pyproject.toml

[build-system]
# torch used at build needs to match the one at runtime
requires = ["setuptools", "wheel", "setuptools-scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "openfold3"
dynamic = ["version"]
authors = [
    { name = "OpenFold Team", email = "support@openfold.io" }
]
description = "OpenFold's Biological Structure Prediction Model based on DeepMind's AlphaFold 3"
readme = "README.md"
license = { text = "Apache-2.0" }
classifiers = [
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
urls.Homepage = "https://openfold.io/"
urls.Documentation = "https://openfold-3.readthedocs.io/en/latest/"
urls.Repository = "https://github.com/aqlaboratory/openfold-3"
urls.Issues = "https://github.com/aqlaboratory/openfold-3/issues"

requires-python = ">=3.10"
dependencies = [
    "numpy",
    "scipy",
    "pandas",
    "torch", # ==2.5.1",
    "ml-collections",
    "pytorch-lightning >=2.1",
    "biotite",
    "rdkit<2026", # aqlaboratory/openfold-3/issues/285 
    "pdbeccdutils",
    "kalign-python",
    "requests",
    "awscli",
    "awscrt",
    "boto3",
    "PyYAML",
    "ijson",
    "memory_profiler",
    "wandb",
    "func_timeout",
    "tqdm",
    "typing-extensions",
    "lmdb",
]

optional-dependencies.dev = [
    "pytest",
    "pytest-xdist",
    "pytest-cov",
    "pytest-benchmark",
    "pytest-regressions",
    "pytest-vcr",
    "ruff",
    "mypy",
    "mypy-baseline",
    "pre-commit",

    # used for documentation
    "sphinx",
    "myst-parser",
    "furo"
]
optional-dependencies.cuequivariance = [
    "cuequivariance>=0.8",
    "cuequivariance-ops-torch-cu12>=0.8",
    "cuequivariance-torch>=0.8",
    "torch>=2.7",
]
optional-dependencies.deepspeed = [
    "deepspeed>=0.18.7",
]

[project.scripts]
run_openfold="openfold3.run_openfold:cli"
setup_openfold="openfold3.setup_openfold:main"
validate-openfold3-rocm="openfold3.entry_points.validate_rocm:main"

# Let's take a decision if these are optional-dependencies or dependency-groups
# See: https://github.com/astral-sh/uv/issues/9011
# Leaving here to not break ongoing docker revamp efforts
[dependency-groups]
test = [
    "pytest",
    "ruff",
    "awscli",
    "aria2",
    "pytest-xdist",
    "pytest-cov",
    "pytest-benchmark",
    "pytest-regressions",
    "pytest-recording",
    "debugpy",
]


[tool.setuptools_scm]
fallback_version = "0.5.0"

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

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

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

# 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
extend-exclude = ["docs"]

[tool.ruff.lint]
select = [
    # pycodestyle
    "E",
    # Pyflakes
    "F",
    # pyupgrade
    "UP",
    # flake8-bugbear
    "B",
    # flake8-simplify
    "SIM",
    # isort
    "I",
    # flake8-tidy-imports (TID252 bans relative imports)
    "TID",
]
ignore = [
    "E741",
    "SIM108",
    "B905",  # explicit strict= for zip
]
extend-safe-fixes = ["UP006"]

[tool.ruff.lint.flake8-tidy-imports]
ban-relative-imports = "all"

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

[tool.mypy]
# So that a bare `mypy` (as used by the typecheck tasks) checks the whole project.
files = ["openfold3", "scripts"]
# The version every pixi environment currently resolves to, and the only one CI
# runs. Pinning it (rather than following the active interpreter) keeps the
# baseline from drifting on an unrelated `pixi update`; bump it deliberately,
# together with a `typecheck-sync`, when the environments move to a new Python.
# Note this means the `requires-python = ">=3.10"` floor above is not type-checked.
python_version = "3.14"
# The baseline is recorded on, and enforced by, linux-64 CI. Without pinning the
# platform, `sys.platform` branches (device selection, MPS vs CUDA fallbacks) are
# analysed on a developer's mac and skipped in CI, so a mac run reports errors
# that CI never sees and vice versa. The cost is that darwin-only branches are
# not type-checked anywhere; consistency with the enforcing platform wins.
platform = "linux"
# Most of our scientific dependencies (rdkit, biotite, pdbeccdutils, wandb, ...)
# ship no stubs. Without this, the baseline would be dominated by import noise.
ignore_missing_imports = true
# mypy-baseline parses one error per line, so the compact format is required.
pretty = false

# rdkit and gemmi are compiled extension modules whose conda-forge builds ship
# inline .pyi stubs on linux-64 but not on osx-arm64 -- same package version,
# different build contents. mypy therefore introspects them in CI and treats
# them as Any on a mac, which made ~15 baseline entries platform-dependent
# (e.g. `Module has no attribute "EmbedMolecule"`, or `tuple[Mol, str]` where a
# mac reports `tuple[Any, str]`). Skipping the import forces Any everywhere, so
# the baseline records the same errors no matter where it is generated. Drop
# this once both builds ship stubs and the stubs are accurate enough to type
# against.
#
# `follow_imports = "skip"` alone is not enough: mypy fully analyses stub files
# regardless of that setting unless `follow_imports_for_stubs` is also on. The
# latter is a no-op for every other module, since `follow_imports` stays at its
# default of "normal" outside this override.
follow_imports_for_stubs = true

[[tool.mypy.overrides]]
module = ["rdkit.*", "gemmi.*"]
follow_imports = "skip"

[tool.mypy-baseline]
# Keep the baseline sorted so its diffs stay reviewable.
sort_baseline = true

[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/",
]