src/pyproject.toml

[build-system]
requires = ["hatchling>=1.21"]
build-backend = "hatchling.build"

[project]
name = "statlens"
version = "0.1.11"
description = "Self-hosted DEA method selector — point a TSV at a Qwen3-32B + LoRA classifier and get the right DESeq2/limma pipeline auto-run."
readme = "README.md"
requires-python = ">=3.10"
license = { text = "Apache-2.0" }
authors = [
    { name = "statLens contributors" },
]
keywords = ["bioinformatics", "differential expression", "DESeq2", "limma", "LLM", "Qwen3", "vLLM"]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

dependencies = [
    # web
    "fastapi>=0.115",
    "uvicorn[standard]>=0.30",
    "python-multipart>=0.0.10",
    "httpx>=0.27",

    # serving — LLaMA-Factory wraps transformers + bitsandbytes for streamable bnb 4-bit
    "llamafactory>=0.9,<1.0",
    "bitsandbytes>=0.43",
    "torch>=2.1",
    # torchaudio 2.11+ requires CUDA 13; pin <2.11 to keep CUDA 12.x users happy.
    # (llamafactory imports torchaudio unconditionally for multimodal templates.)
    "torchaudio<2.11",
    "transformers>=4.45",
    "peft>=0.12",
    "huggingface_hub>=0.25",
    "pyyaml>=6.0",

    # data + plots used by V4 pipelines
    "pandas>=2.0",
    "numpy>=1.26",
    "matplotlib>=3.8",
    "seaborn>=0.13",
    "scipy>=1.13",
    "statsmodels>=0.14",
    "scikit-learn>=1.4",

    # DESeq2 (pure Python; no R)
    "pydeseq2>=0.5",

    # CLI niceties
    "rich>=13.0",
    "click>=8.0",
]

[project.urls]
Homepage   = "https://huggingface.co/domizzz2025/statLens"
Repository = "https://huggingface.co/domizzz2025/statLens"

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

[tool.hatch.build.targets.wheel]
packages = ["statlens"]
# data/ + pipelines/ are inside the package dir and picked up automatically;
# we only need to make sure they're not excluded.
include = [
    "statlens/**/*.py",
    "statlens/**/*.html",
    "statlens/**/*.tsv",
    "statlens/**/*.sh",
    "statlens/**/*.md",
]