["boto3"]
gcs = ["google-cloud-storage"]
cloud = ["boto3", "google-cloud-storage"]

[tool.poetry.group.dev.dependencies]
pytest = "^8.0"
ruff = "^0.6"
mypy = "^1.0"

[tool.poetry.group.docs.dependencies]
sphinx = { version = "^8.2", python = ">=3.14" }
sphinx-rtd-theme = { version = "^3.0", python = ">=3.14" }
myst-parser = { version = "^4.0", python = ">=3.14" }
sphinx-autoapi = { version = "^3.6", python = ">=3.14" }
sphinx-copybutton = { version = "^0.5", python = ">=3.14" }

[tool.ruff]
line-length = 100
target-version = "py39"

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "B"]
ignore = ["UP006", "UP007", "UP035"]

[tool.mypy]
python_version = "3.9"
warn_unused_configs = true
disallow_untyped_defs = false
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src"]
markers = [
    "realworld: integration tests that exercise real datasets and installed metric dependencies",
    "publicmodels: manual smoke tests that download and run small public models",
    "cloudemulators: manual integration tests for S3/GCS-compatible local emulators",
    "distributedruntime: manual smoke tests for real local Ray/Dask runtimes",
    "devicesmoke: manual smoke tests for real CPU/GPU device execution paths",
    "memorystress: manual stress tests for larger memory/subsampling workflows",
]