added sphinx doc generation

7 files changed, 689 insertions, 150 deletions

diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..5acfcec
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PySpike.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PySpike.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PySpike"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PySpike"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000..48ebc7e
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,271 @@
+# -*- coding: utf-8 -*-
+#
+# PySpike documentation build configuration file, created by
+# sphinx-quickstart on Thu Oct 16 15:56:58 2014.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# 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.
+sys.path.insert(0, os.path.abspath('../pyspike'))
+
+def skip(app, what, name, obj, skip, options):
+    if name == "__init__":
+        return False
+    return skip
+
+def setup(app):
+    app.connect("autodoc-skip-member", skip)
+
+# -- 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.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'PySpike'
+copyright = u'2014, 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
+# built documents.
+#
+# The short X.Y version.
+version = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# 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 themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PySpikedoc'
+
+
+# -- 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': '',
+}
+
+# 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 = [
+  ('index', 'PySpike.tex', u'PySpike Documentation',
+   u'Mario Mulansky', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'pyspike', u'PySpike Documentation',
+     [u'Mario Mulansky'], 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 = [
+  ('index', 'PySpike', u'PySpike Documentation',
+   u'Mario Mulansky', 'PySpike', '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
diff --git a/doc/index.rst b/doc/index.rst
new file mode 100644
index 0000000..b94c162
--- /dev/null
+++ b/doc/index.rst
@@ -0,0 +1,22 @@
+.. PySpike documentation master file, created by
+   sphinx-quickstart on Thu Oct 16 15:56:58 2014.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to PySpike's documentation!
+===================================
+
+Reference:
+
+.. toctree::
+   :maxdepth: 2
+
+   pyspike
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/doc/pyspike.rst b/doc/pyspike.rst
new file mode 100644
index 0000000..39adea0
--- /dev/null
+++ b/doc/pyspike.rst
@@ -0,0 +1,38 @@
+pyspike package
+===============
+
+Submodules
+----------
+
+pyspike.distances module
+------------------------
+
+.. automodule:: pyspike.distances
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyspike.function module
+-----------------------
+
+.. automodule:: pyspike.function
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+pyspike.spikes module
+---------------------
+
+.. automodule:: pyspike.spikes
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyspike
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/pyspike/distances.py b/pyspike/distances.py
index 3e97b77..b0af24c 100644
--- a/pyspike/distances.py
+++ b/pyspike/distances.py
@@ -17,15 +17,17 @@ from pyspike import PieceWiseConstFunc, PieceWiseLinFunc
 # isi_profile
 ############################################################
 def isi_profile(spikes1, spikes2):
-    """ Computes the isi-distance profile S_isi(t) of the two given spike
-    trains. Retruns the profile as a PieceWiseConstFunc object. The S_isi
+    """ Computes the isi-distance profile :math:`S_{isi}(t)` of the two given
+    spike trains. Retruns the profile as a PieceWiseConstFunc object. The S_isi
     values are defined positive S_isi(t)>=0.  The spike trains are expected
     to have auxiliary spikes at the beginning and end of the interval. Use the
     function add_auxiliary_spikes to add those spikes to the spike train.
-    Args:
-    - spikes1, spikes2: ordered arrays of spike times with auxiliary spikes.
-    Returns:
-    - PieceWiseConstFunc describing the isi-distance.
+
+    :param spikes1: ordered array of spike times with auxiliary spikes.
+    :param spikes2: ordered array of spike times with auxiliary spikes.
+    :returns: The isi-distance profile :math:`S_{isi}(t)`
+    :rtype: :class:`pyspike.function.PieceWiseConstFunc`
+
     """
     # check for auxiliary spikes - first and last spikes should be identical
     assert spikes1[0] == spikes2[0], \
@@ -52,12 +54,15 @@ Falling back to slow python backend.")
 ############################################################
 def isi_distance(spikes1, spikes2):
     """ Computes the isi-distance I of the given spike trains. The
-    isi-distance is the integral over the isi distance profile S_isi(t):
-     I = \int_^T S_isi(t) dt.
-    Args:
-    - spikes1, spikes2: ordered arrays of spike times with auxiliary spikes.
-    Returns:
-    - double value: The isi-distance I.
+    isi-distance is the integral over the isi distance profile
+    :math:`S_{isi}(t)`:
+
+    .. math:: I = \int_0^T S_{isi}(t) dt.
+
+    :param spikes1: ordered array of spike times with auxiliary spikes.
+    :param spikes2: ordered array of spike times with auxiliary spikes.
+    :returns: The isi-distance I.
+    :rtype: double
     """
     return isi_profile(spikes1, spikes2).avrg()
 
