pyproject.toml

[tool.black]
line-length = 99
target-version = ['py38']
exclude = '''
/(
    \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''

[tool.isort]
profile = "hug"
src_paths = ["glotaran"]
include_trailing_comma = true
line_length = 99
known_first_party = ["glotaran"]
force_single_line = true
remove_redundant_aliases = true

[tool.interrogate]
exclude = ["setup.py", "docs", "*test/*", "benchmark/*"]
ignore-init-module = true
fail-under = 63

[tool.nbqa.addopts]
flake8 = ["--extend-ignore=E402,F404"]


[tool.coverage.run]
branch = true
omit = [
  'setup.py',
  '*/tests/*',
  '*/test/*',
  # comment the above line if you want to see if all tests did run
]

[tool.coverage.report]
# Regexes for lines to exclude from consideration
exclude_lines = [
  # Have to re-enable the standard pragma
  'pragma: no cover',

  # Don't complain about missing debug-only code:
  'def __repr__',
  'if self\.debug',

  # Don't complain if tests don't hit defensive assertion code:
  'raise AssertionError',
  'raise NotImplementedError',

  # Don't complain if non-runnable code isn't run:
  'if 0:',
  'if __name__ == .__main__.:',
  'if TYPE_CHECKING:',
]

[tool.check-manifest]
ignore = [
  "benchmark/**/*",
  "binder/**/*",
  "docs/**/*",
  "*/.pytest_cache/**/*",
  "*/.mypy_cache/**/*",
  ".git-blame-ignore-revs",
  ".gitignore",
  ".pre-commit-config.yaml",
  ".sonarcloud.properties",
  ".sourcery.yaml",
  ".zenodo.json",
  "codecov.yml",
  "flake.nix",
  "flake.lock",
  "INSTALLATION.md",
  "readthedocs.yml",
  "requirements_dev.txt",
  "tox.ini",
  ".gitmodules",
  # This is just a file on the CI if not check out with git submodules option
  "validation",
]


[tool.mypy]
ignore_missing_imports = true
scripts_are_modules = true
show_error_codes = true
warn_unused_configs = true
warn_unused_ignores = true
check_untyped_defs = true

[[tool.mypy.overrides]]
module = "glotaran.builtin.megacomplexes.*"
ignore_errors = true

[[tool.mypy.overrides]]
# Should be rewritten anyway see #1171
module = "glotaran.builtin.io.ascii.*"
ignore_errors = true

[[tool.mypy.overrides]]
module = "glotaran.cli.*"
ignore_errors = true

[[tool.mypy.overrides]]
module = "benchmark.*"
ignore_errors = true

[tool.codespell]
ignore-words-list = "projectio"