add docs

README.rst

@@ -8,6 +8,9 @@ graphtools
 .. image:: https://api.travis-ci.com/KrishnaswamyLab/graphtools.svg?branch=master
     :target: https://travis-ci.com/KrishnaswamyLab/graphtools
     :alt: Travis CI Build
+.. image:: https://img.shields.io/readthedocs/graphtools.svg
+    :target: https://graphtools.readthedocs.io/
+    :alt: Read the Docs
 .. image:: https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow
     :target: https://twitter.com/KrishnaswamyLab
     :alt: Twitter

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = PHATE
+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)

doc/source/api.rst

@@ -0,0 +1,8 @@
+API Reference
+=============
+
+.. automodule:: graphtools
+    :members:
+    :undoc-members:
+    :inherited-members:
+    :show-inheritance:

doc/source/conf.py

@@ -0,0 +1,159 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# PHATE documentation build configuration file, created by
+# sphinx-quickstart on Thu Mar 30 19:50:14 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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 sys
+sys.path.insert(0, os.path.abspath('../..'))
+# print(sys.path)
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The master toctree document.
+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'
+
+# 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'
+# The full version, including alpha/beta/rc tags.
+release = '0.1.3'
+
+# 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 patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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 = '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
+# 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 = ['ystatic']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'graphtoolsdoc'
+
+
+# -- 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, 'graphtools.tex', 'graphtools Documentation',
+     'Jay Stanley and Scott Gigante, Krishnaswamy Lab, 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)
+]
+
+
+# -- 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, 'graphtools', 'graphtools Documentation',
+     author, 'graphtools', 'One line description of project.',
+     'Miscellaneous'),
+]

doc/source/index.rst

@@ -0,0 +1,55 @@
+===========================================================================
+graphtools
+===========================================================================
+
+.. raw:: html
+
+    <a href="https://pypi.org/project/graphtools/"><img src="https://img.shields.io/pypi/v/graphtools.svg" alt="Latest PyPi version"></a>
+
+.. raw:: html
+
+    <a href="https://travis-ci.com/KrishnaswamyLab/graphtools"><img src="https://api.travis-ci.com/KrishnaswamyLab/graphtools.svg?branch=master" alt="Travis CI Build"></a>
+
+.. raw:: html
+
+    <a href="https://graphtools.readthedocs.io/"><img src="https://img.shields.io/readthedocs/graphtools.svg" alt="Read the Docs"></img></a>
+
+.. raw:: html
+
+    <a href="https://twitter.com/KrishnaswamyLab"><img src="https://img.shields.io/twitter/follow/KrishnaswamyLab.svg?style=social&label=Follow" alt="Twitter"></a>
+
+.. raw:: html
+
+    <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>
+
+Tools for building and manipulating graphs in Python.
+
+.. toctree::
+    :maxdepth: 2
+
+    installation
+    api
+
+Quick Start
+===========
+
+To use `graphtools`, create a `graphtools.Graph` class::
+
+    from sklearn import datasets
+    import graphtools
+    digits = datasets.load_digits()
+    G = graphtools.Graph(digits['data'])
+    K = G.kernel
+    P = G.diff_op
+    G = graphtools.Graph(digits['data'], n_landmark=300)
+    L = G.landmark_op
+
+To use `graphtools` with `pygsp`, create a `graphtools.Graph` class with `use_pygsp=True`::
+
+    from sklearn import datasets
+    import graphtools
+    digits = datasets.load_digits()
+    G = graphtools.Graph(digits['data'], use_pygsp=True)
+    N = G.N
+    W = G.W
+    basis = G.compute_fourier_basis()

doc/source/installation.rst

@@ -0,0 +1,81 @@
+Installation
+============
+
+Python installation
+-------------------
+
+Installation with `pip`
+~~~~~~~~~~~~~~~~~~~~~~~
+
+The Python version of PHATE can be installed using::
+
+       pip install --user phate
+
+Installation from source
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The Python version of PHATE can be installed from GitHub by running the following from a terminal::
+
+       git clone --recursive git://github.com/KrishnaswamyLab/PHATE.git
+       cd Python
+       python setup.py install --user
+
+MATLAB installation
+-------------------
+
+1. The MATLAB version of PHATE can be accessed using::
+
+    git clone git://github.com/KrishnaswamyLab/PHATE.git
+    cd PHATE/Matlab
+
+2. Add the PHATE/Matlab directory to your MATLAB path and run any of our `test` scripts to get a feel for PHATE.
+
+R installation
+--------------
+
+In order to use PHATE in R, you must also install the Python package.
+
+Installation from CRAN and PyPi
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Install `phateR` from CRAN by running the following code in R::
+
+    install.packages("phateR")
+
+Install `phate` in Python by running the following code from a terminal::
+
+    pip install --user phate
+
+Installation with `devtools` and `reticulate`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The development version of PHATE can be installed directly from R with `devtools`::
+
+    if (!suppressWarnings(require(devtools))) install.packages("devtools")
+    devtools::install_github("KrishnaswamyLab/phateR")
+
+If you have the development version of `reticulate`, you can also install `phate` in Python by running the following code in R::
+
+    devtools::install_github("rstudio/reticulate")
+    reticulate::py_install("phate")
+
+Installation from source
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+The latest source version of PHATE can be accessed by running the following in a terminal::
+
+    git clone --recursive git://github.com/SmitaKrishnaswamy/PHATE.git
+    cd PHATE/phateR
+    R CMD INSTALL
+    cd ../Python
+    python setup.py install --user
+
+If the `phateR` folder is empty, you have may forgotten to use the `--recursive` option for `git clone`. You can rectify this by running the following in a terminal::
+
+    cd PHATE
+    git submodule init
+    git submodule update
+    cd phateR
+    R CMD INSTALL
+    cd ../Python
+    python setup.py install --user

doc/source/requirements.txt

@@ -0,0 +1,5 @@
+numpy>=1.10.0
+scipy>=0.18.0
+pygsp>=>=0.5.1
+scikit-learn>=0.19.1
+future