content: [project]
  name = "mrna-bench"
  version = "1.2.2"
  description = "Benchmarking suite for mRNA property prediction."
  readme = "README.md"
  authors = [
      { name = "Ruian (Ian) Shi", email = "ian.shi@mail.utoronto.ca" },
      { name = "Taykhoom Dalal", email = "tid4007@med.cornell.edu" },
      { name = "Phil Fradkin", email = "phil.fradkin@gmail.com" },
      { name = "Divya Koyyalagunta", email = "dko4001@med.cornell.edu" }
  ]
  requires-python = ">= 3.10"
  license = { file = "LICENSE" }  # Include a LICENSE file in your repo
  keywords = ["mrna", "genomic foundation model", "benchmark"]
  classifiers = [
      "Programming Language :: Python :: 3",
      "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
      "Operating System :: Unix"
  ]
  dependencies = [
      "tqdm",
      "PyYAML",
      "scikit-learn",
      "numpy<2",
      "pandas<=2.2.2",
      "requests",
      "pyarrow",
      "fastparquet",
      "openpyxl"
  ]
  
  [project.urls]
  Repository = "https://github.com/morrislab/mRNABench"
  
  [project.optional-dependencies]
  base_models = [
      "torch==2.2.2",
      "transformers==4.38.0",
      "flash-attn==2.7.4.post1",
      "mamba-ssm==1.2.0.post1",
      "rna-fm==0.2.2",
      "accelerate==1.8.1",
      "multimolecule==0.0.7",
      "evo-model==0.4"
  ]
  dev = [
      "mypy",
      "flake8",
      "flake8-docstrings",
      "pytest"
  ]
  
  [build-system]
  requires = [
      "setuptools",
      "wheel",
      "pip"
  ]
  build-backend = "setuptools.build_meta"
  
  [tool.setuptools.packages.find]
  include = ["mrna_bench*"]
  