pyproject.toml

[build-system]
# torch used at build needs to match the one at runtime
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "openfold3"
version = "0.4.0"
dependencies = [
  "awscli",
  "awscrt",
  "torch",# ==2.5.1",
  "pytorch-lightning >=2.1",
  "numpy",
  "pandas",
  "PyYAML",
  "requests",
  "scipy",
  "tqdm",
  "typing-extensions",
  "wandb",
  "ml-collections",
  "mkl",
  "aria2",
  "biotite",
  "rdkit",
  "boto3",
  "memory_profiler",
  "func_timeout",
  "lmdb", # == 1.6  # This verison might be required to avoid Error during training
  "ijson",
  "deepspeed",
  "pdbeccdutils",
  # For cutlass >=4, import library is cutlass_cppgen, but deepspeed is
  # currently using cutlass.
  "nvidia-cutlass <4",
  "kalign-python",

  # additional pins

  # Pinned cutlass <4 calls from cuda.__version__, which was removed when
  # cuda-python went fully metapackage
  "cuda-python <12.9.1",
]
authors = [
  {name = "OpenFold Team", email = "support@openfold.io" }
]
description = "OpenFold's Biological Structure Prediction Model based on DeepMind's AlphaFold 3"
readme = "README.md"
requires-python = ">=3.10"
license = { text = "Apache-2.0" }
classifiers = [
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3.10",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]

[project.urls]
Repository = "https://github.com/aqlaboratory/openfold-3"

[project.scripts]
run_openfold="openfold3.run_openfold:cli"
setup_openfold="openfold3.setup_openfold:main"

[dependency-groups]
test = [
  "pytest",
  "ruff",
  "awscli",
  "aria2",
  "pytest-xdist",
  "pytest-cov",
  "pytest-benchmark",
  "debugpy",
]

[project.optional-dependencies]
dev = [
  "pytest",
  "ruff",
  # used for documentation
  "sphinx",
  "myst-parser",
  "furo"
]
cuequivariance = [
  "cuequivariance>=0.6.1",
  "cuequivariance-ops-torch-cu12>=0.6.1",
  "cuequivariance-torch>=0.6.1",
  "torch>=2.7",
]

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
where = ["."]
include = ["openfold3*", "scripts*"] 

[tool.setuptools.package-data]
openfold3 = [
  "projects/*/config/*.yml",
  "tests/test_data/**/*",
  "scripts/*.sh"
]

# much of the cibuildwheel config taken from benfred/implicit
[tool.cibuildwheel]
before-all = "devtools/install_cuda.sh"
manylinux-x86_64-image = "manylinux2014"

[tool.cibuildwheel.linux]
repair-wheel-command = """
AUDITWHEEL_PLAT=manylinux2014_$(uname -m) \
auditwheel repair \
    --exclude libc10.so \
    --exclude libtorch.so \
    --exclude libtorch_cpu.so \
    --exclude libtorch_python.so \
    -w {dest_dir} {wheel}
"""

[tool.cibuildwheel.linux.environment]
CUDACXX = "/usr/local/cuda/bin/nvcc"

[tool.ruff]
line-length = 88

[tool.ruff.lint]
select = [
    # pycodestyle
    "E",
    # Pyflakes
    "F",
    # pyupgrade
    "UP",
    # flake8-bugbear
    "B",
    # flake8-simplify
    "SIM",
    # isort
    "I",
]
ignore = [
    "E741",
    "SIM108",
    "B905",  # explicit strict= for zip
]
extend-safe-fixes = ["UP006"]

[tool.ruff.lint.per-file-ignores]
"**/tests/**" = ["E501"]

[tool.pytest.ini_options]
log_cli = true
log_cli_level = "WARNING"
log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"
testpaths = ["openfold3/tests"]
python_files = ["test_*.py"]
markers = [
    "inference_verification: Tests to verify installation on inference example",
    "slow: Large size test"
]

# Exclude directories during collection
[tool.coverage.run]
omit = [
    "openfold3/tests/*",
]

# Exclude directories from reporting
[tool.coverage.report]
omit = [
    "openfold3/tests/*",
]

# Map /opt/openfold3/openfold3/ (docker path) to openfold3/ (local path) during `coverage combine`
[tool.coverage.paths]
source = [
    "openfold3/",
    "/opt/openfold3/openfold3/",
]