@@ -71,10 +76,12 @@ def spike_profile(spikes1, spikes2):
     values are defined positive S_spike(t)>=0. The spike trains are expected to
     have auxiliary spikes at the beginning and end of the interval. Use the
     function add_auxiliary_spikes to add those spikes to the spike train.
-    Args:
-    - spikes1, spikes2: ordered arrays of spike times with auxiliary spikes.
-    Returns:
-    - PieceWiseLinFunc describing the spike-distance.
+
+    :param spikes1: ordered array of spike times with auxiliary spikes.
+    :param spikes2: ordered array of spike times with auxiliary spikes.
+    :returns: The spike-distance profile :math:`S_{spike}(t).
+    :rtype: :class:`pyspike.function.PieceWiseLinFunc`
+
     """
     # check for auxiliary spikes - first and last spikes should be identical
     assert spikes1[0] == spikes2[0], \
@@ -104,18 +111,20 @@ def spike_distance(spikes1, spikes2):
     """ Computes the spike-distance S of the given spike trains. The
     spike-distance is the integral over the isi distance profile S_spike(t):
      S = \int_^T S_spike(t) dt.
-    Args:
-    - spikes1, spikes2: ordered arrays of spike times with auxiliary spikes.
-    Returns:
-    - double value: The spike-distance S.
+
+    :param spikes1: ordered array of spike times with auxiliary spikes.
+    :param spikes2: ordered array of spike times with auxiliary spikes.
+    :returns: The spike-distance.
+    :rtype: double
+
     """
     return spike_profile(spikes1, spikes2).avrg()
 
 
 ############################################################
-# generic_profile_multi
+# _generic_profile_multi
 ############################################################
-def generic_profile_multi(spike_trains, pair_distance_func, indices=None):
+def _generic_profile_multi(spike_trains, pair_distance_func, indices=None):
     """ Internal implementation detail, don't call this function directly,
     use isi_profile_multi or spike_profile_multi instead.
 
@@ -153,7 +162,7 @@ def generic_profile_multi(spike_trains, pair_distance_func, indices=None):
 ############################################################
 # multi_distance_par
 ############################################################
-def multi_distance_par(spike_trains, pair_distance_func, indices=None):
+def _multi_distance_par(spike_trains, pair_distance_func, indices=None):
     """ parallel implementation of the multi-distance. Not currently used as
     it does not improve the performance.
     """
@@ -210,14 +219,15 @@ def isi_profile_multi(spike_trains, indices=None):
     trains. That is the average isi-distance of all pairs of spike-trains:
     S_isi(t) = 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j},
     where the sum goes over all pairs <i,j>
-    Args:
-    - spike_trains: list of spike trains
-    - indices: list of indices defining which spike trains to use,
-    if None all given spike trains are used (default=None)
-    Returns:
-    - A PieceWiseConstFunc representing the averaged isi distance S_isi(t)
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type state: list or None
+    :returns: The averaged isi profile :math:`<S_{isi}>(t)`
+    :rtype: :class:`pyspike.function.PieceWiseConstFunc`
     """
-    return generic_profile_multi(spike_trains, isi_profile, indices)
+    return _generic_profile_multi(spike_trains, isi_profile, indices)
 
 
 ############################################################
@@ -226,14 +236,14 @@ def isi_profile_multi(spike_trains, indices=None):
 def isi_distance_multi(spike_trains, indices=None):
     """ computes the multi-variate isi-distance for a set of spike-trains.
     That is the time average of the multi-variate spike profile:
-    S_isi = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j},
+    I = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{isi}^{i,j},
     where the sum goes over all pairs <i,j>
-    Args:
-    - spike_trains: list of spike trains
-    - indices: list of indices defining which spike trains to use,
-    if None all given spike trains are used (default=None)
-    Returns:
-    - A double value representing the averaged isi distance S_isi
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :returns: The time-averaged isi distance :math:`I`
+    :rtype: double
     """
     return isi_profile_multi(spike_trains, indices).avrg()
 
