pyproject.toml

[project]
name = "looptrace-loci-vis"
dynamic = ["version"]
requires-python = ">= 3.10, < 3.13"
authors = [
    {name = "Vince Reuter"}
]
description = "This project facilitates viewing, in `napari`, locus-specific spots from `looptrace`."
readme = "README.md"
license = {file = "LICENSE"}
keywords = ["visualisation", "bioinformatics", "chromatin", "napari", "FISH"]
classifiers = [
    "Development Status :: 1 - Planning",
    "License :: OSI Approved :: MIT License",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Typing :: Typed",
]
dependencies = [
    "gertils @ git+https://github.com/gerlichlab/gertils.git@v0.5.1",
    "napari >= 0.4.19; sys_platform == 'darwin'",
    "napari[all] >= 0.4.19; sys_platform != 'darwin'",
    "numpy",
    "numpydoc_decorator >= 2.2.1",
    "pandas",
    "pyqt6 >= 6.5.0; sys_platform == 'darwin'",
    "zarr >= 2.4.12",
]

[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project.urls]
Homepage = "https://github.com/gerlichlab/looptrace-loci-vis"
Repository = "https://github.com/gerlichlab/looptrace-loci-vis.git"
Issues = "https://github.com/gerlichlab/looptrace-loci-vis/issues"

[tool.setuptools.dynamic]
version = { attr = "looptrace_loci_vis.__version__" }

[tool.setuptools.package-data]
looptrace_loci_vis = [ "napari.yaml", "examples/*.csv" ]

[project.entry-points."napari.manifest"]
looptrace-loci-vis = "looptrace_loci_vis:napari.yaml"

[project.optional-dependencies]
formatting = [
    "codespell >= 2.2.4",
    "ruff >= 0.8.0",
]
linting = [
    "mypy >= 1.0.1",
    "pandas-stubs",
    "ruff >= 0.8.0",
]
testsuite = [
    "npe2",
    "pytest >= 7.1.0",
    "pytest-cov >= 5.0.0",
    "typer",
]

[tool.codespell]
skip = ".git,.mypy_cache,.nox,.vscode,__pycache__,poetry.lock"
builtin = "clear,rare,informal,usage,code,names"
ignore-words-list = "jupyter,iff"
check-filenames = true
uri-ignore-words-list = "*"

[tool.mypy]
files = ['looptrace_loci_vis/*.py']
warn_redundant_casts = true
warn_unused_ignores = true
warn_return_any = true
warn_unreachable = true

[[tool.mypy.overrides]]
module = "looptrace_loci_vis.*"
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.pytest.ini_options]
addopts = "-vv --cov looptrace_loci_vis --cov-report term-missing"

[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
    "PLR0913", # Too many arguments in function definition
    "D401", # First line of docstring should be in imperative mood
    "PLC0105", # This suggests suffixing a type variable with variance type (e.g., co/contra)

    # Imports and type annotations
    "ANN003",  # Missing type annotation for kwargs
    "FA100",  # Missing `from __future__ import annotations`, but uses `typing.*`
    "TC002",  # Move third-party import `...` into a type-checking block
    "TC003",  # 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

    # Other
    "PLR0912",  # too many branches (of a conditional)
    "TD002",  # missing author in TODO
    "C901", # function too complex
    "PLR0911", # too many return statements
]

[tool.ruff.lint.per-file-ignores]
"tests/*" = [
    # Ignore some groups of checks in our test code.
    "ANN",  # Type annotations
    "D10",  # Missing docstrings
    "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
]