setup.cfg

[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_files = LICENSE

[options]
packages = find:
package_dir =
	=src
zip_safe = false
include_package_data = true

python_requires = >= 3.9

install_requires =
	# Test failures on 2.x
	numpy ~= 1.13
	sqlalchemy >= 1.4
	# Seq stores data as bytes
	biopython ~= 1.79
	attrs >= 20
	# Minimum for 3.12, also introduces potentially breaking changes
	cattrs >= 23.2
	click >= 7.0
	h5py ~= 3.0
	scipy ~= 1.7
	typing-extensions >= 4.0

tests_require =
	pytest


[options.packages.find]
where = src


[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)
addopts = --doctest-modules --ignore-glob "**/__main__.py"
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*


# 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