pyproject.toml

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

[project]
name = "modelgenerator"
version = "0.1.1-4"
description = "AIDO.ModelGenerator is a software stack powering the development of an AI-driven Digital Organism by enabling researchers to adapt pretrained models and generate finetuned models for downstream tasks."
readme = "README.md"
authors = [
    { name = "GenBio AI" },
    { name = "Caleb Ellington", email = "caleb.ellington@genbio.ai" },
    { name = "Dian Li", email = "dian.li@genbio.ai" },
]
classifiers = [
    "Programming Language :: Python :: 3",
    "Operating System :: OS Independent",
]
keywords = [
    "genbio",
    "foundation models",
    "finetuning",
    "machine learning",
]
dependencies = [
    "torch",
    "torchvision",
    "torchaudio",
    "transformers==4.38.0",
    "datasets",
    "packaging",
    "bitsandbytes",
    "scipy",
    "scikit-learn",
    "wandb",
    "pandas",
    "pyfaidx",
    "peft<=0.13.2",  # Dec 6 2024 release breaks EncoderDecoderCache from transformers
    "torchmetrics>=1.5.0",
    "lightning>=2.4.0",
    "black",
    "jsonargparse[signatures]>=4.26.1",
    "awscli",
    "openfold @ git+https://github.com/genbio-ai/openfold.git@c4aa2fd0d920c06d3fd80b177284a22573528442",
    "dllogger @ git+https://github.com/NVIDIA/dllogger.git@0540a43971f4a8a16693a9de9de73c1072020769",
    "biotite>=1.0.1",
    "einops>=0.8.0",
    "ml-collections>=1.0.0",
    "dm-tree>=0.1.8",
    "biopython>=1.84",
    "omegaconf>=2.3.0",
    "anndata",
]
requires-python = ">=3.10,<3.11"

[project.scripts]
mgen = "modelgenerator.main:cli_main"
mgen-hf = "modelgenerator.huggingface_models.utils:hf_cli_main"

[tool.hatch.build.targets.wheel]
package = ["modelgenerator"]

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

[project.urls]
"Homepage" = "https://genbio-ai.github.io/ModelGenerator"
"Source" = "https://github.com/genbio-ai/ModelGenerator"