pyproject.toml

[build-system]
requires = ["setuptools>=64", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "micov"
requires-python = ">=3.9"
classifiers = [
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: Implementation :: CPython",
    "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",
]
dynamic = ["version"]

dependencies = [
    "click",
    "scipy",
    "pyarrow<16.0.0",
    "polars-u64-idx<1.23.0",
    "numba",
    "matplotlib>=3.9.0",
    "duckdb>=1.2.0",
    "pytest",
]

readme = "README.md"
authors = [
    { name = "Daniel McDonald", email = "damcdonald@ucsd.edu" },
    { name = "Sherlyn Weng", email = "y1weng@ucsd.edu" },
    { name = "Caitlin Guccione", email = "cguccion@ucsd.edu" },
]
license = { file = "LICENSE" }
keywords = ["microbiome", "bioinformatics"]

[project.scripts]
micov = "micov.cli:cli"

# an empty section is needed to allow setuptools to pull version information
[tool.setuptools_scm]

[tool.ruff]
fix = true
line-length = 88
target-version = "py310"

[tool.check-manifest]
ignore = [
    # created by conda-incubator/setup-miniconda@v3 action
    "ci/setup-miniconda-patched-conda_host_env.yml",
]

[tool.ruff.lint]
# adapted from https://github.com/pola-rs/polars/blob/main/py-polars/pyproject.toml
select = [
    "ANN",    # flake8-annotations
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "D",      # flake8-docstrings
    "E",      # pycodestyle
    "F",      # pyflakes
    "FA",     # flake8-future-annotations
    "FBT001", # flake8-boolean-trap
    "I",      # isort
    "ICN",    # flake8-import-conventions
    "INT",    # flake8-gettext
    "PERF",   # perflint
    "PIE",    # flake8-pie
    "PT",     # flake8-pytest-style
    "PYI",    # flake8-pyi
    "RUF",    # ruff-specific rules
    "TCH",    # flake8-type-checking
    "TID",    # flake8-tidy-imports
    "UP",     # pyupgrade
    "W",      # pycodestyle
]
ignore = [
    "ANN",  # annotations are not enforced
    "D203", # puts a space before class docstrings
    "D213", # puts summary on second line
    "D400", # redundant with D415 in place
    "D301", # forces raw string literals
]

[tool.ruff.lint.per-file-ignores]
"micov/tests/*" = ["D", "PT"]

[tool.ruff.lint.pycodestyle]
max-doc-length = 88

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.setuptools.packages.find]
exclude = ["example*", "ci*"]