@@ -246,14 +256,14 @@ def spike_profile_multi(spike_trains, indices=None):
     trains. That is the average spike-distance of all pairs of spike-trains:
     S_spike(t) = 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j},
     where the sum goes over all pairs <i,j>
-    Args:
-    - spike_trains: list of spike trains
-    - indices: list of indices defining which spike-trains to use,
-    if None all given spike trains are used (default=None)
-    Returns:
-    - A PieceWiseLinFunc representing the averaged spike distance S(t)
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type indices: list or None
+    :returns: The averaged spike profile :math:`<S_{spike}>(t)`
+    :rtype: :class:`pyspike.function.PieceWiseLinFunc`
     """
-    return generic_profile_multi(spike_trains, spike_profile, indices)
+    return _generic_profile_multi(spike_trains, spike_profile, indices)
 
 
 ############################################################
@@ -264,12 +274,13 @@ def spike_distance_multi(spike_trains, indices=None):
     That is the time average of the multi-variate spike profile:
     S_{spike} = \int_0^T 2/((N(N-1)) sum_{<i,j>} S_{spike}^{i, j} dt
     where the sum goes over all pairs <i,j>
-    Args:
-    - spike_trains: list of spike trains
-    - indices: list of indices defining which spike-trains to use,
-    if None all given spike trains are used (default=None)
-    Returns:
-    - A double value representing the averaged spike distance S
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type indices: list or None
+    :returns: The averaged spike distance S.
+    :rtype: double
     """
     return spike_profile_multi(spike_trains, indices).avrg()
 
@@ -277,7 +288,7 @@ def spike_distance_multi(spike_trains, indices=None):
 ############################################################
 # generic_distance_matrix
 ############################################################
-def generic_distance_matrix(spike_trains, dist_function, indices=None):
+def _generic_distance_matrix(spike_trains, dist_function, indices=None):
     """ Internal implementation detail. Don't use this function directly.
     Instead use isi_distance_matrix or spike_distance_matrix.
     Computes the time averaged distance of all pairs of spike-trains.
@@ -311,15 +322,16 @@ def generic_distance_matrix(spike_trains, dist_function, indices=None):
 ############################################################
 def isi_distance_matrix(spike_trains, indices=None):
     """ Computes the time averaged isi-distance of all pairs of spike-trains.
-    Args:
-    - spike_trains: list of spike trains
-    - indices: list of indices defining which spike-trains to use
-    if None all given spike-trains are used (default=None)
-    Return:
-    - a 2D array of size len(indices)*len(indices) containing the average
-    pair-wise isi-distance
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type indices: list or None
+    :returns: 2D array with the pair wise time average isi distances
+              :math:`I_{ij}`
+    :rtype: np.array
     """
-    return generic_distance_matrix(spike_trains, isi_distance, indices)
+    return _generic_distance_matrix(spike_trains, isi_distance, indices)
 
 
 ############################################################
@@ -327,12 +339,13 @@ def isi_distance_matrix(spike_trains, indices=None):
 ############################################################
 def spike_distance_matrix(spike_trains, indices=None):
     """ Computes the time averaged spike-distance of all pairs of spike-trains.
-    Args:
-    - spike_trains: list of spike trains
-    - indices: list of indices defining which spike-trains to use
-    if None all given spike-trains are used (default=None)
-    Return:
-    - a 2D array of size len(indices)*len(indices) containing the average
-    pair-wise spike-distance
+
+    :param spike_trains: list of spike trains
+    :param indices: list of indices defining which spike trains to use,
+                    if None all given spike trains are used (default=None)
+    :type indices: list or None
+    :returns: 2D array with the pair wise time average spike distances
+              :math:`S_{ij}`
+    :rtype: np.array
     """
-    return generic_distance_matrix(spike_trains, spike_distance, indices)
+    return _generic_distance_matrix(spike_trains, spike_distance, indices)
diff --git a/pyspike/function.py b/pyspike/function.py
index b161034..ed47f27 100644
--- a/pyspike/function.py
+++ b/pyspike/function.py
@@ -16,15 +16,16 @@ import numpy as np
 ##############################################################
 # PieceWiseConstFunc
 ##############################################################
-class PieceWiseConstFunc:
+class PieceWiseConstFunc(object):
     """ A class representing a piece-wise constant function. """
 
