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upgrade to pyproject.toml
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pyproject.toml

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[build-system]
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requires = ["setuptools >= 77.0.3", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "chebai-proteins"
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version = "0.0.2"
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description = "Repository for protein prediction and classification, built on top of the python-chebai codebase"
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authors = [{name="", email=""}]
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readme = "README.md"
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license = { text = "AGPL-3.0" }
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requires-python = ">=3.9, <3.13"
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dependencies = [
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"chebai @ git+https://github.com/ChEB-AI/python-chebai.git",
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"biopython",
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"fair-esm",
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]
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[project.optional-dependencies]
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dev = ["black", "isort", "pre-commit"]
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plot = ["matplotlib", "seaborn"]
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wandb = ["wandb"]
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[tool.setuptools]
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include-package-data = true
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license-files = ["LICEN[CS]E*"]
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[tool.setuptools.packages.find]
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where = ["."]
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exclude = ["tests*"]
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[tool.setuptools.package-data]
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"*" = ["**/*.txt", "**/*.json"]

setup.py

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