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setup.cfg
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setup.cfg
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# This file is used to configure your project.
# Read more about the various options under:
# http://setuptools.readthedocs.io/en/latest/setuptools.html#configuring-setup-using-setup-cfg-files
[metadata]
name = mbf
description = Functionality for genomics
version = 0.3
author = Florian Finkernagel
author-email = [email protected]
license = mit
url = https://github.com/TyberiusPrime/mbf
long-description = file: README.md
long_description_content_type = text/markdown
# Change if running only on Windows, Mac or Linux (comma-separated)
platforms = any
# Add here all kinds of additional classifiers as defined under
# https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers =
Development Status :: 4 - Beta
Programming Language :: Python
[options]
zip_safe = False
packages = find:
include_package_data = True
package_dir =
=src
# DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
#setup_requires = pyscaffold>=3.1a0,<3.2a0
# Add here dependencies of your project (semicolon/line-separated), e.g.
install_requires =
attrs
bitarray
cutadapt
cython
dppd_plotnine
feather-format
matplotlib-venn
matplotlib-venn
mbf_bam
mbf_gtf
mbf-nested-intervals
natsort
numpy
openpyxl
ordered-set
pandas
plotnine
pyBigWig
pypipegraph
pypipegraph2
pysam
requests
scipy
scikit-learn
statsmodels
tabulate
toml
venn
xlrd
xlwt
#rpy2 # will explode anysnake...
# The usage of test_requires is discouraged, see `Dependency Management` docs
# tests_require = pytest; pytest-cov
# Require a specific Python version, e.g. Python 2.7 or >= 3.4
python_requires = >=3.8
[options.packages.find]
where = src
exclude =
tests
[options.extras_require]
testing =
pytest
pytest-cov
pytest-icdiff
requests-mock
doc =
sphinx
sphinx-bootstrap-theme
numpydoc
[options.entry_points]
console_scripts =
scb_submit = mbf.publish.scb_submit:main
[test]
# py.test options when running `python setup.py test`
# addopts = --verbose
extras = True
[tool:pytest]
# Options for py.test:
# Specify command line options as you would do when invoking py.test directly.
# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
# in order to write a coverage file that can be read by Jenkins.
# --cov-config=.coverage_rc
addopts =
--cov-report term-missing
--verbose
norecursedirs =
dist
build
.tox
testpaths = tests
filterwarnings =
ignore::DeprecationWarning:rpy2.rinterface_lib.sexp:283
ignore::DeprecationWarning:jinja2.utils:485
ignore::DeprecationWarning:jinja2.runtime:318
[aliases]
build = bdist_wheel
release = build upload
[bdist_wheel]
# Use this option if your package is pure-python
universal = 1
[build_sphinx]
source_dir = docs
build_dir = docs/_build
[devpi:upload]
# Options for the devpi: PyPI server and packaging tool
# VCS export must be deactivated since we are using setuptools-scm
no-vcs = 1
formats = bdist_wheel
[flake8]
# Some sane defaults for the code style checker flake8
exclude =
.tox
build
dist
.eggs
docs/conf.py
max-line-length = 88
max-complexity = 21
ignore = E501,W504,W503,E402,E203,E713
select = C,E,F,W,B,B901