[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 = "bionemo-meta"

readme = "README.md"

description = "BioNeMo meta-package."

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 = [

    # **ALL** bionemo sub-packages

    'bionemo-core',

    'bionemo-esm2',

    'bionemo-evo2',

    'bionemo-example_model',

    'bionemo-fw',

    'bionemo-geneformer',

    'bionemo-geometric',

    'bionemo-llm',

    'bionemo-moco',

    'bionemo-scdl',

    'bionemo-size-aware-batching',

    'bionemo-testing',

    'bionemo-webdatamodule',

    # 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-*/"]

[tool.uv.sources]

# external

nemo_run = { git = "https://github.com/NVIDIA/NeMo-Run", rev = "34259bd3e752fef94045a9a019e4aaf62bd11ce2" }

# under 3rdparty/

nemo_toolkit = { workspace = true }

megatron-core = { workspace = true }

# in sub-packages/

bionemo-core = { workspace = true }

bionemo-amplify = { workspace = true }

bionemo-esm2 = { workspace = true }

bionemo-example_model = { workspace = true }

bionemo-fw = { workspace = true }

bionemo-geneformer = { workspace = true }

bionemo-geometric = { workspace = true }

bionemo-llm = { workspace = true }

bionemo-moco = { workspace = true }

bionemo-noodles = { workspace = true }

bionemo-scdl = { workspace = true }

bionemo-size-aware-batching = { workspace = true }

bionemo-testing = { workspace = true }

bionemo-webdatamodule = { 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]

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",

        "./3rdparty/NeMo",

        # bionemo sub-packages

        './sub-packages/bionemo-core/src',

        './sub-packages/bionemo-esm2/src',

        './sub-packages/bionemo-evo2/src',

        './sub-packages/bionemo-example_model/src',

        './sub-packages/bionemo-fw/src',

        './sub-packages/bionemo-geneformer/src',

        './sub-packages/bionemo-geometric/src',

        './sub-packages/bionemo-llm/src',

        './sub-packages/bionemo-moco/src',

        './sub-packages/bionemo-noodles/src',

        './sub-packages/bionemo-scdl/src',

        './sub-packages/bionemo-size-aware-batching/src',

        './sub-packages/bionemo-testing/src',

        './sub-packages/bionemo-webdatamodule/src',

        # internal

        './internal/infra-bionemo/src',

    ] },

]