Merge pull request #34 from materials-data-facility/forge-dev

Forge dev

.gitignore

@@ -10,8 +10,8 @@ Untitled*.ipynb
 
 *temp/*
 
-*/build/*
-*/dist/*
+**/build/
+**/dist/
 *.egg*
 
 travis.tar

README.md

@@ -17,8 +17,8 @@ pip install -e .
 ```
 
 # Documentation and examples
-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).
+Forge documentation can be found on [Read the Docs](https://mdf-forge.readthedocs.io/en/master/) and [GitHub](https://github.com/materials-data-facility/forge/tree/master/docs/).
+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 3.5 or greater.

docs/examples/Example Aggregations.ipynb → docs/examples/Example_Aggregations.ipynb

@@ -4,7 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Aggregating data with MDF"
+    "# Example Aggregations"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Aggregating data with MDF"
    ]
   },
   {
@@ -37,7 +44,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## aggregate_source - NIST XPS DB\n",
+    "### aggregate_source - NIST XPS DB\n",
     "Example: We want to collect all records from the NIST XPS Database and analyze the binding energies. This database has almost 30,000 records, so we have to use `aggregate()`."
    ]
   },
@@ -152,7 +159,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## aggregate - Multiple Datasets\n",
+    "### aggregate - Multiple Datasets\n",
     "Example: We want to analyze how often elements are studied with Gallium (Ga), and what the most frequent elemental pairing is. There are more than 10,000 records containing Gallium data."
    ]
   },

docs/examples/Example Statistics - MDF Datasets.ipynb → docs/examples/Example_Statistics-MDF_Datasets.ipynb

@@ -4,10 +4,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Example Statistics\n",
+    "# Example Statistics - MDF Datasets\n",
     "Example: We want to know how many datasets are in MDF and which datasets have the most records.\n",
     "\n",
-    "## Note: This example is not kept up-to-date with the latest statistics.\n",
+    "**Note: This example is not kept up-to-date with the latest statistics.**\n",
+    "\n",
     "If you want the current MDF statistics, you must run this code yourself."
    ]
   },

docs/sphinx/source/conf.py

@@ -12,23 +12,19 @@
 # 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'))
+import sphinx_bootstrap_theme
+
 
 # -- Project information -----------------------------------------------------
 
 project = 'MDF Forge'
-copyright = 'Apache License, Version 2.0'
-author = 'Jonathon Gaff'
+copyright = '2018, The University of Chicago'
+author = 'The University of Chicago'
 
 # The short X.Y version
-version = '0.5'
+version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.5.1'
+release = ''
 
 
 # -- General configuration ---------------------------------------------------
@@ -42,11 +38,12 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.ifconfig',
+    'sphinx.ext.coverage',
+    'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
     'sphinx.ext.mathjax',
-    'IPython.sphinxext.ipython_console_highlighting',
+    'm2r',
+    'nbsphinx'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -68,7 +65,7 @@
 #    '.md': CommonMarkParser,
 # }
 
-source_suffix = ['.rst', '.md']
+source_suffix = ['.rst', '.md', '.ipynb']
 
 # The master toctree document.
 master_doc = 'index'
@@ -83,7 +80,7 @@
 # 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']
+exclude_patterns = ['_build', '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -93,7 +90,7 @@
 # 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']
+# 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:
@@ -102,7 +99,7 @@
 # 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'
+# autoclass_content = 'class'
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -111,18 +108,19 @@
 # List of themes: basic, alabaster, classic, sphinxdoc, scrolls, agoago, nature,
 # pyramid, haiku, traditional, epub, bizstyle
 #
-html_theme = 'sphinxdoc'
+html_theme = 'bootstrap'
 
 # 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 = {}
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
 
 # 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']
+html_static_path = []
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -164,7 +162,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'mdf-forge.tex', u'mdf-forge Documentation',
+    (master_doc, 'mdf-forge.tex', 'mdf-forge Documentation',
      'Jonathon Gaff', 'manual'),
 ]
 
@@ -174,7 +172,7 @@
