setup.cfg

[metadata]
name = gecco-tool
version = attr: gecco.__version__
author = Martin Larralde
author_email = martin.larralde@embl.de
url = https://gecco.embl.de
description = Gene cluster prediction with Conditional random fields.
long_description = file: README.md
long_description_content_type = text/markdown
license = GPL-3.0-only
platform = x86, x86_64, powerpc, ppc64
classifiers =
  Development Status :: 3 - Alpha
  Intended Audience :: Science/Research
  License :: OSI Approved :: GNU General Public License v3 (GPLv3)
  Operating System :: POSIX
  Programming Language :: Python :: 3 :: Only
  Programming Language :: Python :: 3.7
  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
  Topic :: Scientific/Engineering :: Bio-Informatics
  Topic :: Scientific/Engineering :: Medical Science Apps.
  Typing :: Typed
project_urls =
  Repository = https://github.com/zellerlab/GECCO
  Bug Tracker = https://github.com/zellerlab/GECCO/issues
  Changelog = https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md
  Coverage = https://codecov.io/gh/zellerlab/GECCO/
  Builds = https://git.embl.de/grp-zeller/GECCO/-/pipelines
  Preprint = https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1

[options]
zip_safe = false
packages = find:
include_package_data = true
python_requires = >=3.7
setup_requires =
  setuptools >=39.2
  rich >=12.4.0
  pyhmmer ~=0.10.0
  wheel >=0.30
  pronto ~=2.2
install_requires =
  biopython ~=1.73
  docopt ~=0.6.2
  importlib-metadata >=4.0      ; python_version < '3.10'
  importlib-resources >=1.0     ; python_version < '3.9'
  numpy ~=1.16
  polars >=0.16,<0.21
  psutil ~=5.8
  pyhmmer ~=0.10.0
  pyrodigal ~=3.0
  rich >=12.4.0
  scikit-learn ~=1.0
  scipy ~=1.4
  sklearn-crfsuite ~=0.3.6

[options.extras_require]
train =
  fisher ~=0.1.10
  statsmodels >=0.13,<0.15

[options.packages.find]
include =
  gecco
  gecco.cli
  gecco.cli.commands
  gecco.crf
  gecco.hmmer
  gecco.interpro
  gecco.types

[options.package_data]
gecco = _version.txt, py.typed

[options.entry_points]
gecco.cli.commands =
  annotate = gecco.cli.commands.annotate:Annotate
  convert = gecco.cli.commands.convert:Convert
  cv = gecco.cli.commands.cv:Cv                    [train]
  run = gecco.cli.commands.run:Run
  train = gecco.cli.commands.train:Train           [train]
  help = gecco.cli.commands.help:Help
  predict = gecco.cli.commands.predict:Predict
console_scripts =
  gecco = gecco.cli:main

[bdist_wheel]
universal = true

[coverage:report]
include = gecco/*
show_missing = true
exclude_lines =
  pragma: no cover
  if typing.TYPE_CHECKING:
  @abc.abstractmethod
  @abc.abstractproperty
  raise NotImplementedError
  return NotImplemented

[green]
file-pattern = test_*.py
verbose = 2
no-skip-report = true
quiet-stdout = true
run-coverage = true

[pydocstyle]
match-dir = (?!tests)(?!resources)(?!docs)[^\.].*
match = (?!test)(?!setup)[^\._].*\.py
inherit = false
ignore = D200, D203, D213, D402, D406, D407   # Google conventions

[flake8]
max-line-length = 99
doctests = True
ignore = D200, D203, D213, D406, D407, Q000  # Google conventions
exclude =
  .git
  .eggs
  ci/
  scripts/
  notebook/
  tests/
  docs/
  */build/
  */setup.py

[mypy]
disallow_any_decorated = true
disallow_any_generics = true
disallow_any_unimported = false
disallow_subclassing_any = false
disallow_untyped_calls = true
disallow_untyped_defs = true
ignore_missing_imports = true
warn_unused_ignores = true
warn_return_any = true