pyproject.toml

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

[project]
dynamic= ["version"]
name = "picasso_workflow"
description = "Automation and documentation of DNA-PAINT analysis workflows"
license = {'file' = "LICENSE"}
requires-python = ">=3.10"
dependencies = [
    "matplotlib",
    "seaborn",
    "numpy",
    "pandas",
    "tables",
    "openpyxl==3.1.2",
    "picassosr",
    "moviepy==1.0.3",
    "python-dotenv==1.0.1",
    "pre-commit>=3.5.1",
    "bandit==1.7.8",
    "coverage==7.4.4",
    "pytest==8.1.1",
    "isort==5.13.2",
    "aicspylibczi>=3.1.1",
    "fsspec>=2022.8.0",
    "aicsimageio",
    "psutil",
]
keywords = ["picasso"]

[tool.setuptools]
packages = ["picasso_workflow"]

[tool.black]
line-length = 79
include = "\\.pyi?$"
exclude = '''
/(
    \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''

[tool.mypy]
strict = true

[tool.flake8]
max-line-length = 88
exclude = ".tox,.git,__pycache__,docs"
ignore = "E203,W503"
select = "C,E,F,W,B,B9,I"
# C: complexity
# E: pycodestyle errors
# F: pyflakes errors
# W: pycodestyle warnings
# B: bugbear errors
# B9: bugbear warnings
# I: isort errors
# Plugins
require-code = "True"
ban-relative-imports = "True"
docstring-convention = "google"
# flake8-bugbear
# flake8-eradicate
# flake8-docstrings

[tool.bandit]
exclude = "/tests"
skips = "B105,B404"
baseline = "bandit-baseline.json"
format = "txt"

[tool.pytest-cov]
[pytest-cov.run]
branch = "True"
[pytest-cov.report]
fail_under = 80

[tool.pytest.ini_options]
minversion = "6.0"
addopts = "-ra -q"
testpaths = ["picasso_workflow/tests"]