| [tool.poetry] |
| name = "CodonTransformer" |
| version = "1.6.7" |
| description = "The ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms." |
| authors = ["Adibvafa Fallahpour <Adibvafa.fallahpour@mail.utoronto.ca>"] |
| license = "Apache-2.0" |
| readme = "README.md" |
| homepage = "https://github.com/adibvafa/CodonTransformer" |
| repository = "https://github.com/adibvafa/CodonTransformer" |
| packages = [{ include = "CodonTransformer", from = "model" }] |
| classifiers = [ |
| "Programming Language :: Python :: 3", |
| "License :: OSI Approved :: Apache Software License", |
| "Operating System :: OS Independent", |
| ] |
|
|
| [tool.poetry.dependencies] |
| python = "^3.9" |
| biopython = "^1.83" |
| ipywidgets = "^7.0.0" |
| numpy = "<2.0.0" |
| onnxruntime = "^1.16.3" |
| pandas = "^2.0.0" |
| python_codon_tables = "^0.1.12" |
| pytorch_lightning = "^2.2.1" |
| scikit-learn = "^1.2.2" |
| scipy = "^1.13.1" |
| setuptools = "^70.0.0" |
| torch = "^2.0.0" |
| tqdm = "^4.66.2" |
| transformers = "^4.40.0" |
| CAI-PyPI = "^2.0.1" |
|
|
| [tool.poetry.dev-dependencies] |
| coverage = {version = "^7.0", extras = ["toml"]} |
|
|
| [build-system] |
| requires = ["poetry-core>=1.0.0"] |
| build-backend = "poetry.core.masonry.api" |
|
|
| [tool.ruff] |
| line-length = 88 |
| indent-width = 4 |
| target-version = "py310" |
|
|
| [tool.ruff.lint] |
| select = ["E", "F", "I"] |
| ignore = [] |
|
|
| [tool.ruff.format] |
| quote-style = "double" |
| indent-style = "space" |
| skip-magic-trailing-comma = false |
| line-ending = "auto" |
|
|
| [tool.coverage.run] |
| omit = [ |
| |
| "/tmp/*", |
| ] |
|
|
