From ea61fc2ed03e42b3ea159b7ef7886d005c90e29f Mon Sep 17 00:00:00 2001
From: Mario Mulansky <mario.mulansky@gmx.net>
Date: Tue, 3 Feb 2015 15:13:22 +0100
Subject: update docs to the structural changes

---
 Readme.rst              |  4 ++--
 doc/conf.py             |  4 ++--
 doc/pyspike.rst         | 47 +++++++++++++++++++++++++++++++++++------------
 pyspike/DiscreteFunc.py |  6 +++---
 pyspike/spikes.py       |  2 +-
 5 files changed, 43 insertions(+), 20 deletions(-)

diff --git a/Readme.rst b/Readme.rst
index bcf6fa9..debd32e 100644
--- a/Readme.rst
+++ b/Readme.rst
@@ -11,7 +11,7 @@ All computation intensive parts are implemented in C via cython_ to reach a comp
 
 PySpike provides the same fundamental functionality as the SPIKY_ framework for Matlab, which additionally contains spike-train generators, more spike train distance measures and many visualization routines.
 
-All source codes are published under the BSD_License_.
+All source codes are available on `Github <https://github.com/mariomulansky/PySpike>`_  and are published under the BSD_License_.
 
 .. [#] Kreuz T, Haas JS, Morelli A, Abarbanel HDI, Politi A, *Measuring spike train synchrony.* J Neurosci Methods 165, 151 (2007) `[pdf] <http://wwwold.fi.isc.cnr.it/users/thomas.kreuz/images/Kreuz_JNeurosciMethods_2007_Spike-Train-Synchrony.pdf>`_
 
@@ -201,7 +201,7 @@ The parameter :code:`interval` is optional and if neglected the whole spike trai
 
 
 SPIKE synchronization
-..............
+.....................
 
 **Important note:**
 
diff --git a/doc/conf.py b/doc/conf.py
index 48ebc7e..5427bb1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -57,7 +57,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'PySpike'
-copyright = u'2014, Mario Mulansky'
+copyright = u'2014-2015, Mario Mulansky'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -254,7 +254,7 @@ man_pages = [
 #  dir menu entry, description, category)
 texinfo_documents = [
   ('index', 'PySpike', u'PySpike Documentation',
-   u'Mario Mulansky', 'PySpike', 'One line description of project.',
+   u'Mario Mulansky', 'PySpike', 'Measure of spike train synchrony.',
    'Miscellaneous'),
 ]
 
diff --git a/doc/pyspike.rst b/doc/pyspike.rst
index 39adea0..6aa36e7 100644
--- a/doc/pyspike.rst
+++ b/doc/pyspike.rst
@@ -4,35 +4,58 @@ pyspike package
 Submodules
 ----------
 
-pyspike.distances module
-------------------------
+pyspike.isi_distance module
+----------------------------------------
 
-.. automodule:: pyspike.distances
+.. automodule:: pyspike.isi_distance
     :members:
     :undoc-members:
     :show-inheritance:
 
-pyspike.function module
------------------------
+pyspike.spike_distance module
+----------------------------------------
 
-.. automodule:: pyspike.function
+.. automodule:: pyspike.spike_distance
     :members:
     :undoc-members:
     :show-inheritance:
 
-pyspike.spikes module
----------------------
+pyspike.spike_sync module
+----------------------------------------
 
-.. automodule:: pyspike.spikes
+.. automodule:: pyspike.spike_sync
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyspike.PieceWiseConstFunc module
+----------------------------------------
+
+.. automodule:: pyspike.PieceWiseConstFunc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyspike.PieceWiseLinFunc module
+----------------------------------------
+
+.. automodule:: pyspike.PieceWiseLinFunc
     :members:
     :undoc-members:
     :show-inheritance:
 
+pyspike.DiscreteFunc module
+----------------------------------------
 
-Module contents
----------------
+.. automodule:: pyspike.DiscreteFunc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyspike.spikes module
+----------------------------------------
 
-.. automodule:: pyspike
+.. automodule:: pyspike.spikes
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/pyspike/DiscreteFunc.py b/pyspike/DiscreteFunc.py
index 2283e03..bd13e1f 100644
--- a/pyspike/DiscreteFunc.py
+++ b/pyspike/DiscreteFunc.py
@@ -23,10 +23,10 @@ class DiscreteFunc(object):
         """ Constructs the discrete function.
 
         :param x: array of length N defining the points at which the values are
-        defined.
+                  defined.
         :param y: array of length N degining the values at the points x.
         :param multiplicity: array of length N defining the multiplicity of the
-        values.
+                             values.
         """
         # convert parameters to arrays, also ensures copying
         self.x = np.array(x)
@@ -174,7 +174,7 @@ class DiscreteFunc(object):
 
     def avrg(self, interval=None):
         """ Computes the average of the interval sequence:
-        :math:`a = 1/N sum f_n ` where N is the number of intervals.
+        :math:`a = 1/N sum f_n` where N is the number of intervals.
 
         :param interval: averaging interval given as a pair of floats, a
                          sequence of pairs for averaging multiple intervals, or
diff --git a/pyspike/spikes.py b/pyspike/spikes.py
index 6a3353e..c7a1e40 100644
--- a/pyspike/spikes.py
+++ b/pyspike/spikes.py
@@ -54,7 +54,7 @@ def spike_train_from_string(s, sep=' ', is_sorted=False):
     :param s: the string with (ordered) spike times
     :param sep: The separator between the time numbers, default=' '.
     :param is_sorted: if True, the spike times are not sorted after loading,
-    if False, spike times are sorted with `np.sort`
+                      if False, spike times are sorted with `np.sort`
     :returns: array of spike times
     """
     if not(is_sorted):
-- 
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