pyproject.toml

[tool.poetry]
name = "fcsparser"
version = "0.2.8"
description = "A python package for reading raw fcs files"
authors = ["Eugene Yurtsev <eyurtsev@gmail.com>"]
license = "MIT"
readme = "README.rst"
repository = "https://github.com/eyurtsev/fcsparser"
keywords = ["flow cytometry", "data analysis", "cytometry", "parser", "data"]
classifiers = [
  "Intended Audience :: Science/Research",
  "Programming Language :: Python :: 3",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Topic :: Scientific/Engineering :: Medical Science Apps.",
]

[tool.poetry.dependencies]
python = "^3.8.0"
pandas = ">=1.5.3"
numpy = "^1"

[tool.poetry.group.dev.dependencies]
jupyterlab = "^3"

[tool.poetry.group.test.dependencies]
pytest = "^7.4.2"
black = { version = "^23.1.0", extras = ["jupyter"] }
poethepoet = "^0.18.1"
ruff = "^0.0.292"
pytest-cov = "^4.1.0"

[tool.poetry.group.typing.dependencies]
mypy = "^0.991"

[tool.poe.tasks]
black = "black"
ruff = "ruff"
pytest.cmd = "py.test --durations=5 -W error::RuntimeWarning --cov --cov-config=.coveragerc --cov-report xml --cov-report term-missing:skip-covered"
mypy = "mypy . --pretty --show-error-codes"
fix = { shell = "poe black . && poe ruff --fix ." }
fix_docs = "black docs"
# Using a --preview feature. Commit your code prior to use this fix.
fix_strings = "black kor --preview"
test = { shell = "poe black . --check --diff && poe ruff . && poe pytest && poe mypy" }
# Use to auto-generate docs
apidoc = "sphinx-apidoc -o docs/source/generated kor"

[tool.ruff]
select = [
  "E", # pycodestyle
  "F", # pyflakes
  "I", # isort
]

# Same as Black.
line-length = 88

[tool.mypy]
disallow_untyped_defs = "True"
ignore_missing_imports = "True"

[tool.coverage.run]
omit = ["tests/*"]


[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"