Update ComPath, Bio2BEL, and PyBEL (#14)

* Update compath

* Update bio2bel

* Update .flake8

* Update setup.cfg

* Updates

* Update client.py

* Update bio2bel requirement

* Update README.rst

[skip ci]

* Update metadata

[skip ci]

* Update metadata

* Update for bio2bel 3.9

* Update for failing tox

* Get up to date

* Update .travis.yml

* Update

* Update client.py

.bumpversion.cfg

@@ -19,9 +19,9 @@ values =
 [bumpverion:part:build]
 values = [0-9A-Za-z-]+
 
-[bumpversion:file:src/bio2bel_kegg/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
+[bumpversion:file:setup.cfg]
+search = version = {current_version}
+replace = version = {new_version}
 
 [bumpversion:file:docs/source/conf.py]
 search = release = '{current_version}'

.flake8

@@ -18,9 +18,8 @@ max-complexity = 10
 import-order-style = pycharm
 application-import-names =
     bio2bel_kegg
-    bio2bel_hgnc
     bio2bel
-	compath_utils
+    pyobo
     pybel
     tests
 format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.gitignore

@@ -102,3 +102,4 @@ ENV/
 
 .idea
 .pytest_cache
+tests/resources/.DS_Store

.travis.yml

@@ -2,7 +2,7 @@ sudo: false
 cache: pip
 language: python
 python:
-- 3.6
+  - '3.9'
 stages:
   - lint
   - docs
@@ -15,7 +15,6 @@ jobs:
     - stage: lint
       env: TOXENV=manifest
     - env: TOXENV=flake8
-    - env: TOXENV=vulture
     - env: TOXENV=mypy
     - env: TOXENV=pyroma
     - env: TOXENV=xenon
@@ -27,15 +26,14 @@ jobs:
     # test stage
     - stage: test
       env: TOXENV=py
-matrix:
   allow_failures:
-      - env: TOXENV=vulture
-      - env: TOXENV=mypy
+    - env: TOXENV=mypy
+    - env: TOXENV=xenon
 install:
-    - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
+  - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
 script:
-- tox
+  - tox
 after_success:
-    - sh -c 'if [ "$TOXENV" = "py" ]; then tox -e coverage-report; codecov; fi'
+  - sh -c 'if [ "$TOXENV" = "py" ]; then tox -e coverage-report; codecov; fi'
 notifications:
   slack: pybel:n2KbWKBum3musnBg3L76gGwq

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017-2018 Charles Tapley Hoyt and Daniel Domingo-Fernández
+Copyright (c) 2017-2020 Daniel Domingo-Fernández and Charles Tapley Hoyt
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -3,30 +3,37 @@ Bio2BEL KEGG |build| |coverage| |documentation| |zenodo|
 This package allows the enrichment of BEL networks with KEGG information by wrapping its RESTful API.
 Furthermore, it is integrated in the `ComPath environment <https://github.com/ComPath>`_ for pathway database comparison.
 
+If you find this package useful, please consider citing [domingofernandez2018]_:
+
+.. [domingofernandez2018] Domingo-Fernandez, D., *et al* (2018). `ComPath: an ecosystem for exploring, analyzing,
+   and curating mappings across pathway databases <https://doi.org/10.1038/s41540-018-0078-8>`_.
+   *Npj Systems Biology and Applications*, __5__(1), 3.
+
+**Warning** This package creates ``partOf`` relationships in BEL, but does not convert KEGG mechanistic
+relationships to BEL. That functionality is implemented in the
+`PathMe project <https://github.com/pathwaymerger/pathme>`_.
+
 Installation |pypi_version| |python_versions| |pypi_license|
 ------------------------------------------------------------
 ``bio2bel_kegg`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_kegg>`_ with the
 following code in your favorite terminal:
 
 .. code-block:: sh
 
-    $ python3 -m pip install bio2bel_kegg
+    $ pip install bio2bel_kegg
 
-or from the latest code on `GitHub <https://github.com/bio2bel/kegg>`_ with:
+or from the latest code on `GitHub <https://github.com/bio2bel/kegg>`_ in development mode with:
 
 .. code-block:: sh
 
-    $ python3 -m pip install git+https://github.com/bio2bel/kegg.git@master
+    $ git clone https://github.com/bio2bel/kegg.git
+    $ cd kegg
+    $ pip install -e .
 
