pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "readfish"
authors = [
    { name = "Alexander Payne" },
    { name = "Rory Munro", email = "rory.munro@nottingham.ac.uk" },
    { name = "Matt Loose", email = "matt.loose@nottingham.ac.uk"}
]
license = "MIT"
readme = "README.md"
requires-python = ">=3.8"
description = "ONT adaptive sampling"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: Implementation :: CPython",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = []
dependencies = [
    "minknow_api",
    "numpy",
    "cattrs",
    "rtoml",
    "more_itertools",
    'exceptiongroup ; python_version<"3.11"',
    "readfish_summarise >= 0.2.7",
    "readfish[all]",
]
dynamic = ["version"]

[project.scripts]
readfish = "readfish._cli_base:main"

[project.optional-dependencies]
# Development dependencies
docs = ["sphinx-copybutton", "furo", "myst-parser", "faqtory"]
tests = ["pytest", "coverage[toml]"]
tests-mappy = ["readfish[tests,mappy,dorado]"]
dev = ["readfish[all,docs,tests]", "pre-commit"]
# Running dependencies, this is a little bit clunky but works for now
mappy = ["mappy"]
mappy-rs = ["mappy-rs >= 0.0.6"]
dorado = ["ont-pybasecall-client-lib>=7.4.12"]
all = ["readfish[mappy,mappy-rs,dorado]"]

[project.urls]
Documentation = "https://looselab.github.io/readfish"
"Bug Tracker" = "https://github.com/LooseLab/readfish/issues"
"Source Code" = "https://github.com/LooseLab/readfish"

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.version]
path = "src/readfish/__about__.py"

[tool.black]
line-length = 88

[tool.ruff]
ignore = ["E501"]


[tool.pytest.ini_options]
testpaths = [
    "tests/*test.py",
    "src/readfish",
]
markers = [
    "alignment: marks tests which rely on loading or using Mappy or Mappy-rs aligners, used to test with both. (deselect with '-m \"not slow\", select with '-k alignment')",
]
addopts = ["-ra", "--doctest-modules", "--ignore=src/readfish/read_until/base.py"]

[tool.coverage.report]
omit = [
    "src/readfish/plugins/dorado.py",
    "src/readfish/_read_until_client.py",
    "src/readfish/plugins/guppy.py",
]