doc: change style of docs to alabaster

Change style of docs from bootstrap to alabaster. Clean up and
simplify overall. Make the notebooks work correctly as part of the
table of contents by including in a rst file rather than using
index.ipynb as the main notebook index file. Also, stop using mock to
allow solve_fe docs. The solve_fe function can now be imported without
sfepy being required so remove all the mock paraphernalia from
conf.py.

Author: wd15

Diff for: README.md

@@ -1,14 +1,5 @@
-<p align="center">
-<img src="https://raw.githubusercontent.com/materialsinnovation/pymks/master/doc/pymks_logo.ico"
-     height="60"
-     alt="PyMKS logo"
-     class="inline">
-</p>
-
-<h1> <p align="center"><sup><strong>
-PyMKS &ndash; The Materials Knowledge System in Python
-</strong></sup></p>
-</h1>
+
+# PyMKS Overview
 
 <a href="https://travis-ci.org/materialsinnovation/pymks" target="_blank">
 <img src="https://api.travis-ci.org/materialsinnovation/pymks.svg"

Diff for: doc/API.rst

@@ -4,8 +4,15 @@
 API
 ===
 
+.. toctree::
+   :maxdepth: 2
+
+
 .. jinja::
 
+   Table
+   =====
+
    {% set functions = ['plot_microstructures', 'generate_delta', 'generate_multiphase', 'generate_checkerboard', 'solve_cahn_hilliard', 'solve_fe', 'coeff_to_real', 'paircorr_from_twopoint'] | sort %}
 
    {% set classes = ['PrimitiveTransformer', 'LegendreTransformer', 'TwoPointCorrelation', 'FlattenTransformer', 'LocalizationRegressor', 'ReshapeTransformer'] | sort %}
@@ -20,11 +27,16 @@ API
        {{ class }}
    {% endfor %}
 
+   Functions
+   =========
+
    {% for function in functions %}
    .. autofunction:: pymks.{{ function }}
 
    {% endfor %}
 
+   Classes
+   =======
 
    {% for class in classes %}
    .. autoclass:: pymks.{{ class }}

Diff for: doc/EXAMPLES.rst

@@ -3,9 +3,35 @@
 Examples
 ========
 
+Overview
+--------
+
+Start with the following notebooks if you are new to PyMKS.
+
+.. toctree::
+   :maxdepth: 2
+
+   rst/notebooks/intro.ipynb
+   rst/notebooks/checkerboard.ipynb
+
+Homogenization
+--------------
+
+.. toctree::
+   :maxdepth: 2
+
+   rst/notebooks/stress.ipynb
+   rst/notebooks/fiber.ipynb
+
+Localization
+------------
+
 .. toctree::
    :maxdepth: 2
 
-   spatial_stats.rst
-   homogenization.rst
-   localization.rst
+   rst/notebooks/elasticity.ipynb
+   rst/notebooks/multiphase.ipynb
+   rst/notebooks/elasticity3d.ipynb
+   rst/notebooks/filter.ipynb
+   rst/notebooks/cahn_hilliard.ipynb
+   rst/notebooks/cahn_hilliard_legendre.ipynb

Diff for: doc/pymks_logo.ico renamed to doc/_static/pymks_logo.ico

@@ -0,0 +1,7 @@
+<p>
+  <span class="navbar-version">
+    <b>
+      version: {{ release }}
+    </b>
+  </span>
+</p>