     def __init__(self, x, y):
         """ Constructs the piece-wise const function.
-        Args:
-        - x: array of length N+1 defining the edges of the intervals of the pwc
-        function.
-        - y: array of length N defining the function values at the intervals.
+
+        :param x: array of length N+1 defining the edges of the intervals of
+                  the pwc function.
+        :param y: array of length N defining the function values at the
+                  intervals.
         """
         # convert parameters to arrays, also ensures copying
         self.x = np.array(x)
@@ -32,19 +33,19 @@ class PieceWiseConstFunc:
 
     def copy(self):
         """ Returns a copy of itself
-        Returns:
-        - PieceWiseConstFunc copy
+
+        :rtype: :class:`PieceWiseConstFunc`
         """
         return PieceWiseConstFunc(self.x, self.y)
 
     def almost_equal(self, other, decimal=14):
         """ Checks if the function is equal to another function up to `decimal`
         precision.
-        Args:
-        - other: another PieceWiseConstFunc object
-        Returns:
-        True if the two functions are equal up to `decimal` decimals,
-        False otherwise
+
+        :param: other: another :class:`PieceWiseConstFunc`
+        :returns: True if the two functions are equal up to `decimal` decimals,
+                  False otherwise
+        :rtype: bool
         """
         eps = 10.0**(-decimal)
         return np.allclose(self.x, other.x, atol=eps, rtol=0.0) and \
@@ -53,6 +54,14 @@ class PieceWiseConstFunc:
     def get_plottable_data(self):
         """ Returns two arrays containing x- and y-coordinates for immeditate
         plotting of the piece-wise function.
+
+        :returns: (x_plot, y_plot) containing plottable data
+        :rtype: pair of np.array
+
+        Example::
+
+            x, y = f.get_plottable_data()
+            plt.plot(x, y, '-o', label="Piece-wise const function")
         """
 
         x_plot = np.empty(2*len(self.x)-2)
@@ -67,9 +76,10 @@ class PieceWiseConstFunc:
 
     def avrg(self):
         """ Computes the average of the piece-wise const function:
-        a = 1/T int f(x) dx where T is the length of the interval.
-        Returns:
-        - the average a.
+        :math:`a = 1/T int_0^T f(x) dx` where T is the length of the interval.
+
+        :returns: the average a.
+        :rtype: double
         """
         return np.sum((self.x[1:]-self.x[:-1]) * self.y) / \
             (self.x[-1]-self.x[0])
@@ -77,8 +87,9 @@ class PieceWiseConstFunc:
     def add(self, f):
         """ Adds another PieceWiseConst function to this function.
         Note: only functions defined on the same interval can be summed.
-        Args:
-        - f: PieceWiseConst function to be added.
+
+        :param f: :class:`PieceWiseConstFunc` function to be added.
+        :rtype: None
         """
         assert self.x[0] == f.x[0], "The functions have different intervals"
         assert self.x[-1] == f.x[-1], "The functions have different intervals"
@@ -99,8 +110,10 @@ that PySpike is installed by running\n 'python setup.py build_ext --inplace'! \
 
     def mul_scalar(self, fac):
         """ Multiplies the function with a scalar value
-        Args:
-        - fac: Value to multiply
+
+        :param fac: Value to multiply
+        :type fac: double
+        :rtype: None
         """
         self.y *= fac
 
