pyproject.toml

[tool.poetry]
name = "dcicpyvcf"
version = "3.1.0"
description = "Variant Call Format (VCF) parser for Python"
# A VCFv4.0 and 4.1 parser for Python."
# Online version of PyVCF documentation is available at http://pyvcf.rtfd.org/
authors = ["4DN-DCIC Team <support@4dnucleome.org>"]  # Forked
license = "MIT"
readme = "README.rst"
keywords = ["dcicpyvcf", "pyvcf", "vcf"]
homepage = "https://github.com/4dn-dcic/PyVCF"
repository = "https://github.com/4dn-dcic/PyVCF.git"
packages = [
  { include="vcf", from="." }
]

classifiers = [
  # How mature is this project? Common values are
  #   3 - Alpha
  #   4 - Beta
  #   5 - Production/Stable
  'Development Status :: 4 - Beta',

  # Indicate who your project is intended for
  'Intended Audience :: Developers',
  'Intended Audience :: Science/Research',

  'Topic :: Scientific/Engineering :: Bio-Informatics',

  # Pick your license as you wish (should match "license" above)
  'License :: OSI Approved :: BSD License',
  'License :: OSI Approved :: MIT License',

  # Yeah, this is just English
  'Natural Language :: English',

  # Specify the Python versions you support here. In particular, ensure
  # that you indicate whether you support Python 2, Python 3 or both.
  'Programming Language :: Cython',
  '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 :: 3.12',

  'Programming Language :: Python :: Implementation :: CPython',
  'Programming Language :: Python :: Implementation :: PyPy',

  'Operating System :: OS Independent',
]
include = [
  "LICENSE",
]

[tool.poetry.dependencies]

python = ">=3.8.0,<3.13"

cython = "*"
pysam = "^0.22.1"
setuptools = "*"

[tool.poetry.dev-dependencies]

# Coverage
codacy-coverage = ">=1.3.11"
coverage = ">=6.5.0"

# Linting generally
flake8 = ">=3.9.2"

# pygments is used by PyCharm
pygments = ">=2.14.0"

# PyTest and its auxiliary support files
pytest = ">=7.2.1"  # ">=6.2.5"
pytest-cov = ">=4.0.0"  # "2.12.1" # >=
pytest-mock = ">=3.10.0"  # 3.6.1"  # >=
pytest-runner = ">=6.0.0"  # "5.3.1"  # >=

# Docs build dependencies
sphinx = ">=3.5.4"  # should be 5.1.1?
sphinx-rtd-theme = ">=1.2.0"

[tool.poetry.scripts]

# make-sample-fastq-file = "submit_cgap.scripts.make_sample_fastq_file:main"

[tool.coverage.report]

# https://coverage.readthedocs.io/en/latest/config.html
exclude_lines = [
  "if __name__ == .__main__.:",
  "pragma: no cover"
]

[build-system]

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