pyproject.toml

[tool.poetry]
name = "gertils"
version = "0.6.1"
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 :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "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 = ">=3.10.0,<3.13"
dask = "^2023.5.1"
numpy = "^1.24.2"
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"
mypy = "1.0.1"
nox = "^2022.11.21"
pydantic = "^1.10.4"
pytest = "^7.1.0"
pytest-cov = "^5.0.0"
ruff = ">=0.3"

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

[tool.poetry.group.format.dependencies]
codespell = "^2.2.2"
ruff = ">=0.3"

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

[tool.poetry.group.lint.dependencies]
hypothesis = "^6.68.2"
mypy = "^1.0.1"
nox = "^2022.11.21"
pydantic = "^1.10.4"
pytest = "^7.1.0"
ruff = ">=0.3"

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

[tool.poetry.group.nox.dependencies]
nox = "^2022.11.21"

[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,.mypy_cache,.nox,.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.mypy]
files = ['*.py', 'gertils/*.py', 'tests/*.py']
plugins = ["pydantic.mypy"]
warn_redundant_casts = true
warn_unused_ignores = true
warn_return_any = true
warn_unreachable = true
enable_error_code = ["ignore-without-code"]

[[tool.mypy.overrides]]
module = "gertils.*"
disallow_untyped_defs = true
disallow_untyped_calls = true
disallow_incomplete_defs = true
check_untyped_defs = true
disallow_any_unimported = true
disallow_any_explicit = true
disallow_any_generics = true
disallow_subclassing_any = true
implicit_optional = false
strict_optional = true

[tool.ruff]
# Black uses line-length = 88, but allows exceptions when breaking the line
# would lead to other rule violations. Use 100 as a maximum hard limit:
line-length = 100
target-version = "py310"

[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.per-file-ignores]
"gertils/__init__.py" = [
    "F401",  # import unused
]
"noxfile.py" = [
    # The noxfile is dev-only; we don't care much about form.
    "ANN",  # Missing type annotations
    "D",  # Missing docstrings
]
"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
]