pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling", "hatch-vcs>=0.3", "setuptools-scm>=7.1"]

[project]
authors = [
  {name = "Jannes Spangenberg", email = "jannes.spangenberg@uni-jena.de"}
]
classifiers = [
  "Programming Language :: Python",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
  "Intended Audience :: Science/Research"
]
dependencies = [
  "numpy >=1.26.0",
  "pandas >=2.2.0",
  "seaborn >=0.13.0",
  "matplotlib >=3.2.0",
  "read5_ont >=1.2.5",
  "pysam >=0.22.0",
  "psutil >=6.0.0",
]
description = "Segmentation/resquiggling tool for ONT signals."
dynamic = ["version"]
license = {text = "GNUv3"}
name = "dynamont"
readme = "README.md"
requires-python = ">=3.10"

[project.optional-dependencies]
test = [
  "pytest",
  "pytest-cov",
  "mypy"
]

[project.scripts]
dynamont-resquiggle = "src.python.segmentation.segment:main"
dynamont-train = "src.python.segmentation.train:main"

[project.urls]
repository = "https://github.com/JannesSP/dynamont"

[tool.coverage.report]
exclude_lines = [
  "pragma: no cover",
  # This covers both typing.TYPE_CHECKING and plain TYPE_CHECKING, with any amount of whitespace
  "if\\s+(typing\\.)?TYPE_CHECKING:",
  'if __name__ == "__main__":'
]
omit = [
  "src/python/_version.py",
  "test/*"
]

[tool.distutils.bdist_wheel]
universal = true

[tool.hatch.build.hooks.vcs]
version-file = "src/python/_version.py"

[tool.hatch.build.targets.wheel]
packages = ["src"]

[tool.hatch.build.targets.sdist]
include = [
  "src/python",
  "pyproject.toml",
  "README.rst",
  "LICENSE"
]

[tool.hatch.version]
source = "vcs"

[tool.mypy]
disallow_untyped_defs = true
files = ["src/python/**/*.py"]
python_version = "3.10"
warn_no_return = true

[tool.pytest.ini_options]
addopts = [
  "-vv",
  "--color=yes",
  "--cov-append",
  "--cov-branch",
  "--cov-report=term-missing",
  "--cov=src/python",
  "--tb=native",
  "--strict-markers",
  "--durations=20"
]
markers = [
  "serial: execute test serially (to avoid race conditions)",
  "slow: tests can take a long time (deselect with '-m \"not slow\"')"
]
norecursedirs = [".*", "*.egg*", "build", "dist", "conda.recipe", "examples", "env", "envs", "scripts"]