various documentation updates

7 files changed, 38 insertions, 20 deletions

diff --git a/.gitignore b/.gitignore
index e691660..dde7e83 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,5 @@
 *.pyc
 gensvm/*.so
+README
+build/*
+cover/*
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 9a203e1..ae918c0 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,2 +1,2 @@
 Change Log
-==========
+----------
diff --git a/Makefile b/Makefile
index c330cd5..353cddc 100644
--- a/Makefile
+++ b/Makefile
@@ -31,7 +31,8 @@ install2: ## Install for the current user using the python2 command
 test: in ## Run nosetests using the default nosetests command
 	nosetests -v
 
-test2: develop2 ## Run nosetests using the nosetests2 command
+test2: ## Run nosetests using the nosetests2 command
+	python2 setup.py build_ext -i
 	nosetests2 -v
 
 cover: test ## Test unit test coverage using default nosetests
diff --git a/README.rst b/README.rst
index 0182103..5e68024 100644
--- a/README.rst
+++ b/README.rst
@@ -14,6 +14,11 @@ The source code of this package is available on GitHub at:
 Installation
 ------------
 
+**Before** GenSVM can be installed, a working NumPy installation is required.  
+Please see `the installation instructions for NumPy 
+<https://docs.scipy.org/doc/numpy-1.13.0/user/install.html>`_, then install 
+GenSVM using the instructions below.
+
 GenSVM can be easily installed through pip:
 
 .. code:: bash
@@ -23,15 +28,15 @@ GenSVM can be easily installed through pip:
 Usage
 -----
 
-The package contains two classes to fit the GenSVM model: :class:`GenSVM` and 
-:class:`GenSVMGridSearchCV`. These classes respectively fit a single GenSVM 
-model or fit a series of models for a parameter grid search. The interface to 
-these classes is the same as that of classifiers in `Scikit-Learn <http://scikit-learn.org/stable/index.html>`_ so users 
-familiar with `Scikit-Learn <http://scikit-learn.org/stable/index.html>`_ should have no trouble using this package. Below 
+The package contains two classes to fit the GenSVM model: `GenSVM`_ and 
+`GenSVMGridSearchCV`_.  These classes respectively fit a single GenSVM model 
+or fit a series of models for a parameter grid search. The interface to these 
+classes is the same as that of classifiers in `Scikit-Learn`_  so users 
+familiar with Scikit-Learn should have no trouble using this package.  Below 
 we will show some examples of using the GenSVM classifier and the 
 GenSVMGridSearchCV class in practice.
 
-In the examples We assume that we have loaded the `iris dataset
+In the examples we assume that we have loaded the `iris dataset
 <http://scikit-learn.org/stable/auto_examples/datasets/plot_iris_dataset.html>`_ 
 from Scikit-Learn as follows:
 
@@ -53,7 +58,7 @@ computation time of GenSVM and is `generally recommended for SVMs
 
 
 Example 1: Fitting a single GenSVM model
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Let's start by fitting the most basic GenSVM model on the training data:
 
@@ -121,7 +126,7 @@ For other parameters that can be tuned in the GenSVM model, see `GenSVM`_.
 
 
 Example 2: Fitting a GenSVM model with a "warm start"
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 One of the key features of the GenSVM classifier is that training can be 
 accelerated by using so-called "warm-starts". This way the optimization can be 
@@ -170,7 +175,7 @@ can be used to do a grid search of parameters.
 
 
 Example 3: Running a GenSVM grid search
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Often when we're fitting a machine learning model such as GenSVM, we have to 
 try several parameter configurations to figure out which one performs best on 
@@ -180,8 +185,7 @@ overfitting. To do this efficiently and to make use of warm starts, the
 `GenSVMGridSearchCV`_ class is available. This class works in the same way as 
 the `GridSearchCV 
 <http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.GridSearchCV.html>`_ 
-class of `Scikit-Learn <http://scikit-learn.org/stable/index.html>`_, but uses 
-the GenSVM C library for speed.
+class of `Scikit-Learn`_, but uses the GenSVM C library for speed.
 
 To do a grid search, we first have to define the parameters that we want to 
 vary and what values we want to try:
@@ -216,8 +220,8 @@ found in the grid search:
     >>> gg.score(X_test, y_test)
     1.0
 
-A nice feature borrowed from `Scikit-Learn <http://scikit-learn.org>`_ is that 
-the results from the grid search can be represented as a ``pandas`` DataFrame:
+A nice feature borrowed from `Scikit-Learn`_ is that the results from the grid 
+search can be represented as a ``pandas`` DataFrame:
 
 .. code:: python
 
@@ -262,6 +266,15 @@ License
 -------
 
 This package is licensed under the GNU General Public License version 3.  
+
 Copyright G.J.J. van den Burg, excluding the sections of the code that are 
 explicitly marked to come from Scikit-Learn.
 
+.. _Scikit-Learn:
+    http://scikit-learn.org/stable/index.html
+
+.. _GenSVM:
+    https://gensvm.readthedocs.io/en/latest/#gensvm
+
+.. _GenSVMGridSearchCV:
+    https://gensvm.readthedocs.io/en/latest/#gensvmgridsearchcv
diff --git a/docs/cls_gensvm.rst b/docs/cls_gensvm.rst
index 082df8f..4e67631 100644
--- a/docs/cls_gensvm.rst
+++ b/docs/cls_gensvm.rst
@@ -10,7 +10,7 @@
    errors. It is this flexibility that makes it perform well on diverse
    datasets.
    
-   The :func:`.~GenSVM.fit` and :func:`~GenSVM.predict` methods of this class
+   The :func:`~GenSVM.fit` and :func:`~GenSVM.predict` methods of this class
    use the GenSVM C library for the actual computations.
    
    :param p: Parameter for the L_p norm of the loss function (1.0 <= p <= 2.0)
diff --git a/docs/conf.py b/docs/conf.py
index 8a02df3..e3eb6b9 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -136,7 +136,7 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = {'collapse_navigation': True}
 
 # 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,
diff --git a/docs/index.rst b/docs/index.rst
index 7f539b8..7a28f0e 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -3,19 +3,20 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
+.. toctree::
 
 .. include:: ../README.rst
 
 Classes
-=======
+-------
 
 GenSVM
-------
+^^^^^^
 
 .. include:: ./cls_gensvm.rst
 
 GenSVMGridSearchCV
-------------------
+^^^^^^^^^^^^^^^^^^
 
 .. include:: ./cls_gridsearch.rst