biofoundation/pyproject.toml at main · Open-Athena/biofoundation · GitHub

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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "biofoundation"
version = "0.1.0"
description = "An ecosystem for users of biological foundation models"
requires-python = ">=3.12"
dependencies = [
    "biopython>=1.85",
    "datasets>=4.0.0",
    "einops",
    "jaxtyping",
    "numpy",
    "pandas",
    "pyarrow>=21.0.0",
    "scikit-learn",
    "transformers[torch]",
    "bioframe",
]

[project.optional-dependencies]
mamba = [
  "causal-conv1d==1.5.0.post8",
  "mamba-ssm==2.2.4",
]
gpn = [
  "gpn @ git+https://github.com/songlab-cal/gpn",
]
glm-experiments = [
  "lightning>=2.0.0",
  "hydra-core>=1.3.0,<2.0.0",
]

[tool.uv.sources]
torch = { index = "pytorch-cu128" }
causal-conv1d = { git = "https://github.com/Dao-AILab/causal-conv1d", tag = "v1.5.0.post8" }
mamba-ssm = { git = "https://github.com/state-spaces/mamba", tag = "v2.2.4" }

[tool.uv]
no-build-isolation-package = ["mamba-ssm", "causal-conv1d"]

[[tool.uv.dependency-metadata]]
name = "mamba-ssm"
version = "2.2.4"
requires-dist = ["torch", "einops"]

[[tool.uv.dependency-metadata]]
name = "causal-conv1d"
version = "1.5.0.post8"
requires-dist = ["torch", "einops"]

[tool.ruff.lint]
# Disable F722 (syntax error in forward annotation) for jaxtyping compatibility
ignore = ["F722"]

[dependency-groups]
dev = [
    "pre-commit>=4.3.0",
    "ruff>=0.12.11",
    "mypy>=1.17.0",
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
]

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.wheel]
packages = ["biofoundation"]

[tool.mypy]
strict = true
ignore_missing_imports = true
exclude = ["tests/"]