@@ -113,13 +126,13 @@ class PieceWiseLinFunc:
 
     def __init__(self, x, y1, y2):
         """ Constructs the piece-wise linear function.
-        Args:
-        - x: array of length N+1 defining the edges of the intervals of the pwc
-        function.
-        - y1: array of length N defining the function values at the left of the
-        intervals.
-        - y2: array of length N defining the function values at the right of
-        the intervals.
+
+        :param x: array of length N+1 defining the edges of the intervals of
+                  the pwc function.
+        :param y1: array of length N defining the function values at the left
+                  of the intervals.
+        :param y2: array of length N defining the function values at the right
+                  of the intervals.
         """
         # convert to array, which also ensures copying
         self.x = np.array(x)
@@ -128,19 +141,19 @@ class PieceWiseLinFunc:
 
     def copy(self):
         """ Returns a copy of itself
-        Returns:
-        - PieceWiseLinFunc copy
+
+        :rtype: :class`PieceWiseLinFunc`
         """
         return PieceWiseLinFunc(self.x, self.y1, self.y2)
 
     def almost_equal(self, other, decimal=14):
         """ Checks if the function is equal to another function up to `decimal`
         precision.
-        Args:
-        - other: another PieceWiseLinFunc object
-        Returns:
-        True if the two functions are equal up to `decimal` decimals,
-        False otherwise
+
+        :param: other: another :class:`PieceWiseLinFunc`
+        :returns: True if the two functions are equal up to `decimal` decimals,
+                  False otherwise
+        :rtype: bool
         """
         eps = 10.0**(-decimal)
         return np.allclose(self.x, other.x, atol=eps, rtol=0.0) and \
@@ -150,6 +163,14 @@ class PieceWiseLinFunc:
     def get_plottable_data(self):
         """ Returns two arrays containing x- and y-coordinates for immeditate
         plotting of the piece-wise function.
+
+        :returns: (x_plot, y_plot) containing plottable data
+        :rtype: pair of np.array
+
+        Example::
+
+            x, y = f.get_plottable_data()
+            plt.plot(x, y, '-o', label="Piece-wise const function")
         """
         x_plot = np.empty(2*len(self.x)-2)
         x_plot[0] = self.x[0]
@@ -162,27 +183,20 @@ class PieceWiseLinFunc:
 
     def avrg(self):
         """ Computes the average of the piece-wise linear function:
-        a = 1/T int f(x) dx where T is the length of the interval.
-        Returns:
-        - the average a.
+        :math:`a = 1/T int_0^T f(x) dx` where T is the length of the interval.
+
+        :returns: the average a.
+        :rtype: double
         """
         return np.sum((self.x[1:]-self.x[:-1]) * 0.5*(self.y1+self.y2)) / \
             (self.x[-1]-self.x[0])
 
-    def abs_avrg(self):
-        """ Computes the absolute average of the piece-wise linear function:
-        a = 1/T int |f(x)| dx where T is the length of the interval.
-        Returns:
-        - the average a.
-        """
-        return np.sum((self.x[1:]-self.x[:-1]) * 0.5 *
-                      (np.abs(self.y1)+np.abs(self.y2)))/(self.x[-1]-self.x[0])
-
     def add(self, f):
         """ Adds another PieceWiseLin function to this function.
         Note: only functions defined on the same interval can be summed.
-        Args:
-        - f: PieceWiseLin function to be added.
+
+        :param f: :class:`PieceWiseLinFunc` function to be added.
+        :rtype: None
         """
         assert self.x[0] == f.x[0], "The functions have different intervals"
         assert self.x[-1] == f.x[-1], "The functions have different intervals"
@@ -209,8 +223,10 @@ that PySpike is installed by running\n 'python setup.py build_ext --inplace'! \
 
     def mul_scalar(self, fac):
         """ Multiplies the function with a scalar value
-        Args:
-        - fac: Value to multiply
+
+        :param fac: Value to multiply
+        :type fac: double
+        :rtype: None
         """
         self.y1 *= fac
         self.y2 *= fac
@@ -218,12 +234,12 @@ that PySpike is installed by running\n 'python setup.py build_ext --inplace'! \
 
 def average_profile(profiles):
     """ Computes the average profile from the given ISI- or SPIKE-profiles.
-    Args:
-    - profiles: list of PieceWiseConstFunc or PieceWiseLinFunc representing
-    ISI- or SPIKE-profiles to be averaged
-    Returns:
-    - avrg_profile: PieceWiseConstFunc or PieceWiseLinFunc containing the
-    average profile.
+
+    :param profiles: list of :class:`PieceWiseConstFunc` or
+                     :class:`PieceWiseLinFunc` representing ISI- or
+                     SPIKE-profiles to be averaged.
+    :returns: the averages profile :math:`<S_{isi}>` or :math:`<S_{spike}>`.
+    :rtype: :class:`PieceWiseConstFunc` or :class:`PieceWiseLinFunc`
     """
     assert len(profiles) > 1
 