 # 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',
+    (master_doc, 'mdf-forge', 'mdf-forge Documentation',
      [author], 1)
 ]
 
@@ -187,7 +185,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'mdf-forge', u'mdf-forge Documentation',
+    (master_doc, 'mdf-forge', 'mdf-forge Documentation',
      author, 'mdf-forge', 'One line description of project.',
      'Miscellaneous'),
 ]
@@ -208,7 +206,7 @@
 # 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_init_with_doc = True
 napoleon_include_private_with_doc = False
 napoleon_include_special_with_doc = True
 napoleon_use_admonition_for_examples = False

docs/sphinx/source/example_list.rst

@@ -0,0 +1,8 @@
+Forge Examples
+==============
+
+.. toctree::
+
+    examples/Example_Aggregations
+    examples/Example_Statistics-MDF_Datasets
+

docs/sphinx/source/examples

@@ -0,0 +1 @@
+../../examples

docs/sphinx/source/index.rst

@@ -1,110 +1,15 @@
-.. highlight:: rst
 
-MDF Forge
-=========
 
-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.
+Index
+=====
 
-..  toctree::
-    :titlesonly:
+.. toctree::
+   :maxdepth: 2
+   :titlesonly:
 
-    forge_quickstart
-
-Installation
-============
-
-.. code-block:: bash
-
-   pip install mdf_forge
-
-..  toctree::
-    :titlesonly:
-
-    installation_guide.rst
-
-For Developers
---------------
-
-.. image:: https://img.shields.io/pypi/v/mdf_forge.svg
-   :target: https://pypi.python.org/pypi/mdf-forge
-.. image:: https://travis-ci.org/materials-data-facility/forge.svg?branch=master
-   :target: https://travis-ci.org/materials-data-facility/forge
-.. image:: https://coveralls.io/repos/github/materials-data-facility/forge/badge.svg?branch=master
-   :target: https://coveralls.io/github/materials-data-facility/forge?branch=master
-
-.. code-block:: bash
-
-   git clone https://github.com/materials-data-facility/forge.git
-   cd forge
-   pip install -e .
-
-..  toctree::
-    :maxdepth: 2
-
-    requirements_link
-    mdf_forge
-
-Documentation and examples
-==========================
-
-Documentation, including tutorials and examples, can be found in the
-``docs`` directory.
-
-Tutorials
----------
-
-#. Introduction (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/tutorials/1%20-%20Introduction.ipynb/>`_)
-#. Core Query Builder Functions (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/tutorials/2%20-%20Core%20Query%20Builder%20Functions.ipynb/>`_)
-#. Expanded Query Builder Functions (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/tutorials/3%20-%20Expanded%20Query%20Builder%20Functions.ipynb/>`_)
-#. General Helper Functions (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/tutorials/4%20-%20General%20Helper%20Functions.ipynb/>`_)
-#. Field-Specific Helper Functions (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/tutorials/5%20-%20Field-Specific%20Helper%20Functions.ipynb/>`_)
-#. Data Retrieval Functions (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/tutorials/6%20-%20Data%20Retrieval%20Functions.ipynb/>`_)
-
-Examples
---------
-
-#. Example Aggregations (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/examples/Example%20Aggregations.ipynb/>`_)
-#. Example Statistics - MDF Datasets (`Jupyter Notebook <https://github.com/materials-data-facility/forge/blob/master/docs/examples/Example%20Statistics%20-%20MDF%20Datasets.ipynb/>`_)
-
-Requirements
-============
-
--  Forge requires Python 2.7 or >=3.3
--  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`_).
-
-Contributions
-=============
-
-If you find a bug or want a feature, feel free to open an issue here on
-GitHub (and please tag it accordingly). If you want to contribute code
-yourself, we’re more than happy to accept merge requests.
-
-Support
-=======
-
-This work was performed under financial assistance award 70NANB14H012
-from U.S. Department of Commerce, National Institute of Standards and
-Technology as part of the `Center for Hierarchical Material Design
-(CHiMaD)`_. This work was also supported by the National Science
-Foundation as part of the `Midwest Big Data Hub`_ under NSF Award
-Number: 1636950 “BD Spokes: SPOKE: MIDWEST: Collaborative: Integrative
-Materials Design (IMaD): Leverage, Innovate, and Disseminate”.
-
-.. _free Globus ID: https://www.globusid.org/create
-.. _Center for Hierarchical Material Design (CHiMaD): http://chimad.northwestern.edu
-.. _Midwest Big Data Hub: http://midwestbigdatahub.org
-
-----
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+   MDF Forge Client <mdf_forge>
+   Tutorials <tutorial_list>
+   Examples <example_list>
 
 
+.. mdinclude:: ../../../README.md