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setup.cfg
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##########################
# Setup.py Configuration #
##########################
[metadata]
name = pathme
version = 0.1.14-dev
description = Harmonizing pathway databases using Biological Expression Language (BEL)
long_description = file: README.rst
# URLs associated with the project
url = https://github.com/PathwayMerger/PathMe
download_url = https://pypi.org/project/pathme/
project_urls =
Bug Tracker = https://github.com/PathwayMerger/PathMe/issues
Source Code = https://github.com/PathwayMerger/PathMe
Documentation = https://pathme.readthedocs.io/en/latest/
# Author information
author = Daniel Domingo-Fernández, Sarah Mubeen, Josep Marin Llao, Charles Tapley Hoyt
author_email = [email protected]
maintainer = Daniel Domingo-Fernández
maintainer_email = [email protected]
# License Information
license = Apache 2.0 License
license_file = LICENSE
# Search tags
classifiers =
Development Status :: 4 - Beta
Environment :: Console
Intended Audience :: Developers
Intended Audience :: Science/Research
License :: OSI Approved :: Apache Software License
Operating System :: OS Independent
Programming Language :: Python
Programming Language :: Python :: 3.7
Programming Language :: Python :: 3 :: Only
Topic :: Scientific/Engineering :: Bio-Informatics
keywords =
Pathway Databases
Systems Biology
Networks Biology
Biological Expression Language
[options]
install_requires =
click==7.0
pandas
tqdm
numpy
diffupath
rdflib==4.2.2
bio2bel==0.2.1
bio2bel_hgnc==0.2.2
bio2bel_chebi==0.2.1
bio2bel_kegg==0.2.5
bio2bel_wikipathways==0.2.3
bio2bel_reactome==0.2.3
compath_utils==0.2.1
pybel==0.13.2
pybel-tools>=0.7.2
pybel-cx==0.1.3
# Random options
zip_safe = false
include_package_data = True
python_requires = >=3.7
# Where is my code
packages = find:
package_dir =
= src
[options.packages.find]
where = src
[options.extras_require]
docs =
sphinx
sphinx-rtd-theme
sphinx-click
sphinx-autodoc-typehints
[options.entry_points]
console_scripts =
pathme = pathme.cli:main
######################
# Doc8 Configuration #
# (doc8.ini) #
######################
[doc8]
max-line-length = 120
##########################
# Coverage Configuration #
# (.coveragerc) #
##########################
[coverage:run]
branch = True
source = pathme
omit =
src/pathme/__main__.py
src/pathme/cli.py
tests/*
docs/*
[coverage:paths]
source =
src/pathme
.tox/*/lib/python*/site-packages/pathme
[coverage:report]
show_missing = True
exclude_lines =
def __str__
def __repr__