pyproject.toml

[tool.poetry]
name = "fcsjanitor"
version = "0.8.0"
description = "Clean up CyTOF FCS files as per the Standard Biotools recommendations"
authors = ["Miles Smith <miles-smith@omrf.org>"]
license = "GPL-3.0"
readme = "README.md"

[tool.poetry.dependencies]
python = "^3.10"
pytometry = "^0.1.2"
scanpy = "^1.9.1"
tqdm = "^4.66.1"
numpy = "^1.23.4"
loguru = "^0.7.2"
typer = "^0.9.0"
rich = "^13.6.0"
flowkit = "^1.0.1"

[tool.poetry.group.dev.dependencies]
black = "^23.9.1"
pytest = "^7.4.2"
mypy = "^1.0.0"
ruff = "^0.0.292"
types-python-dateutil = "^2.8.19.14"

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

[tool.poetry.scripts]
janitor = "fcsjanitor.cli:app"

[tool.mypy]
# mypy configurations: http://bit.ly/2zEl9WI
python_version = 3.10
pretty = true
allow_redefinition = false
check_untyped_defs = true
disallow_any_generics = true
disallow_incomplete_defs = true
follow_imports_for_stubs = false
ignore_missing_imports = false
implicit_reexport = false
strict_optional = true
strict_equality = true
no_implicit_optional = true
warn_no_return = true
warn_unused_ignores = true
warn_redundant_casts = true
warn_unused_configs = true
warn_return_any = true
warn_unreachable = true
show_error_codes = true
show_column_numbers = true
show_error_context = true

[tool.isort]
known_typing = "typing,types,typing_extensions,mypy,mypy_extensions"
sections = "FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER"
include_trailing_comma = true
default_section = "FIRSTPARTY"
multi_line_output = 3
indent = 4
force_grid_wrap = 0
use_parentheses = true
line_length = 80

[tool.black]
line-length = 120
target-version = ["py310"]
skip-string-normalization = true

[tool.ruff]
target-version = "py310"
line-length = 120
select = [
    "A",
    "ARG",
    "B",
    "C",
    "DTZ",
    "E",
    "EM",
    "F",
    "FBT",
    "I",
    "I001",
    "ICN",
    "ISC",
    "N",
    "PLC",
    "PLE",
    "PLR",
    "PLW",
    "Q",
    "RUF",
    "S",
    "T",
    "TID",
    "UP",
    "W",
    "YTT",
]
# E127, E128 are hard to silence in certain nested formatting situations.
# E265, E266 talk about comment formatting which is too opinionated.
# E402 warns on imports coming after statements. There are important use cases
# like demandimport (https://fburl.com/demandimport) that require statements
# before imports.
# E501 is not flexible enough, we're using B950 instead.
# E722 is a duplicate of B001.
# P207 is a duplicate of B003.
# W503 talks about operator formatting which is too opinionated.
# E203 conflicts with Black
ignore = [
    "B027",
    "E265",
    "E266",
    "E402",
    "E501",
    "E722",
    "E203",
    "E241",
    "FBT003",
    "S105",
    "S106",
    "S107",
    "C901",
    "PLR0911",
    "PLR0912",
    "PLR0913",
    "PLR0915",
]
unfixable = [
    "F401",
    "UP007",
]
exclude = [
    ".git",
    ".hg",
    "__pycache__",
    "_bin/*",
    "_build/*",
    "_ig_fbcode_wheel/*",
    "buck-out/*",
    "third-party-buck/*",
    "third-party2/*",
    "dist",
    ".venv",
    ".nox",
    ".mypy_cache",
    ".pytype",
    ".svn",
    "__pypackages__",
]
src = ["src"]

[tool.ruff.mccabe]
max-complexity = 50

[tool.ruff.isort]
known-first-party = ["readcounts"]

[tool.ruff.flake8-tidy-imports]
ban-relative-imports = "all"