pyproject.toml

[tool.poetry]
name = "azimuth"
version = "4.1.0"
description = "Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency"
authors = ["Miles Smith <mileschristiansmith@gmail.com>"]
license = "BSD 3-clause"
homepage = "https://github.com/milescsmith/azimuth"
classifiers =[
    "Development Status::4 - Beta",
    "Intended Audience::Developers",
    "License             ::OSI Approved:: BSD-3",
    "Programming Language::Python::3.6",
    "Programming Language::Python::3.7",
]
include = ["azure_modules/*.pickle", "data/*"]
keywords = ["CRISPR"]

[tool.poetry.dependencies]
python = ">=3.10,<3.11"
GPy = {git = "https://github.com/KOLANICH-ML/GPy", branch = "pyproject.toml"}
biopython = "^1.81"
scipy = "^1.11"
scikit-learn = "^1.3"
pandas = "^2.1"
hyperopt = "^0.2"
paramz = {git = "https://github.com/MartinBubel/paramz.git", branch = "fix-numpy-types"}
dill = "^0.3"
theanets = {git = "https://github.com/lmjohns3/theanets"}
# Cython = "^0.29.24"
typer = "^0.9"
openpyxl = "^3.1"
loguru = "^0.7.2"
rich = "^13.7.0"
better-exceptions = "^0.3.3"

[tool.poetry.group.dev.dependencies]
Sphinx = "^7.2"
MonkeyType = "^23.3"
pytest = "^7.4"
ruff = "^0.1"
mypy = "^1.7"
sourcery = "^1.14"
black = "^23.11"
sphinx-autodoc-typehints = "^1.25.2"

[tool.poetry.scripts]
"azimuth" = "azimuth.__main__:app"

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

[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",
]
ignore = [
    "B027",
    "UP007",
    "FBT001",
    "FBT002",
    "FBT003",
    "N802",
    "N803",
    "N806",
    "S105",
    "S106",
    "S107",
    "C901",
    "PLR0911",
    "PLR0912",
    "PLR0913",
    "PLR0915",
    "PLR2004",
]
unfixable = [
    "F401",
]
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.flake8-tidy-imports]
ban-relative-imports = "all"

# mypy global options:

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
exclude = [
    '^file1\.py$',  # TOML literal string (single-quotes, no escaping necessary)
    "^file2\\.py$",  # TOML basic string (double-quotes, backslash and other characters need escaping)
]
follow_imports = false
follow_imports_for_stubs = true
warn_unreachable = true
pretty = true
ignore_missing_imports = true