mirror of
https://github.com/RosettaCommons/foundry.git
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5e7b739ed3
* Add initial files * add files * Move projects.aa_design -> rfd3 * Make format * Delete test files * Add configs * Mc * Fixed tests * remove test files
178 lines
4.3 KiB
TOML
178 lines
4.3 KiB
TOML
[project]
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name = "modelforge"
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dynamic = ["version"]
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description = "Shared utilities and training infrastructure for biomolecular structure prediction models."
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readme = "README.md"
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requires-python = ">=3.12"
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authors = [
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{ name = "Institute for Protein Design", email = "contact@ipd.uw.edu" },
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]
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license = { file = "LICENSE.md" }
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classifiers = [
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"Natural Language :: English",
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"Operating System :: POSIX :: Linux",
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"Operating System :: MacOS",
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"Operating System :: Microsoft :: Windows",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: Implementation :: CPython",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"License :: OSI Approved :: BSD License",
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]
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dependencies = [
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# ... configuration & CLI
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"rootutils>=1.0.7,<1.1",
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"hydra-core>=1.3.0,<1.4",
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"environs>=11.0.0,<12",
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# ... logging
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"wandb>=0.15.10,<1",
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"rich>=13.9.4",
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# ... typing & documentation
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"jaxtyping>=0.2.17,<1",
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"beartype>=0.18.0,<1",
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"typer>=0.9.0,<1",
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# ... ml tools (core)
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"torch>=2.2.0,<3",
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"lightning>=2.5.0",
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"loralib>=0.1.1",
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"einops>=0.8.0,<1",
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"einx>=0.1.0,<1",
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"opt_einsum>=3.4.0,<4",
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"dm-tree>=0.1.6,<1",
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]
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[project.optional-dependencies]
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rfd3 = [
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"pydantic>=2.8",
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]
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rf3 = [
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"cuequivariance_ops_cu12>=0.6.1; sys_platform == 'linux'",
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"cuequivariance_ops_torch_cu12>=0.6.1; sys_platform == 'linux'",
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"cuequivariance_torch>=0.6.1; sys_platform == 'linux'",
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]
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all = [
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"modelforge[rfd3]",
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"modelforge[rf3]",
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]
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dev = [
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# Linters & formatters
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"assertpy",
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"ruff==0.8.3",
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"ipdb",
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# Debugger/interactive
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"debugpy>=1.8.5,<2",
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"ipykernel>=6.29.4,<7",
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# Testing tools
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"pytest>=8.2.0,<9", # testing framework
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"pytest-testmon>=2.1.1,<3", # run only tests related to changed code
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"pytest-xdist>=3.6.1,<4", # run tests in parallel
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"pytest-dotenv>=0.5.2,<1", # load environment variables from .env file
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"pytest-cov>=4.1.0,<5", # generate coverage report
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"pytest-benchmark>=5.0.0,<6", # benchmark tests for speed
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"atomworks==1.0.2",
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]
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[project.scripts]
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rf3 = "rf3.cli:app"
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rfd3 = "rfd3.cli:app"
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# Build settings ----------------------------------------------------------------------
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[build-system]
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requires = [
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"hatchling",
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"hatch-vcs == 0.4",
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]
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build-backend = "hatchling.build"
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[tool.hatch.version]
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source = "vcs"
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fallback-version = "0.0.0"
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[tool.hatch.build.hooks.vcs]
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version-file = "src/modelhub/version.py"
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[tool.hatch.metadata]
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allow-direct-references = true
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[tool.hatch.build.targets.wheel]
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packages = [
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"src/modelhub",
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"models/rf3/src/rf3",
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"models/rfd3/src/rfd3",
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]
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# Formatting & linting settings -------------------------------------------------------
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[tool.ruff]
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line-length = 88
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indent-width = 4
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target-version = "py310"
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exclude = [
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".bzr",
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".direnv",
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".eggs",
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".git",
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".git-rewrite",
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".hg",
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".ipynb_checkpoints",
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".mypy_cache",
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".nox",
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".pants.d",
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".pyenv",
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".pytest_cache",
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".pytype",
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".ruff_cache",
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".svn",
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".tox",
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".venv",
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".vscode",
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"__pypackages__",
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"_build",
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"buck-out",
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"build",
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"dist",
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"node_modules",
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"site-packages",
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"env",
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".venv",
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"venv",
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"*.ipynb",
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"dev.py",
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"archive",
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]
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[tool.ruff.format]
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# Like Black, use double quotes for strings.
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quote-style = "double"
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# Like Black, indent with spaces, rather than tabs.
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indent-style = "space"
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# Like Black, respect magic trailing commas.
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skip-magic-trailing-comma = false
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# Like Black, automatically detect the appropriate line ending.
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line-ending = "auto"
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# Enable auto-formatting of code examples in docstrings. Markdown,
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# reStructuredText code/literal blocks and doctests are all supported.
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docstring-code-format = true
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docstring-code-line-length = 88
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[tool.ruff.lint]
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# Allow unused variables when underscore-prefixed.
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dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
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# Sort imports
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extend-select = ["I", "F401"]
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ignore = [
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"F722", # for jaxtyping shape annotation
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"F821", # temporary to avoid jaxtyping warnings, see: https://github.com/astral-sh/ruff/issues/17386
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"E741", # enable us to use variables like "L"
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]
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[tool.pyright]
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typeCheckingMode = "off"
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