maxToki/pyproject.toml at main · NVIDIA-Digital-Bio/maxToki · GitHub

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[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

# We can likely clean up the meta-package once https://github.com/astral-sh/uv/issues/6935 has a resolution.
[project]
name = "maxtoki"
readme = "README.md"
description = "MaxToki: Single-cell gene expression model built on BioNeMo Framework."
authors = [{ name = "BioNeMo Team", email = "bionemofeedback@nvidia.com" }]
requires-python = ">=3.10"
classifiers = ["Private :: Do Not Upload", "Programming Language :: Python :: 3.10"]
license = { file = "LICENSE/license.txt" }
version = "2.0.0"
dependencies = [
    'bionemo-core',
    'bionemo-maxtoki',
    'bionemo-llm',
    # external
    'nemo_run',
    'torch==2.3.*',
    # internal code
    "infra-bionemo",
]

[project.optional-dependencies]
build = ['flash-attn', 'pip']

[tool.uv.workspace]
members = ["3rdparty/*", "internal/infra-bionemo/", "sub-packages/bionemo-core", "sub-packages/bionemo-llm", "sub-packages/bionemo-maxtoki", "sub-packages/bionemo-testing"]

[tool.uv.sources]
# external
nemo_run = { git = "https://github.com/NVIDIA/NeMo-Run", rev = "34259bd3e752fef94045a9a019e4aaf62bd11ce2" }
# under 3rdparty/
# nemo_toolkit = { workspace = false }
megatron-core = { workspace = true }
# in sub-packages/
bionemo-core = { workspace = true }
bionemo-maxtoki = { workspace = true }
bionemo-llm = { workspace = true }
bionemo-testing = { workspace = true }
# in internal/
infra-bionemo = { workspace = true }

[tool.uv]
dev-dependencies = [
    "click",
    "ipdb",
    "nbval",
    "pre-commit",
    "pyright",
    "ruff",
    "tach",
    "tenacity",
]
no-build-isolation-package = ["flash-attn"]
cache-keys = [{ git = { commit = true } }]

[tool.black]
line-length = 119
target-version = ['py310']
skip-string-normalization = true

[tool.ruff]
line-length = 119

[tool.ruff.lint]
ignore = ["C901", "D100", "E501", "E741", "RUF005", "RUF010"]
select = [
    "C",   # Pylint conventions
    "D",   # Documentation formatting
    "E",   # style stuff, whitespaces
    "F",   # important pyflakes lints
    "I",   # import sorting
    "RUF", # Some Ruff-specific lints, unused noqas, etc.
    "W",   # Pylint warnings
]

# Ignore import violations in all `__init__.py` files.
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["D104", "E402", "F401", "F403", "F811"]
"test_*.py" = ["D"]
"conftest.py" = ["D"]
"scripts/*.py" = ["D"]
"**/*.ipynb" = ["D"]

[tool.ruff.lint.isort]
lines-after-imports = 2
known-first-party = ["bionemo", "infra_bionemo"]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.pytest.ini_options]
xfail_strict = true
norecursedirs = ["3rdparty"]
addopts = [
    "--durations-min=30.0",
    "--durations=0",
    "--ignore=3rdparty",
]
markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]

[tool.pyright]
include = ["./internal/", "./scripts/", "./sub-packages/"]
exclude = ["*/tests/"]
executionEnvironments = [
    { "root" = ".", pythonVersion = "3.10", extraPaths = [
        # 3rd party, git submodules
        "./3rdparty/Megatron-LM",
        # bionemo sub-packages
        './sub-packages/bionemo-core/src',
        './sub-packages/bionemo-maxtoki/src',
        './sub-packages/bionemo-llm/src',
        # internal
        './internal/infra-bionemo/src',
    ] },
]