OneScience-Group/CodonTransformer

1[tool.poetry]2name = "CodonTransformer"3version = "1.6.7"4description = "The ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms."5authors = ["Adibvafa Fallahpour <Adibvafa.fallahpour@mail.utoronto.ca>"]6license = "Apache-2.0"7readme = "README.md"8homepage = "https://github.com/adibvafa/CodonTransformer"9repository = "https://github.com/adibvafa/CodonTransformer"10packages = [{ include = "CodonTransformer", from = "model" }]11classifiers = [12    "Programming Language :: Python :: 3",13    "License :: OSI Approved :: Apache Software License",14    "Operating System :: OS Independent",15]16 17[tool.poetry.dependencies]18python = "^3.9"19biopython = "^1.83"20ipywidgets = "^7.0.0"21numpy = "<2.0.0"22onnxruntime = "^1.16.3"23pandas = "^2.0.0"24python_codon_tables = "^0.1.12"25pytorch_lightning = "^2.2.1"26scikit-learn = "^1.2.2"27scipy = "^1.13.1"28setuptools = "^70.0.0"29torch = "^2.0.0"30tqdm = "^4.66.2"31transformers = "^4.40.0"32CAI-PyPI = "^2.0.1"33 34[tool.poetry.dev-dependencies]35coverage = {version = "^7.0", extras = ["toml"]}36 37[build-system]38requires = ["poetry-core>=1.0.0"]39build-backend = "poetry.core.masonry.api"40 41[tool.ruff]42line-length = 8843indent-width = 444target-version = "py310"45 46[tool.ruff.lint]47select = ["E", "F", "I"]48ignore = []49 50[tool.ruff.format]51quote-style = "double"52indent-style = "space"53skip-magic-trailing-comma = false54line-ending = "auto"55 56[tool.coverage.run]57omit = [58    # omit pytorch-generated files in /tmp59    "/tmp/*",60]61