helical/pyproject.toml at release · helicalAI/helical · GitHub

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

[project]
name = "helical"
version = "3.1.1"

authors = [
  { name="Helical Team", email="support@helical-ai.com" },
]
description = "Helical Python SDK"
readme = "README.md"
requires-python = ">=3.12,<3.13"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
    "Operating System :: OS Independent",
]

license = {file = "LICENSE"}

dependencies = [
    'requests>=2.32.3',
    'pandas==2.2.2',
    'anndata>=0.11',
    'numpy>=2.1.3,<2.3',  # scipy 1.13.1 requires numpy<2.3
    'scikit-learn>=1.5.0',
    'scipy==1.13.1',
    # Pinned exact: prebuilt flash-attn/mamba/causal-conv1d wheels only reach
    # torch 2.10, and only as cu13+cp312 builds. Bump deliberately (needs new
    # accelerator wheels + matching CUDA 13 / Python 3.12), not incidentally.
    'torch==2.10.0',
    'accelerate==1.14.0',
    'transformers>=5.3.0',  # security floor: clears CVE-2026-4372 (fixed 5.3.0)
    'scikit-misc>=0.5.2',
    'einops==0.8.1',
    'omegaconf==2.3.0',
    'hydra-core==1.3.2',
    'pybiomart',
    'datasets==3.6.0',
    'sentencepiece>=0.2.0',
    'bitsandbytes>=0.48.2',
    # Directly imported by helical but previously only satisfied transitively
    # (scanpy via scib, now removed) or by a dirty CI env. Declared explicitly so
    # a clean install has them: scanpy (scgpt/c2s/uce/tahoe model code),
    # requests-cache (utils/downloader.py, used by every model), torchmetrics +
    # catalogue (tahoe backbone).
    'scanpy>=1.11',
    'requests-cache>=1.2',
    'torchmetrics>=1.0',
    'catalogue>=2.0',
]

constraint-dependencies = [
    # version-floor guard against the protobuf-3.20 break — removing it loses that floor
    'protobuf>=3.20.0',
]

[project.optional-dependencies]
# Test/lint tooling (formerly requirements-dev.txt). Install with `.[dev]`.
dev = [
    'pytest==9.0.3',
    'pytest-cov==7.1.0',
    'pytest-mock==3.15.1',
    'nbmake==1.5.4',
    'black==26.3.1',
]

mamba-ssm = [
    'mamba-ssm==2.3.2.post1',
    'causal-conv1d==1.6.2.post1',
]

evo-2 = [
    'biopython==1.85',
    'transformer-engine[pytorch]==1.13.0',
]

[tool.hatch.metadata]
allow-direct-references = true # Allows installing package from git

# Default PyPI torch==2.10.0 is a cu12 build (pins cuda-bindings==12.9.4), which
# collides with the cu13 RAPIDS/cuda-python stack. Pull torch from the cu130
# index so it resolves to its CUDA 13 build (cuda-bindings 13.x); the nvidia
# index supplies the cu13 nvidia-*/cuda-bindings deps that build pulls in.
[[tool.uv.index]]
name = "pytorch-cu130"
url = "https://download.pytorch.org/whl/cu130"
explicit = true

[[tool.uv.index]]
name = "nvidia"
url = "https://pypi.nvidia.com"

[tool.uv.sources]
torch = { index = "pytorch-cu130" }

[project.urls]
Homepage = "https://github.com/helicalAI/helical"
Issues = "https://github.com/helicalAI/helical/issues"
Documentation = "https://helical.readthedocs.io/"
Repository = "https://github.com/helicalAI/helical"