krewlyzer/pyproject.toml at main · msk-access/krewlyzer · GitHub

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[project]
name = "krewlyzer"
version = "0.7.0"
description = "Feature extraction tools for circulating tumor DNA from GRCh37 aligned BAM files"
authors = [{name = "Ronak Shah", email = "shahr2@mskcc.org"}]
requires-python = ">=3.8"
readme = "README.md"
license = { file = "LICENSE" }
dependencies = [
    "typer>=0.15.0",
    "pysam>=0.22.0",
    "pandas>=2.2.0",
    "numpy>=1.20.0",
    "rich>=13.9.0",
    "pyarrow>=15.0.0"
]

[project.optional-dependencies]
docs = [
    "mkdocs>=1.5.0",
    "mkdocs-material>=9.5.0"
]
test = [
    "pytest>=7.0.0",
    "pytest-mock>=3.10.0"
]
dev = [
    "pytest>=7.0.0",
    "pytest-mock>=3.10.0",
    "black==26.1.0",
    "ruff==0.15.4",
    "mypy==1.19.1",
]

[project.urls]
"Homepage" = "https://github.com/msk-access/krewlyzer"

[project.scripts]
krewlyzer = "krewlyzer.cli:app"

[build-system]
requires = ["maturin>=1.0,<2.0"]
build-backend = "maturin"

[tool.maturin]
python-source = "src"
manifest-path = "rust/Cargo.toml"
module-name = "krewlyzer._core"
# CRITICAL: Exclude data directory to keep wheel <100MB for PyPI
# Without this, maturin includes ALL source files by default!
exclude = ["src/krewlyzer/data/**/*"]
# Data source by installation method:
#   - Docker: bundled in image
#   - git clone + pip install -e .: uses source directory directly
#   - pip install: requires KREWLYZER_DATA_DIR env var pointing to cloned data

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
markers = [
    "unit: Fast unit tests with no I/O",
    "integration: Tool integration tests",
    "e2e: End-to-end workflow tests",
    "slow: Tests that take >10s",
    "rust: Tests requiring Rust backend",
]
filterwarnings = [
    "ignore::DeprecationWarning",
]

[tool.coverage.run]
source = ["krewlyzer"]
omit = ["*/tests/*"]

[tool.ruff]
line-length = 88  # Match black
target-version = "py310"

[tool.ruff.lint]
# E402: Module-level imports after code — deliberate pattern for CLI modules
#       that require typer.Option() / Rich setup before importing submodules.
# F821: Undefined name — forward-reference type annotations for baseline
#       dataclasses that are only imported at runtime inside functions.
ignore = ["E402", "F821"]

[tool.ruff.lint.per-file-ignores]
# Availability check pattern: `from krewlyzer import _core` is used to test
# whether the Rust extension is installed, even though _core isn't referenced.
"tests/unit/test_rust_python_equivalence.py" = ["F401"]
"tests/unit/test_bgzf_reader.py" = ["F401"]
"tests/integration/test_region_entropy.py" = ["F401"]

[tool.black]
line-length = 88
target-version = ["py310"]

[tool.mypy]
python_version = "3.10"
# _core is a Rust extension — no stubs available. Suppress all missing import
# errors globally so developers don't need stub files installed.
ignore_missing_imports = true
# Suppress noisy warnings that don't apply to Rust-bridged return types.
warn_return_any = false
warn_unused_ignores = false
no_error_summary = true

[[tool.mypy.overrides]]
# Fully suppress all mypy analysis of the Rust _core extension module.
# The Rust/PyO3 interface is the authoritative source of truth for these types.
module = ["krewlyzer._core", "krewlyzer._core.*"]
ignore_missing_imports = true
ignore_errors = true