Merge pull request #47 from KrishnaswamyLab/dev

graphtools v1.4.0

Author: scottgigante

.travis.yml

@@ -17,6 +17,7 @@
 
   script:
     - pip install -U .[test]
+    - if [ "$TRAVIS_PYTHON_VERSION" != "3.5" ]; then black . --check --diff; fi
     - python setup.py test
     - pip install -U .[doc]
     - cd doc; make html

CONTRIBUTING.md

@@ -0,0 +1,39 @@
+
+Contributing to graphtools
+============================
+
+There are many ways to contribute to `graphtools`, with the most common ones
+being contribution of code or documentation to the project. Improving the
+documentation is no less important than improving the library itself. If you
+find a typo in the documentation, or have made improvements, do not hesitate to
+submit a GitHub pull request.
+
+But there are many other ways to help. In particular answering queries on the
+[issue tracker](https://github.com/KrishnaswamyLab/graphtools/issues),
+investigating bugs, and [reviewing other developers' pull
+requests](https://github.com/KrishnaswamyLab/graphtools/pulls)
+are very valuable contributions that decrease the burden on the project
+maintainers.
+
+Another way to contribute is to report issues you're facing, and give a "thumbs
+up" on issues that others reported and that are relevant to you. It also helps
+us if you spread the word: reference the project from your blog and articles,
+link to it from your website, or simply star it in GitHub to say "I use it".
+
+Code Style and Testing
+----------------------
+
+`graphtools` is maintained at close to 100% code coverage. Contributors are encouraged to write tests for their code, but if you do not know how to do so, please do not feel discouraged from contributing code! Others can always help you test your contribution.
+
+Code style is dictated by [`black`](https://pypi.org/project/black/#installation-and-usage). To automatically reformat your code when you run `git commit`, you can run `./autoblack.sh` in the root directory of this project to add a hook to your `git` repository.
+
+Code of Conduct
+---------------
+
+We abide by the principles of openness, respect, and consideration of others
+of the Python Software Foundation: https://www.python.org/psf/codeofconduct/.
+
+Attribution
+---------------
+
+This `CONTRIBUTING.md` was adapted from [scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/master/CONTRIBUTING.md).

README.rst

@@ -23,6 +23,9 @@ graphtools
 .. image:: https://img.shields.io/github/stars/KrishnaswamyLab/graphtools.svg?style=social&label=Stars
     :target: https://github.com/KrishnaswamyLab/graphtools/
     :alt: GitHub stars
+.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+    :target: https://github.com/psf/black
+    :alt: Code style: black
 
 Tools for building and manipulating graphs in Python.
 

autoblack.sh

@@ -0,0 +1,14 @@
+cat <<EOF >> .git/hooks/pre-commit
+#!/bin/sh
+
+set -e
+
+files=\$(git diff --staged --name-only --diff-filter=d -- "*.py")
+
+for file in \$files; do
+  black -q \$file
+  git add \$file
+done
+EOF
+chmod +x .git/hooks/pre-commit
+

doc/source/conf.py

@@ -19,7 +19,9 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+root_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
+sys.path.insert(0, root_dir)
 # print(sys.path)
 
 # -- General configuration ------------------------------------------------
@@ -31,40 +33,43 @@
 # 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.autodoc',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.napoleon',
-              'sphinx.ext.doctest',
-              'sphinx.ext.coverage',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.viewcode',
-              'sphinxcontrib.bibtex']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.doctest",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinxcontrib.bibtex",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['ytemplates']
+templates_path = ["ytemplates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'graphtools'
-copyright = '2018 Krishnaswamy Lab, Yale University'
-author = 'Jay Stanley and Scott Gigante, Krishnaswamy Lab, Yale University'
+project = "graphtools"
+copyright = "2018 Krishnaswamy Lab, Yale University"
+author = "Scott Gigante and Jay Stanley, Yale University"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-version = '0.1.3'
+version_py = os.path.join(root_dir, "graphtools", "version.py")
 # The full version, including alpha/beta/rc tags.
-release = '0.1.3'
+release = open(version_py).read().strip().split("=")[-1].replace('"', "").strip()
+# The short X.Y version.
+version = release.split("-")[0]
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -79,7 +84,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -90,7 +95,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'default'
+html_theme = "default"
 
 # 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
@@ -101,13 +106,13 @@
 # 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 = ['ystatic']
+html_static_path = ["ystatic"]
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'graphtoolsdoc'
+htmlhelp_basename = "graphtoolsdoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -116,15 +121,12 @@
     # 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',
@@ -134,19 +136,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'graphtools.tex', 'graphtools Documentation',
-     'Jay Stanley and Scott Gigante, Krishnaswamy Lab, Yale University', 'manual'),
+    (
+        master_doc,
+        "graphtools.tex",
+        "graphtools Documentation",
+        "Scott Gigante and Jay Stanley, Yale University",
+        "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, 'graphtools', 'graphtools Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "graphtools", "graphtools Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -155,7 +159,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'graphtools', 'graphtools Documentation',
-     author, 'graphtools', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "graphtools",
+        "graphtools Documentation",
+        author,
+        "graphtools",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]

doc/source/index.rst

@@ -30,6 +30,10 @@ graphtools
 
     <a href="https://github.com/KrishnaswamyLab/graphtools/"><img src="https://img.shields.io/github/stars/KrishnaswamyLab/graphtools.svg?style=social&label=Stars" alt="GitHub stars"></a>
 
+.. raw:: html
+
+    <a href="https://github.com/psf/black/"><img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black"></a>
+
 Tools for building and manipulating graphs in Python.
 
 .. toctree::
@@ -65,4 +69,4 @@ To use `graphtools` with `pygsp`, create a `graphtools.Graph` class with `use_py
 Help
 ====
 
-If you have any questions or require assistance using graphtools, please contact us at https://krishnaswamylab.org/get-help
+If you have any questions or require assistance using graphtools, please contact us at https://krishnaswamylab.org/get-help