A number of minor documentation cleanups.

diff --git a/doc/conf.py b/doc/conf.py
index d469d8b553ce167d043628bfed74297286925b1b..43786fd28fac7d3226d213f0e03de90d4dda0579 100644 (file)
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -25,7 +25,8 @@ import hooke
 
 # 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.doctest', 'sphinx.ext.coverage',
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
+              'sphinx.ext.doctest', 'sphinx.ext.coverage',
               'numpydoc']
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/doc/config.txt b/doc/config.txt
index 6f0359b638d72502d5d93362cc62c2d6d1612bde..c5d594fb8c4df10c12516ab6fb0b9fb1bd3f2fd6 100644 (file)
--- a/doc/config.txt
+++ b/doc/config.txt
@@ -30,9 +30,9 @@ To print a well commented example config file to stdout.
 Finding configuration files
 ---------------------------
 
-The default search path follows the `Filesystem Hierarchy
-Standard`_, and so will probably need adjustment for non-*nix systems.
-The default path list is
+The default search path follows the `Filesystem Hierarchy Standard`_,
+and so will probably need adjustment for non-*nix systems.  The
+default path list is
 
 * /usr/share/hooke/hooke.cfg
 * /etc/hooke/hooke.cfg

diff --git a/doc/gui.txt b/doc/gui.txt
index a22c71982e9048628c63ca8a4a12b562207b98ee..25c0f48d8883f198c9a8dd01f10e27218285155d 100644 (file)
--- a/doc/gui.txt
+++ b/doc/gui.txt
@@ -1,4 +1,7 @@
-# Interface
+*****************
+The GUI interface
+*****************
+
 by Rolf Schmidt <rschmidt@alcor.concordia.ca>
 
 You can dock/undock all windows except for plot tab (I would like to
@@ -16,11 +19,12 @@ In the 'Folders' pane you can double-click playlists (with hkp
 extension) to open them (you cannot double-click curves to open them)
 
 Commands in the 'Commands'-pane that work
-- autopeak (only partially, everything that has to do with clicking on the plot does not work)
-- genlist
-- loadlist
-- convfilt
-- flatfilt
+
+* autopeak (only partially, everything that has to do with clicking on the plot does not work)
+* genlist
+* loadlist
+* convfilt
+* flatfilt
 
 When you open or generate a playlist, Hooke seems to hang. This is
 actually not the case, just wait. Hooke loads all the curves into

diff --git a/doc/hacking.txt b/doc/hacking.txt
index 86e969bfe43b92195a263161c4340edcdb85352c..ab8d9dc565684304b8ec1858ef5abeaa4d16f6a2 100644 (file)
--- a/doc/hacking.txt
+++ b/doc/hacking.txt
@@ -2,14 +2,18 @@
 Hacking Hooke
 *************
 
+.. toctree::
+   :maxdepth: 2
+
+   testing.txt
 
 Architecture
 ============
 
 To clean up the internals, were going to go crazy on the
 object-oriented front, and try to keep the core functionality free of
-any dependencies other than the `Python Standard Library`_ and `Numpy`_
-/ `Scipy`_.
+any dependencies other than the `Python Standard Library`_ and Numpy_
+/ Scipy_.
 
 .. _Python Standard Library: http://docs.python.org/library/
 .. _Numpy: http://numpy.scipy.org/
@@ -29,6 +33,7 @@ files.
 
 On the testing side, the need to stick to the standard library relaxes
 (developers can install extra packages), so we can use nose_.  See
-the `Testing`_ section for more information.
+the Testing_ section for more information.
 
+.. _nose: http://somethingaboutorange.com/mrl/projects/nose/0.11.3/
 .. _Testing: testing.txt

diff --git a/doc/index.txt b/doc/index.txt
index cb6b97b64e3b6cbaecae5ae9ddf5d0a5415fc2f2..3e88c31f3f5878553b072af6fd2e5a8275ce7809 100644 (file)
--- a/doc/index.txt
+++ b/doc/index.txt
@@ -27,6 +27,7 @@ Contents:
 
    install.txt
    tutorial.txt
+   config.txt
    hacking.txt
    hooke/hooke.txt
    doc.txt
@@ -59,8 +60,8 @@ If you have troubles in using Hooke:
 1. Search the `issue tracker`_.
 2. Look at the `trouble shooting wiki page`_.
 3. Search the `discussion group`_.
-3. Ask a question in the discussion group.
-4. File a bug on the issue tracker.
+4. Ask a question in the discussion group.
+5. File a bug on the issue tracker.
 
 .. _issue tracker: http://code.google.com/p/hooke/issues/list
 .. _trouble shooting wiki page:

diff --git a/doc/install.txt b/doc/install.txt
index a8b754c06dd1a6efe0ffffd4d8cccafa091239a4..96d07d011b146c536dc967c448b5daf7e188e09a 100644 (file)
--- a/doc/install.txt
+++ b/doc/install.txt
@@ -17,11 +17,11 @@ You'll need the following Python modules:
 * Matplotlib_ (for generating plots)
 * wxPython_ (for the GUI)
 
-.. Numpy: http://numpy.scipy.org/
-.. Scipy: http://www.scipy.org/
-.. Python: http://www.python.org/
-.. Matplotlib: http://matplotlib.sourceforge.net/
-.. wxPython: http://www.wxpython.org/
+.. _Numpy: http://numpy.scipy.org/
+.. _Scipy: http://www.scipy.org/
+.. _Python: http://www.python.org/
+.. _Matplotlib: http://matplotlib.sourceforge.net/
+.. _wxPython: http://www.wxpython.org/
 
 Getting the source
 ==================

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 1158aad3974ffa022b777fb16023be28fd781130..8f68f90ce1509f79e9368c65828e8d6a1b636169 100644 (file)
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -8,6 +8,11 @@ Benedetti, EPFL, Lausanne)
 .. _A short video showing Hooke in action:
   https://documents.epfl.ch/users/f/fb/fbenedet/www/hooke_short_demostration.ogv
 
+.. toctree::
+   :maxdepth: 2
+
+   gui.txt
+
 Introduction
 ============
 
@@ -44,6 +49,8 @@ Installation_), the equivalent command is::
 
 You may need to give the full path for Python on Windows systems.
 
+.. _plugins: hooke/hooke.plugin.txt
+
 As Hooke launches, you should see something like the following in your
 terminal::
 
@@ -218,9 +225,11 @@ TODO: multiple cycles?  Solution: blank lines for "breaks", add option
 to extract specific sections using Python's slice notation.
 
 
-Interacting with the plot (no plots in command line mode...)
+Interacting with the plot
 -------------------------
 
+(no plots in command line mode...)
+
 Measuring distances and forces
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/hooke/__init__.py b/hooke/__init__.py
index 7a2af6c25bb6af3d0f5fdef9958d9157e4fd3522..b90ff3d8f016e52a1717013bc565ccfcc93731db 100644 (file)
--- a/hooke/__init__.py
+++ b/hooke/__init__.py
@@ -1,6 +1,6 @@
 # COPYRIGHT
 
-"""The hooke module does all the legwork for Hooke_ (BE).
+"""The hooke module does all the legwork for Hooke_.
 
 .. _hooke: http://code.google.com/p/hooke/