pyproject.toml

[tool.poetry]
name = "gertils"
version = "0.7.0"
description = "General computing utilities for data processing and analysis in the Gerlich group at IMBA"
authors = [
    "Vince Reuter <vince.reuter@gmail.com>",
]
readme = "README.md"
license = "MIT"
repository = "https://github.com/gerlichlab/gertils"
classifiers = [
    "Development Status :: 1 - Planning",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Utilities",
    "Typing :: Typed",
]
include = ["py.typed"]

[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[tool.poetry.dependencies]
# These are the main runtime dependencies.
python = ">=3.11,<3.14"
dask = ">=2023.5.1"
numpy = ">=1.24.2,<3"
numpydoc_decorator = "^2.2.1"
zarr = "^2.4.12"

[tool.poetry.group.dev]
optional = true

[tool.poetry.group.dev.dependencies]
# The dev group is for developers' convenience. 
# Consider each new dependency to another group as a dev group candidate.
codespell = "^2.2.2"
hypothesis = "^6.68.2"
pre-commit = "^4.0"
pyright = "==1.1.411"
pytest = "^7.1.0"
pytest-cov = "^5.0.0"
ruff = "==0.7.4"

[tool.poetry.group.lint]
optional = true

[tool.poetry.group.lint.dependencies]
# Everything that the pre-commit hooks run, for the checks job in CI.
codespell = "^2.2.2"
hypothesis = "^6.68.2"
pre-commit = "^4.0"
# The version looptrace pins, so the projects are type-checked by the same pyright.
pyright = "==1.1.411"
pytest = "^7.1.0"
# The version looptrace pins, so the projects are formatted and linted by the same ruff.
ruff = "==0.7.4"

[tool.poetry.group.test]
optional = true

[tool.poetry.group.test.dependencies]
hypothesis = "^6.68.2"
pytest = "^7.1.0"
pytest-cov = "^5.0.0"

[tool.codespell]
skip = ".git,.vscode,__pycache__,pyproject.toml,poetry.lock"
builtin = "clear,rare,informal,usage,code,names"
ignore-words-list = "jupyter,iff"  # prevent jupyter -> jupiter, iff -> if
check-filenames = true
uri-ignore-words-list = "*" # prevent spelling correction in URL-like values.

[tool.pyright]
include = ["gertils", "tests"]
# The package itself gets strict checking; the tests get the standard level.
strict = ["gertils"]
reportUnnecessaryTypeIgnoreComment = "error"

[tool.ruff]
# No line-length: ruff's default of 88, as in the other repositories behind looptrace.
target-version = "py311"

[tool.ruff.lint]
select = ["ALL"]
ignore = [
    # Missing members
    "ANN10",  # Deprecated: Missing type annotation for self/cls in (class)method
    "D105",  # Missing docstring in magic method
    "ANN204", # Missing return type annotation for special method
    
    # Opinionated syntax
    "D203", # Ignore this to instead opt for class body or docstring to possibly start right away under class.
    "D213", # Ignore this to instead opt for summary part of docstring to be on first physical line.
    "TRY003", # Avoid specifying long messages outside the exception class
    "C408",  # Unnecessary `dict` call (rewrite as a literal)
    "EM",  # Exception must not use a (f-)string literal, assign to variable first
    "FIX002",  # Line contains TODO, consider resolving the issue
    "D400",  # First line should end with a period
    "D415",  # First line should end with a period, question mark, or exclamation point
    "N818",  # Exception should be named with an Error suffix
    
    # Imports and type annotations
    "FA100",  # Missing `from __future__ import annotations`, but uses `typing.*`
    "TCH002",  # Move third-party import `...` into a type-checking block
    "TCH003",  # Move standard library import `...` into a type-checking block
    "UP007",  # Use `X | Y` for type annotations

    # Ruff recommends avoiding these checks when using `ruff format`. Since
    # `ruff format` is a drop-in replacement for `black`, we avoid the same
    # checks here (https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
    # has more details):
    "W191",  # tab-indentation
    "E111",  # indentation-with-invalid-multiple
    "E114",  # indentation-with-invalid-multiple-comment
    "E117",  # over-indented
    "D206",  # indent-with-spaces
    "D300",  # triple-single-quotes
    "Q000",  # bad-quotes-inline-string
    "Q001",  # bad-quotes-multiline-string
    "Q002",  # bad-quotes-docstring
    "Q003",  # avoidable-escaped-quote
    "COM812",  # missing-trailing-comma
    "COM819",  # prohibited-trailing-comma
    "ISC001",  # single-line-implicit-string-concatenation
    "ISC002",  # multi-line-implicit-string-concatenation
    "E501",  # line-too-long
]

[tool.ruff.lint.pydocstyle]
# numpydoc_decorator's @doc writes the docstring of the functions it decorates when the
# module is imported, so ruff, which only reads the source, doesn't see one. The setting
# applies only to functions and methods, so classes keep their `# noqa: D101`.
ignore-decorators = ["numpydoc_decorator.doc"]

[tool.ruff.lint.per-file-ignores]
"typings/*" = [
    # Stubs copy the signatures of third-party code, which we can't change.
    "FBT001",  # Boolean-typed positional argument in function definition
    "FBT002",  # Boolean default positional argument in function definition
    "PLR0913",  # Too many arguments in function definition
]
"tests/*" = [
    # Ignore some groups of checks in our test code.
    "ANN",  # Type annotations
    "D10",  # Missing docstrings
    "TCH00",  # Imports and type checking blocks
    "INP001", # File `...` is part of an implicit namespace package. Add an `__init__.py`.

    # Ignore some more specific checks in our test code.
    "D401",  # First line of docstring should be in imperative mood
    "N802",  # Function name `...` should be lowercase
    "S101",  # Use of `assert` detected
]