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setup.cfg
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setup.cfg
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[metadata]
name = gambit
description = Genomic Approximation Method for Bacterial Identification and Tracking
version = attr: gambit.__version__
author = Jared Lumpe
author_email = jared@jaredlumpe.com
url = http://github.com/jlumpe/gambit
license = AGPL-3.0-or-later
license_file = LICENSE
[options]
packages = find:
zip_safe = false
include_package_data = true
python_requires = >= 3.7
install_requires =
numpy~=1.13
sqlalchemy~=1.1
biopython~=1.79
alembic~=1.0
attrs>=20
cattrs~=1.0
click>=7.0
h5py~=3.0
scipy~=1.7
tests_require =
pytest
[options.entry_points]
console_scripts =
gambit = gambit.cli:cli
# Aliases for setuptools commands
[aliases]
test = pytest
# Pytest settings
[tool:pytest]
# Run tests in tests/, obviously
# Also check docstrings in package
testpaths = tests gambit
# Run doctests on all modules (except __main__.py and alembic config directory)
addopts = --doctest-modules --ignore-glob "**/__main__.py" --ignore "gambit/db/migrate/alembic/"
doctest_optionflags = NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
# Treat functions/classes prefixed with "benchmark" as tests, for files in tests/benchmarks/.
python_functions = test_* benchmark_*
python_classes = Test* Benchmark*
# Custom markers
markers =
testdb_nqueries: number of query files from test database to use when testing CLI.
# Flake8 settings
[flake8]
# Ignore these codes:
ignore =
# TABS ARE BETTER
W191,
# indentation contains mixed spaces and tabs - spaces for alignment
E101,
# Blank line at end of file - we require this in .editorconfig
W391
# Exclude these paths:
exclude = docs
# Check style of doctests (not working?)
doctests = True