 Setup
 -----
 KEGG can be downloaded and populated from either the Python REPL or the automatically installed command line utility.
 
-The following resources will be automatically installed and loaded in order to fully populate the tables of the
-database:
-
-- `Bio2BEL HGNC <https://github.com/bio2bel/hgnc>`_
-
 Python REPL
 ~~~~~~~~~~~
 .. code-block:: python
@@ -43,7 +50,8 @@ Command Line Utility
 
 Other Command Line Utilities
 ----------------------------
-- Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_kegg web` (http://localhost:5000/admin/)
+- Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_kegg web`
+  (http://localhost:5000/admin/)
 - Export gene sets for programmatic use :code:`python3 -m bio2bel_kegg export`
 
 Citation

docs/source/conf.py

@@ -17,7 +17,7 @@
 source_suffix = '.rst'
 master_doc = 'index'
 project = 'Bio2BEL KEGG'
-copyright = '2018, Daniel Domingo-Fernández and Charles Tapley Hoyt'
+copyright = '2017-2020, Daniel Domingo-Fernández and Charles Tapley Hoyt'
 author = 'Daniel Domingo-Fernández and Charles Tapley Hoyt'
 
 release = '0.2.6-dev'
@@ -52,7 +52,7 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
-    'networkx': ('https://networkx.github.io/', None),
+    'networkx': ('https://networkx.github.io/documentation/latest/', None),
     'sqlalchemy': ('https://docs.sqlalchemy.org/en/latest', None),
     'pybel': ('https://pybel.readthedocs.io/en/latest/', None),
 }

setup.cfg

@@ -0,0 +1,111 @@
+##########################
+# Setup.py Configuration #
+##########################
+[metadata]
+name = bio2bel_kegg
+version = 0.2.6-dev
+description = A package for converting KEGG gene sets into BEL
+long_description = file: README.rst
+
+# URLs associated with the project
+url = https://github.com/bio2bel/kegg
+download_url = https://github.com/bio2bel/kegg/releases
+project_urls =
+    Bug Tracker = https://github.com/bio2bel/kegg/issues
+    Source Code = https://github.com/bio2bel/kegg
+
+# Author information
+author = Daniel Domingo-Fernández and Charles Tapley Hoyt
+author_email = daniel.domingo.fernandez@scai.fraunhofer.de and cthoyt@gmail.com
+maintainer = Charles Tapley Hoyt
+maintainer_email = cthoyt@gmail.com
+
+# License Information
+license = MIT
+license_file = LICENSE
+
+# Search tags
+classifiers =
+    Development Status :: 4 - Beta
+    Environment :: Console
+    Intended Audience :: Developers
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+    Programming Language :: Python
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3 :: Only
+    Topic :: Scientific/Engineering :: Bio-Informatics
+keywords =
+    Biological Expression Language
+    BEL
+    Systems Biology
+    KEGG
+
+[options]
+install_requires =
+    pybel>=0.15.0,<0.16.0
+    click
+    bio2bel[web]>=0.4.0,<0.5.0
+    pyobo>=0.2.2
+    tqdm
+    sqlalchemy
+    requests
+    pandas
+
+# 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]
+bio2bel =
+    kegg = bio2bel_kegg
+compath =
+    kegg = bio2bel_kegg
+console_scripts =
+    bio2bel_kegg = bio2bel_kegg.cli:main
+
+######################
+# Doc8 Configuration #
+# (doc8.ini)         #
+######################
+[doc8]
+max-line-length = 120
+
+##########################
+# Coverage Configuration #
+# (.coveragerc)          #
+##########################
+[coverage:run]
+branch = True
+source = bio2bel_kegg
+omit =
+    tests/*
+    docs/*
+
+[coverage:paths]
+source =
+    src/bio2bel_kegg
+    .tox/*/lib/python*/site-packages/bio2bel_kegg
+
+[coverage:report]
+show_missing = True
+exclude_lines =
+    def __str__
+    def __repr__