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setup.cfg
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setup.cfg
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[metadata]
name = sgkit
author = sgkit Developers
author_email = [email protected]
license = Apache
description = Statistical genetics toolkit
long_description_content_type=text/x-rst
long_description =
**sgkit** is an open source project for analyzing and manipulating genetic
variation data.
url = https://github.com/sgkit-dev/sgkit
classifiers =
Development Status :: 3 - Alpha
License :: OSI Approved :: Apache Software License
Operating System :: OS Independent
Intended Audience :: Science/Research
Programming Language :: Python
Programming Language :: Python :: 3
Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.11
Programming Language :: Python :: 3.12
Topic :: Scientific/Engineering
[options]
packages = sgkit
zip_safe = False # https://mypy.readthedocs.io/en/latest/installed_packages.html
include_package_data = True
python_requires = >=3.9
install_requires =
numpy < 2
xarray
dask[array] >= 2022.01.0, <= 2024.8.0
distributed >= 2022.01.0, <= 2024.8.0
dask-ml
scipy
zarr >= 2.10.0, != 2.11.0, != 2.11.1, != 2.11.2, < 3
numba
typing-extensions
fsspec != 2021.6.*
scikit-learn
pandas
setuptools >= 41.2 # For pkg_resources
setup_requires =
setuptools >= 41.2
setuptools_scm
[options.extras_require]
# For plink we need dask[dataframe], we already have
# dask[array] in install_requires, and since
# https://github.com/pypa/pip/issues/4957, pip
# will essentially ignore dask[dataframe] in the extras.
# We can workaround this by either adding pip flag
# --use-feature 2020-resolver, or installing
# dask[dataframe] in the install_requires, or just listing
# the 2 missing dependencies from dataframe, the way we do
# here, when pip finally gets a resolver, this won't be
# a problem. Here we opt for listing the 2 dependencies
# since this is the least user invasive solution.
plink =
partd
bed-reader
bgen =
rechunker
cbgen < 1.0.5; platform_system != "Windows"
cbgen == 1.0.1; platform_system == "Windows"
[coverage:report]
fail_under = 100
[tool:pytest]
addopts = --doctest-modules --ignore=validation --cov-fail-under=100
norecursedirs = .eggs build docs
filterwarnings =
error
ignore::DeprecationWarning
[flake8]
ignore =
# whitespace before ':' - doesn't work well with black
E203
E402
# line too long - let black worry about that
E501
# do not assign a lambda expression, use a def
E731
# line break before binary operator
W503
[isort]
profile = black
default_section = THIRDPARTY
known_first_party = sgkit
known_third_party = allel,dask,fire,glow,hail,hypothesis,invoke,msprime,numba,numpy,pandas,pkg_resources,pyspark,pytest,setuptools,sgkit_plink,sklearn,sphinx,typing_extensions,xarray,yaml,zarr
multi_line_output = 3
include_trailing_comma = True
force_grid_wrap = 0
use_parentheses = True
line_length = 88
[mypy-callee.*]
ignore_missing_imports = True
[mypy-dask.*]
ignore_missing_imports = True
[mypy-fsspec.*]
ignore_missing_imports = True
[mypy-dask_ml.*]
ignore_missing_imports = True
[mypy-numpy.*]
ignore_missing_imports = True
[mypy-pandas.*]
ignore_missing_imports = True
[mypy-numba.*]
ignore_missing_imports = True
[mypy-pytest.*]
ignore_missing_imports = True
[mypy-statsmodels.*]
ignore_missing_imports = True
[mypy-hypothesis.*]
ignore_missing_imports = True
[mypy-zarr.*]
ignore_missing_imports = True
[mypy-numcodecs.*]
ignore_missing_imports = True
[mypy-setuptools]
ignore_missing_imports = True
[mypy-sklearn.*]
ignore_missing_imports = True
[mypy-cbgen.*]
ignore_missing_imports = True
[mypy-rechunker.*]
ignore_missing_imports = True
[mypy-bed_reader.*]
ignore_missing_imports = True
[mypy-sphinx.*]
ignore_missing_imports = True
[mypy-yarl.*]
ignore_missing_imports = True
[mypy-allel.*]
ignore_missing_imports = True
[mypy-networkx.*]
ignore_missing_imports = True
[mypy-toolz.*]
ignore_missing_imports = True
[mypy-scipy.*]
ignore_missing_imports = True
[mypy-sgkit.*]
allow_redefinition = True
[mypy-sgkit.*.tests.*]
disallow_untyped_calls = False
disallow_untyped_defs = False
disallow_untyped_decorators = False
[mypy-validation.*]
ignore_errors = True