diff --git a/pyspike/spikes.py b/pyspike/spikes.py
index 68c8bc1..6b6e2e7 100644
--- a/pyspike/spikes.py
+++ b/pyspike/spikes.py
@@ -15,15 +15,16 @@ import numpy as np
 ############################################################
 def add_auxiliary_spikes(spike_train, time_interval):
     """ Adds spikes at the beginning and end of the given time interval.
-    Args:
-    - spike_train: ordered array of spike times
-    - time_interval: A pair (T_start, T_end) of values representing the start
-    and end time of the spike train measurement or a single value representing
-    the end time, the T_start is then assuemd as 0. Auxiliary spikes will be
-    added to the spike train at the beginning and end of this interval, if they
-    are not yet present.
-    Returns:
-    - spike train with additional spikes at T_start and T_end.
+
+    :param spike_train: ordered array of spike times
+    :param time_interval: A pair (T_start, T_end) of values representing the
+                          start and end time of the spike train measurement or
+                          a single value representing the end time, the T_start
+                          is then assuemd as 0. Auxiliary spikes will be added
+                          to the spike train at the beginning and end of this
+                          interval, if they are not yet present.
+    :type time_interval: pair of doubles or double
+    :returns: spike train with additional spikes at T_start and T_end.
 
     """
     try:
@@ -49,12 +50,11 @@ def add_auxiliary_spikes(spike_train, time_interval):
 ############################################################
 def spike_train_from_string(s, sep=' ', sort=True):
     """ Converts a string of times into an array of spike times.
-    Args:
-    - s: the string with (ordered) spike times
-    - sep: The separator between the time numbers, default=' '.
-    - sort: If True, the spike times are order via `np.sort`, default=True.
-    Returns:
-    - array of spike times
+
+    :param s: the string with (ordered) spike times
+    :param sep: The separator between the time numbers, default=' '.
+    :param sort: If True, the spike times are order via `np.sort`, default=True
+    :returns: array of spike times
     """
     if sort:
         return np.sort(np.fromstring(s, sep=sep))
@@ -75,15 +75,18 @@ def load_spike_trains_from_txt(file_name, time_interval=None,
     end of each spike train. However, if `time_interval == None`, no auxiliary
     spikes are added, but note that the Spike and ISI distance both require
     auxiliary spikes.
-    Args:
-    - file_name: The name of the text file.
-    - time_interval: A pair (T_start, T_end) of values representing the start
-    and end time of the spike train measurement or a single value representing
-    the end time, the T_start is then assuemd as 0. Auxiliary spikes will be
-    added to the spike train at the beginning and end of this interval.
-    - separator: The character used to seprate the values in the text file.
-    - comment: Lines starting with this character are ignored.
-    - sort: If true, the spike times are order via `np.sort`, default=True.
+
+    :param file_name: The name of the text file.
+    :param time_interval: A pair (T_start, T_end) of values representing the
+                          start and end time of the spike train measurement
+                          or a single value representing the end time, the
+                          T_start is then assuemd as 0. Auxiliary spikes will
+                          be added to the spike train at the beginning and end
+                          of this interval.
+    :param separator: The character used to seprate the values in the text file
+    :param comment: Lines starting with this character are ignored.
+    :param sort: If true, the spike times are order via `np.sort`, default=True
+    :returns: list of spike trains
     """
     spike_trains = []
     spike_file = open(file_name, 'r')
@@ -102,10 +105,9 @@ def load_spike_trains_from_txt(file_name, time_interval=None,
 ############################################################
 def merge_spike_trains(spike_trains):
     """ Merges a number of spike trains into a single spike train.
-    Args:
-    - spike_trains: list of arrays of spike times
-    Returns:
-    - array with the merged spike times
+
+    :param spike_trains: list of arrays of spike times
+    :returns: spike train with the merged spike times
     """
     # get the lengths of the spike trains
     lens = np.array([len(st) for st in spike_trains])