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pyproject.toml
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128 lines (115 loc) · 4.09 KB
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[project]
name = "dyno-phi"
dynamic = ["version"]
description = "Phi CLI and biomodals for the dyno protein design platform"
readme = "README.md"
requires-python = ">=3.9"
license = { text = "MIT" }
authors = [
{ name = "Dyno Therapeutics" },
]
keywords = ["protein-design", "bioinformatics", "cli", "alphafold", "esmfold", "proteinmpnn"]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
# CLI only requires rich + stdlib
dependencies = [
"rich>=14.0",
]
[project.optional-dependencies]
# Install when deploying or developing biomodals locally
biomodals = [
"modal>=0.69.0",
"google-cloud-storage>=2.18.0",
"requests>=2.32.0",
"pydantic>=2.0",
"biopython>=1.81",
"biotite>=1.0.0",
"numpy>=1.26.0",
]
dev = [
"pytest>=8.0",
"pytest-asyncio>=0.24",
"pytest-cov>=6.0",
"ruff>=0.8",
"mypy>=1.13",
"types-requests",
"types-PyYAML",
]
[project.scripts]
phi = "phi.cli:main"
[project.urls]
Homepage = "https://dynotx.com"
Repository = "https://github.com/dynotx/phi-cli"
Issues = "https://github.com/dynotx/phi-cli/issues"
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[tool.hatch.version]
path = "src/phi/_version.py"
[tool.hatch.build.targets.wheel]
packages = ["src/phi", "biomodals"]
# ── Ruff ──────────────────────────────────────────────────────────────────────
[tool.ruff]
target-version = "py39"
line-length = 100
[tool.ruff.lint]
select = [
"E", # pycodestyle errors
"W", # pycodestyle warnings
"F", # pyflakes
"I", # isort
"B", # flake8-bugbear
"C4", # flake8-comprehensions
"UP", # pyupgrade
"SIM", # flake8-simplify
]
ignore = [
"E501", # line too long (handled by formatter)
"B008", # do not perform function calls in argument defaults
"B904", # allow raising without from
]
[tool.ruff.lint.per-file-ignores]
# Biomodals run inside Modal GPU containers. They use older patterns (percent
# formatting, bare open(), zip() without strict=) that are intentional and
# safe in that context. E402 is expected (late imports inside Modal entrypoints).
"biomodals/*.py" = ["E402", "SIM115", "B905", "UP031", "UP038", "SIM108", "B007", "W293"]
# ── MyPy ──────────────────────────────────────────────────────────────────────
[tool.mypy]
python_version = "3.9"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
ignore_missing_imports = true
# Biomodals run in Modal GPU containers with many third-party libs that lack
# stubs. Relax the strict rules that apply to src/phi/ so we only enforce what
# matters locally: missing imports are already suppressed globally.
[[tool.mypy.overrides]]
module = ["biomodals", "biomodals.*", "biomodals.utils", "biomodals.utils.*"]
disallow_untyped_defs = false
disallow_incomplete_defs = false
warn_return_any = false
ignore_missing_imports = true
disable_error_code = ["import-untyped", "call-arg", "arg-type"]
# ── Pytest ────────────────────────────────────────────────────────────────────
[tool.pytest.ini_options]
minversion = "8.0"
addopts = ["-ra", "--strict-markers"]
testpaths = ["tests"]
pythonpath = ["."]
asyncio_mode = "auto"