Update repository meta

.flake8

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+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+#########################
+[flake8]
+ignore =
+    S403 # pickle
+    S301 # pickle
+    W503 # line break before binary operator
+exclude =
+    .tox,
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    build,
+    dist,
+    tests/fixtures/*,
+    *.pyc,
+    *.egg-info,
+    .cache,
+    .eggs,
+    data
+max-line-length = 120
+max-complexity = 20
+import-order-style = pycharm
+application-import-names =
+    indra_cogex
+    indra
+    tests
+format = ${cyan}%(path)s${reset}:${yellow_bold}%(row)d${reset}:${green_bold}%(col)d${reset}: ${red_bold}%(code)s${reset} %(text)s

.github/workflows/tests.yml

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+name: Tests
+
+on: [ push, pull_request ]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ 3.8, 3.9 ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install tox
+      - name: Check manifest
+        run: tox -e manifest
+      - name: Check code quality with flake8
+        run: tox -e flake8
+      - name: Check package metadata with Pyroma
+        run: tox -e pyroma
+      - name: Check static typing with MyPy
+        run: tox -e mypy
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ 3.8, 3.9 ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install tox
+      - name: Check RST conformity with doc8
+        run: tox -e doc8
+      - name: Check docstring coverage
+        run: tox -e docstr-coverage
+      - name: Check documentation build with Sphinx
+        run: tox -e docs
+  tests:
+    name: Tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ 3.8, 3.9 ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install tox
+      - name: Test with pytest
+        run:
+          tox -e py

MANIFEST.in

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+graft src
+graft tests
+
+recursive-include docs Makefile
+recursive-include docs/source *.py
+recursive-include docs/source *.rst
+recursive-include docs/source *.png
+
+global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle
+
+exclude .appveyor.yml .bumpversion.cfg .coveragerc .flake8 .travis.yml .readthedocs.yml tox.ini .pre-commit-config.yaml
+exclude import.sh
+include LICENSE *.md *.rst

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = INDRA CoGEx
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+
+import os
+import re
+import sys
+from datetime import date
+
+sys.path.insert(0, os.path.abspath('../../src'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'indra_cogex'
+copyright = f'{date.today().year}, Benjamin M. Gyori'
+author = 'Benjamin M. Gyori'
+
+# The full version, including alpha/beta/rc tags.
+release = '1.0.0'
+
+# The short X.Y version.
+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-]+)*))?',
+    release,
+)
+version = parsed_version.expand('\g<major>.\g<minor>.\g<patch>')
+
+if parsed_version.group('release'):
+    tags.add('prerelease')
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = False
+
+# A list of prefixes that are ignored when creating the module index. (new in Sphinx 0.6)
+modindex_common_prefix = ["indra_cogex."]
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autosummary',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.coverage',
+    'sphinx.ext.intersphinx',
+    "sphinx.ext.todo",
+    # 'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx_autodoc_typehints',
+    # 'sphinx_click.ext',
+    # 'sphinx_automodapi.automodapi',
+    # 'texext',
+]
+
+# generate autosummary pages
+autosummary_generate = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+# html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#
+if os.path.exists('logo.png'):
+    html_logo = 'logo.png'
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'INDRACoGExdoc'
+
+# -- Options for LaTeX output ------------------------------------------------
+
+# latex_elements = {
+#     The paper size ('letterpaper' or 'a4paper').
+#
+#     'papersize': 'letterpaper',
+#
+#     The font size ('10pt', '11pt' or '12pt').
+#
+#     'pointsize': '10pt',
+#
+#     Additional stuff for the LaTeX preamble.
+#
+#     'preamble': '',
+#
+#     Latex figure (float) alignment
+#
+#     'figure_align': 'htbp',
+# }
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+# latex_documents = [
+#     (
+#         master_doc,
+#         'indra_cogex.tex',
+#         'INDRA CoGEx Documentation',
+#         author,
+#         'manual',
+#     ),
+# ]
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (
+        master_doc,
+        'indra_cogex',
+        'INDRA CoGEx Documentation',
+        [author],
+        1,
+    ),
+]
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        'indra_cogex',
+        'INDRA CoGEx Documentation',
+        author,
+        'Benjamin M. Gyori',
+        'INDRA CoGEx (Context Graph Extension) is an automatically assembled '
+        'biomedical knowledge graph which integrates causal mechanisms from '
+        'INDRA with non-causal contextual relations including properties, ontology, and data.',
+        'Miscellaneous',
+    ),
+]
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+# epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+# epub_exclude_files = ['search.html']
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    'https://docs.python.org/3/': None,
+}
+
+autoclass_content = 'both'

docs/source/index.rst

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+INDRA CoGEx |release| Documentation
+===================================
+.. toctree::
+   :maxdepth: 2
+   :caption: Getting Started
+   :name: start
+
+Indices and Tables
+------------------
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`