Updates for ComPath, Bio2BEL, and PyBEL (#11)

Closes #9

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.4-dev
+current_version = 0.3.0-dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?
@@ -19,9 +19,9 @@ values =
 [bumpverion:part:build]
 values = [0-9A-Za-z-]+
 
-[bumpversion:file:src/bio2bel_wikipathways/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
+[bumpversion:file:setup.cfg]
+search = version = {current_version}
+replace = version = {new_version}
 
 [bumpversion:file:src/bio2bel_wikipathways/constants.py]
 search = VERSION = '{current_version}'
@@ -30,4 +30,3 @@ replace = VERSION = '{new_version}'
 [bumpversion:file:docs/source/conf.py]
 search = release = '{current_version}'
 replace = release = '{new_version}'
-

.flake8

@@ -23,8 +23,7 @@ import-order-style = pycharm
 application-import-names =
     bio2bel_wikipathways
     bio2bel
-    bio2bel_hgnc
+    pyobo
     pybel
-    compath_utils
     tests
 format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.travis.yml

@@ -2,7 +2,7 @@ sudo: false
 cache: pip
 language: python
 python:
-- 3.6
+  - "3.8"
 stages:
   - lint
   - docs
@@ -23,9 +23,8 @@ jobs:
     # test stage
     - stage: test
       env: TOXENV=py
-matrix:
   allow_failures:
-      - env: TOXENV=xenon
+    - env: TOXENV=xenon
 install:
   - sh -c 'if [ "$TOXENV" = "py" ]; then pip install tox codecov; else pip install tox; fi'
 script:

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Bio2BEL
+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

@@ -4,31 +4,38 @@ This package allows the enrichment of BEL networks with WikiPathways information
 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 WikiPathways 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_wikipathways`` can be installed easily from `PyPI <https://pypi.python.org/pypi/bio2bel_wikipathways>`_ with
 the following code in your favorite terminal:
 
 .. code-block:: sh
 
-    $ python3 -m pip install bio2bel_wikipathways
+    $ pip install bio2bel_wikipathways
 
-or from the latest code on `GitHub <https://github.com/bio2bel/wikipathways>`_ with:
+or from the latest code on `GitHub <https://github.com/bio2bel/wikipathways>`_ in development mode with:
 
 .. code-block:: sh
 
-    $ python3 -m pip install git+https://github.com/bio2bel/wikipathways.git@master
+    $ git clone https://github.com/bio2bel/wikipathways.git
+    $ cd wikipathways
+    $ pip install -e .
 
 Setup
 -----
 WikiPathways 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
@@ -45,8 +52,8 @@ Command Line Utility
 
 Other Command Line Utilities
 ----------------------------
-- Run an admin site for simple querying and exploration :code:`python3 -m bio2bel_wikipathways web` (http://localhost:5000/admin/)
-- Export gene sets for programmatic use :code:`python3 -m bio2bel_wikipathways export`
+- Run an admin site for simple querying and exploration :code:`bio2bel_wikipathways web` (http://localhost:5000/admin/)
+- Export gene sets for programmatic use :code:`bio2bel_wikipathways export`
 
 Citation
 --------

docs/source/conf.py

@@ -17,10 +17,10 @@
 source_suffix = '.rst'
 master_doc = 'index'
 project = 'Bio2BEL WikiPathways'
-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 = '0.2.4-dev'
+release = '0.3.0-dev'
 
 parsed_version = re.match(
     '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?',
@@ -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),
 }

docs/source/index.rst

@@ -10,7 +10,6 @@ Bio2BEL WikiPathways
    cli
    models
    constants
-   parser
    web
 
 Indices and tables

setup.cfg

@@ -0,0 +1,114 @@
+##########################
+# Setup.py Configuration #
+##########################
+[metadata]
+name = bio2bel_wikipathways
+version = 0.3.0-dev
+description = A package for converting WikiPathways gene sets into BEL
+long_description = file: README.rst
+
+# URLs associated with the project
+url = https://github.com/bio2bel/wikipathways
+download_url = https://github.com/bio2bel/wikipathways/releases
+project_urls =
+    Bug Tracker = https://github.com/bio2bel/wikipathways/issues
+    Source Code = https://github.com/bio2bel/wikipathways
+
+# Author information
+author = Daniel Domingo-Fernández and Charles Tapley Hoyt
+author_email = [email protected] and [email protected]
+maintainer = Charles Tapley Hoyt
+maintainer_email = [email protected]
+
+# 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 :: 3.9
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3 :: Only
+    Topic :: Scientific/Engineering :: Bio-Informatics
+keywords =
+    Biological Expression Language
+    BEL
+    Systems Biology
+    WikiPathways
+
+[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 =
+    wikipathways = bio2bel_wikipathways
+compath =
+    wikipathways = bio2bel_wikipathways
+console_scripts =
+    bio2bel_wikipathways = bio2bel_wikipathways.cli:main
+
+######################
+# Doc8 Configuration #
+# (doc8.ini)         #
+######################
+[doc8]
+max-line-length = 120
+
+##########################
+# Coverage Configuration #
+# (.coveragerc)          #
+##########################
+[coverage:run]
+branch = True
+source = bio2bel_wikipathways
+omit =
+    tests/*
+    docs/*
+    scripts/*
+
+[coverage:paths]
+source =
+    src/bio2bel_wikipathways
+    .tox/*/lib/python*/site-packages/bio2bel_wikipathways
+
+[coverage:report]
+show_missing = True
+exclude_lines =
+    def __str__
+    def __repr__