Merge pull request #28 from materials-data-facility/forge-dev

Add docs on Read the Docs, other improvements

.gitignore

@@ -15,5 +15,5 @@ Untitled*.ipynb
 *.egg*
 
 travis.tar
-.coverage
+.coverage*
 

.travis.yml

@@ -7,11 +7,13 @@ python:
 - '3.6'
 install:
 - pip install -e .
-- pip install pytest pytest-cov coveralls flake8
+- pip install -r test_requirements.txt
 env:
 - TEST_ENV=travis
 script:
-- flake8 . && travis_wait 50 py.test
+- if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then flake8 . && travis_wait 50 py.test;
+  else flake8 . && travis_wait 50 py.test --nbval-lax; fi;
+#- flake8 . && travis_wait 50 py.test --nbval-lax
 before_install:
 - openssl aes-256-cbc -K $encrypted_39a50b90a369_key -iv $encrypted_39a50b90a369_iv
   -in travis.tar.enc -out travis.tar -d

README.md

@@ -1,5 +1,5 @@
 # Forge
-[![PyPI](https://img.shields.io/pypi/v/mdf_forge.svg)](https://pypi.python.org/pypi/mdf-forge) [![Build Status](https://travis-ci.org/materials-data-facility/forge.svg?branch=master)](https://travis-ci.org/materials-data-facility/forge) [![Coverage Status](https://coveralls.io/repos/github/materials-data-facility/forge/badge.svg?branch=master)](https://coveralls.io/github/materials-data-facility/forge?branch=master)
+[![PyPI](https://img.shields.io/pypi/v/mdf_forge.svg)](https://pypi.python.org/pypi/mdf-forge) [![Build Status](https://travis-ci.org/materials-data-facility/forge.svg?branch=master)](https://travis-ci.org/materials-data-facility/forge) [![Coverage Status](https://coveralls.io/repos/github/materials-data-facility/forge/badge.svg?branch=master)](https://coveralls.io/github/materials-data-facility/forge?branch=master) [![Read the Docs](https://readthedocs.org/projects/mdf-forge/badge/?version=master)](http://mdf-forge.readthedocs.io/en/master/)
 
 Forge is the Materials Data Facility Python package to interface and leverage the MDF Data Discovery service. Forge allows users to perform simple queries and facilitiates moving and synthesizing results.
 
@@ -17,10 +17,12 @@ pip install -e .
 ```
 
 # Documentation and examples
-Documentation, including tutorials and examples, can be found in the `docs` directory.
+Forge documentation can be found on [Read the Docs](http://mdf-forge.readthedocs.io/en/master/).
+Tutorials and examples can be found in the `docs` directory. The Jupyter notebooks can be viewed on GitHub or run interactively with ![Jupyter](http://jupyter.org/install).
 
 # Requirements
-* Forge requires Python 2.7 or >=3.3 
+* Forge requires Python 3.4 or greater.
+  * **Note**: Python 2.7 support has been deprecated. Forge releases after version 0.6.2 will not work in Python 2. Please upgrade to Python 3.
 * To access data in the MDF, you must have an account recognized by Globus Auth (including Google, ORCiD, many academic institutions, or a [free Globus ID](https://www.globusid.org/create)).
 
 # Contributions

docs/examples/Example Machine Learning - OQMD.ipynb → docs/examples/Example Machine Learning - OQMD.old_ipynb

@@ -87,25 +87,19 @@
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
+   "outputs": [],
    "source": [
     "The MDF stores multiple versions of the OQMD metadata. First, we need to get the latest version"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Latest version: 9\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "oqmd_version = mdf.get_dataset_version('oqmd')\n",
     "print('Latest version: {}'.format(oqmd_version))"
@@ -119,18 +113,8 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 5,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Found 4897 compounds\n"
-     ]
-    }
-   ],
    "source": [
     "query_string = 'mdf.source_name:oqmd_v{0} AND (oqmd_v{0}.configuration:static '\\\n",
     "    'OR oqmd_v{0}.configuration:standard) AND dft.converged:True'.format(oqmd_version)\n",
@@ -726,12 +710,10 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {
     "collapsed": true
    },
-   "outputs": [],
    "source": []
   }
  ],

docs/sphinx/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = mdf-forge
+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/sphinx/source/conf.py

@@ -0,0 +1,224 @@
+# -*- 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/stable/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 sys
+sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('../../..'))
+sys.path.insert(0, os.path.abspath('../../../mdf_forge'))
+sys.path.insert(0, os.path.abspath('../../../tests'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'MDF Forge'
+copyright = 'Apache License, Version 2.0'
+author = 'Jonathon Gaff'
+
+# The short X.Y version
+version = '0.5'
+# The full version, including alpha/beta/rc tags
+release = '0.5.1'
+
+
+# -- 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.intersphinx',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.mathjax',
+    'IPython.sphinxext.ipython_console_highlighting',
+]
+
+# 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']
+#
+# Using Sphinx with Markdown
+# https://github.com/serra/sphinx-with-markdown
+
+
+# Use Markdown and reStructuredText in the same Sphinx project.
+# from recommonmark.parser import CommonMarkParser
+
+# source_parsers = {
+#    '.md': CommonMarkParser,
+# }
+
+source_suffix = ['.rst', '.md']
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of modules to be mocked up. This is useful when some external dependencies are not met
+# at build time and break the building process.
+# You may only specify the root package of the dependencies themselves and ommit the sub-modules:
+# See also:
+# http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_mock_importshttps://github.com/sphinx-doc/sphinx/issues/4182
+autodoc_mock_imports = ['mdf_toolbox', 'pytest', 'globus_sdk.exc']
+
+# This value selects what content will be inserted into the main body of an autoclass directive.
+# The possible values are:
+# “class ”: Only the class ’ docstring is inserted. This is the default.
+# You “can still document init as a separate method using automethod or “the members option
+# to autoclass.
+# “both”: Both the class ’ and the init method’s docstring are concatenated and inserted.
+# “init”: Only the init method’s docstring is inserted.
+autoclass_content = 'both'
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# List of themes: basic, alabaster, classic, sphinxdoc, scrolls, agoago, nature,
+# pyramid, haiku, traditional, epub, bizstyle
+#
+html_theme = 'sphinxdoc'
+
+# 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 = {}
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'mdf-forgedoc'
+
+
+# -- 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, 'mdf-forge.tex', u'mdf-forge Documentation',
+     'Jonathon Gaff', '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, 'mdf-forge', u'mdf-forge Documentation',
+     [author], 1)
+]
+
+# If true, show URL addresses after external links.
+# man_show_urls = False
+
+# -- 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, 'mdf-forge', u'mdf-forge Documentation',
+     author, 'mdf-forge', 'One line description of project.',
+     'Miscellaneous'),
+]
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False
+
+# -- Extension configuration -------------------------------------------------
+# Napoleon settings
+# see http://www.sphinx-doc.org/en/stable/ext/napoleon.html
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = True
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for inter sphinx: refer to the Python standard library.
+# intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}