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setup.cfg
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setup.cfg
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##########################
# Setup.py Configuration #
##########################
[metadata]
name = pybel
version = 0.15.6-dev
description = Parsing, validation, compilation, and data exchange of Biological Expression Language (BEL)
long_description = file: README.rst
# URLs associated with the project
url = https://github.com/pybel/pybel
download_url = https://github.com/pybel/pybel/releases
project_urls =
Bug Tracker = https://github.com/pybel/pybel/issues
Source Code = https://github.com/pybel/pybel
Documentation = https://pybel.readthedocs.io
# Author information
author = Charles Tapley Hoyt
author_email = cthoyt@gmail.com
maintainer = Charles Tapley Hoyt
maintainer_email = cthoyt@gmail.com
# License Information
license = MIT
license_file = LICENSE
# Search tags
classifiers =
Development Status :: 5 - Production/Stable
Environment :: Console
Intended Audience :: Developers
Intended Audience :: Science/Research
License :: OSI Approved :: MIT License
Operating System :: OS Independent
Programming Language :: Python
Programming Language :: Python :: 3.10
Programming Language :: Python :: 3.9
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.7
Programming Language :: Python :: 3.6
Programming Language :: Python :: 3 :: Only
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Chemistry
keywords =
Biological Expression Language
BEL
Domain Specific Language
DSL
Systems Biology
Networks Biology
[options]
install_requires =
dataclasses; python_version < "3.7"
pickle5; python_version < "3.8"
networkx>=2.4
sqlalchemy
click
click-plugins
bel_resources>=0.0.3
more_itertools
requests
requests_file
pyparsing
tqdm
humanize
tabulate
pandas
jsonschema
bioregistry
ratelimit
pystow>=0.1.2
psycopg2-binary
# Random options
zip_safe = false
include_package_data = True
python_requires = >=3.6
# Where is my code
packages = find:
package_dir =
= src
[options.packages.find]
where = src
[options.extras_require]
indra =
indra
jupyter =
jinja2
ipython
neo4j =
py2neo
grounding =
pyobo
protmapper
docs =
sphinx
sphinx-rtd-theme
sphinx-click
sphinx-autodoc-typehints
[options.entry_points]
console_scripts =
pybel = pybel.cli:main
pybel.importer =
bel = pybel.io.lines:from_bel_script
bel.gz = pybel.io.lines:from_bel_script_gz
bel.nodelink.json = pybel.io.nodelink:from_nodelink_file
bel.nodelink.json.gz = pybel.io.nodelink:from_nodelink_gz
bel.jsonl = pybel.io.sbel:from_sbel_file
bel.jsonl.gz = pybel.io.sbel:from_sbel_gz
bel.cx.json = pybel.io.cx:from_cx_file
bel.cx.json.gz = pybel.io.cx:from_cx_gz
bel.graphdati.json = pybel.io.graphdati:from_graphdati_file
bel.graphdati.json.gz = pybel.io.graphdati:from_graphdati_gz
bel.jgif.json = pybel.io.jgif:from_jgif_file
bel.jgif.json.gz = pybel.io.jgif:from_jgif_gz
bel.pickle = pybel.io.gpickle:from_pickle
bel.gpickle = pybel.io.gpickle:from_pickle
bel.pkl = pybel.io.gpickle:from_pickle
bel.pickle.gz = pybel.io.gpickle:from_pickle_gz
bel.gpickle.gz = pybel.io.gpickle:from_pickle_gz
bel.pkl.gz = pybel.io.gpickle:from_pickle_gz
indra.json = pybel.io.indra:from_indra_statements_json_file
pybel.exporter =
bel = pybel.canonicalize:to_bel_script
bel.gz = pybel.canonicalize:to_bel_script_gz
bel.nodelink.json = pybel.io.nodelink:to_nodelink_file
bel.nodelink.json.gz = pybel.io.nodelink:to_nodelink_gz
bel.jsonl = pybel.io.sbel:to_sbel_file
bel.jsonl.gz = pybel.io.sbel:to_sbel_gz
bel.cx.json = pybel.io.cx:to_cx_file
bel.cx.json.gz = pybel.io.cx:to_cx_gz
bel.graphdati.json = pybel.io.graphdati:to_graphdati_file
bel.graphdati.json.gz = pybel.io.graphdati:to_graphdati_gz
bel.jgif.json = pybel.io.jgif:to_jgif_file
bel.jgif.json.gz = pybel.io.jgif:to_jgif_gz
bel.pickle = pybel.io.gpickle:to_pickle
bel.gpickle = pybel.io.gpickle:to_pickle
bel.pkl = pybel.io.gpickle:to_pickle
bel.pickle.gz = pybel.io.gpickle:to_pickle_gz
bel.gpickle.gz = pybel.io.gpickle:to_pickle_gz
bel.pkl.gz = pybel.io.gpickle:to_pickle_gz
indra.json = pybel.io.indra:to_indra_statements_json_file
# No re-import
bel.unodelink.json = pybel.io.umbrella_nodelink:to_umbrella_nodelink_file
bel.unodelink.json.gz = pybel.io.umbrella_nodelink:to_umbrella_nodelink_gz
tsv = pybel.io.triples.api:to_triples_file
gsea = pybel.io.extras:to_gsea
# Importers for PyKEEN
pykeen.triples.extension_importer =
# Import BEL script to PyKEEN
bel = pybel.io.pykeen:get_triples_from_bel
# Import BEL Graph pickle to PyKEEN
bel.gpickle = pybel.io.pykeen:get_triples_from_bel_pickle
bel.pickle = pybel.io.pykeen:get_triples_from_bel_pickle
bel.pkl = pybel.io.pykeen:get_triples_from_bel_pickle
# Import BEL NodeLink JSON to PyKEEN
bel.nodelink.json = pybel.io.pykeen:get_triples_from_bel_nodelink
pykeen.triples.prefix_importer =
# Import BEL from BEL Commons to PyKEEN
bel-commons = pybel.io.pykeen:get_triples_from_bel_commons
######################
# Doc8 Configuration #
# (doc8.ini) #
######################
[doc8]
max-line-length = 120
##########################
# Coverage Configuration #
# (.coveragerc) #
##########################
[coverage:run]
branch = True
source = pybel
omit =
src/pybel/__main__.py
src/pybel/cli.py
src/pybel/io/indra.py
src/pybel/io/web.py
tests/*
docs/*
scripts/*
[coverage:paths]
source =
src/pybel
.tox/*/lib/python*/site-packages/pybel
[coverage:report]
show_missing = True
exclude_lines =
def __str__
def __repr__