mirror of
https://github.com/evolutionaryscale/esm.git
synced 2026-06-04 17:14:23 +08:00
143 lines
3.1 KiB
TOML
143 lines
3.1 KiB
TOML
[project]
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name = "esm"
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version = "3.3.0"
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description = "EvolutionaryScale open model repository"
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readme = "README.md"
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requires-python = ">=3.12,<3.13"
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license = {file = "LICENSE.md"}
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authors = [
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{name = "EvolutionaryScale Team"}
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]
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maintainers = [
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{name = "Zeming Lin", email = "zeming+esm@evolutionaryscale.ai" }
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"Programming Language :: Python :: 3.12",
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]
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dependencies = [
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"torch>=2.2.0",
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"transformers @ git+https://github.com/Biohub/transformers.git@main",
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"ipython",
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"einops",
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"biotite>=1.0.0",
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"rdkit",
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"msgpack-numpy",
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"biopython",
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"scikit-learn",
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"brotli",
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"attrs",
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"pandas",
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"cloudpathlib",
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"httpx",
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"tenacity",
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"zstd",
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"ipywidgets",
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"py3dmol",
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"pydssp",
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"boto3",
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"pygtrie",
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"dna_features_viewer",
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"accelerate",
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]
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# Pytest
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[tool.pytest.ini_options]
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addopts = """
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--cov=esm
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--cov-report term-missing:skip-covered
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-n auto
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--ignore=tests/oss_pytests/test_oss_client.py
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"""
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[tool.setuptools]
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package-dir = {"" = "."}
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include-package-data = true
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[tool.setuptools.packages.find]
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where = ["."]
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include = ["esm*"]
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[tool.setuptools.package-data]
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esm = ["data/*"]
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[tool.pixi.workspace]
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channels = ["conda-forge"]
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platforms = ["linux-64", "osx-arm64"]
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# These are build dependencies, to ensure pip support, keep run-time deps above in `dependencies`
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[tool.pixi.dependencies]
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pkg-config = "*"
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cmake = "*"
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pip = "*"
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twine = "*"
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python = "3.12.*"
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[tool.pixi.pypi-dependencies]
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esm = { path = ".", editable = true }
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[tool.pixi.tasks]
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build-wheel = "python -m pip wheel --no-deps -w dist ."
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upload-wheel = "python -m twine upload --repository pypi"
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[tool.pixi.feature.dev.dependencies]
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matplotlib = "*"
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pre-commit = "*"
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pytest = "*"
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pytest-cov = "*"
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pytest-xdist = "*"
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seaborn = "*"
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pyright = "==1.1.399"
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[tool.pixi.feature.dev.tasks]
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lint-all = "pre-commit run --all-files --show-diff-on-failure"
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cov-test = "pytest -v --junitxml=pytest.xml --cov=esm"
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[tool.pixi.environments]
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default = {features = [], solve-group = "default"}
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dev = {features = ["dev"], solve-group = "default"}
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[tool.ruff]
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extend-include = ["*.ipynb"]
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[tool.ruff.lint]
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# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`), sort imports ('I')
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select = ["E4", "E7", "E9", "F", "I"]
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ignore = [
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# allow variable == False (tensors should do this)
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"E712",
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# allow assigning of lambdas
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"E731",
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# Allow ambiguous variables, e.g. we use O for oxygen
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"E741",
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# Ignore errors from jaxtyping hints
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# https://docs.kidger.site/jaxtyping/faq/#flake8-or-ruff-are-throwing-an-error
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"F722",
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# TODO: Fix the few offenders in a follow up PR
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"E721",
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]
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[tool.ruff.lint.isort]
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split-on-trailing-comma = false
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known-third-party = ["wandb"]
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[tool.ruff.format]
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skip-magic-trailing-comma = true
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docstring-code-format = true
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docstring-code-line-length = "dynamic"
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[tool.isort]
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known_third_party = ["wandb"]
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[tool.pyright]
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useLibraryCodeForTypes = true
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reportPrivateImportUsage = false
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typeCheckingMode = "basic"
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[tool.importlinter]
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root_package = "esm"
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