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CoSMoMVPA · Dec 1, 2016 · 2ed6471 · 2ed6471
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diff --git a/doc/source/cimec2014.rst b/doc/source/cimec2014.rst
@@ -22,12 +22,12 @@ Contents
 .. toctree::
     :maxdepth: 1
 
-    modindex
-    modindex_hdr
-    modindex_skl
+    matindex
+    matindex_hdr
+    matindex_skl
 
-    modindex_run
-    modindex_skl_run
+    matindex_run
+    matindex_skl_run
 
 Matlab outputs: matlab_pb_toc_
 
@@ -37,14 +37,14 @@ Miscellaneous
 .. toctree::
     :maxdepth: 1
 
-    modindex_test
-    modindex_demo
+    matindex_test
+    matindex_demo
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
-* :ref:`modindex`
+* :ref:`matindex`
 * :ref:`search`
 
 .. _matlab_pb_toc: _static/publish/index.html

diff --git a/doc/source/cimec2016.rst b/doc/source/cimec2016.rst
@@ -24,12 +24,12 @@ Contents
 .. toctree::
     :maxdepth: 1
 
-    modindex
-    modindex_hdr
-    modindex_skl
+    matindex
+    matindex_hdr
+    matindex_skl
 
-    modindex_run
-    modindex_skl_run
+    matindex_run
+    matindex_skl_run
 
 Matlab outputs: matlab_pb_toc_
 
@@ -39,14 +39,14 @@ Miscellaneous
 .. toctree::
     :maxdepth: 1
 
-    modindex_test
-    modindex_demo
+    matindex_test
+    matindex_demo
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
-* :ref:`modindex`
+* :ref:`matindex`
 * :ref:`search`
 
 .. _matlab_pb_toc: _static/publish/index.html

diff --git a/doc/source/contribute.rst b/doc/source/contribute.rst
@@ -931,7 +931,7 @@ To indicate that a code block is an exercise, place a line containing ``% >@@>``
 
 Documentation tests
 +++++++++++++++++++
-When providing examples it is a good idea to write them in the shape of examples, so that running :ref:`cosmo_run_tests` will actually test whether the code runs as advertised. Many `modules <modindex.html>`_ have such doctests; you can spot them in the ``Examples:`` section of the help info, where the expected output is preceded by ``>``. For example:
+When providing examples it is a good idea to write them in the shape of examples, so that running :ref:`cosmo_run_tests` will actually test whether the code runs as advertised. Many `modules <matindex.html>`_ have such doctests; you can spot them in the ``Examples:`` section of the help info, where the expected output is preceded by ``>``. For example:
 
     .. include:: matlab/cosmo_strsplit_hdr.txt
 

diff --git a/doc/source/cosmo2013.rst b/doc/source/cosmo2013.rst
@@ -22,12 +22,12 @@ Contents
 .. toctree::
     :maxdepth: 1
 
-    modindex
-    modindex_hdr
-    modindex_skl
+    matindex
+    matindex_hdr
+    matindex_skl
 
-    modindex_run
-    modindex_skl_run
+    matindex_run
+    matindex_skl_run
 
 Matlab outputs: matlab_pb_toc_
 
@@ -37,14 +37,14 @@ Miscellaneous
 .. toctree::
     :maxdepth: 1
 
-    modindex_test
-    modindex_demo
+    matindex_test
+    matindex_demo
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
-* :ref:`modindex`
+* :ref:`matindex`
 * :ref:`search`
 
 .. _matlab_pb_toc: _static/publish/index.html

diff --git a/doc/source/ex_dataset_basics.rst b/doc/source/ex_dataset_basics.rst
@@ -49,7 +49,7 @@ Before starting this exercise, please make sure you have read about:
 - :ref:`cosmomvpa_dataset`
 - :ref:`matlab_octave_logical_masking`
 
-Using some basic :ref:`CoSMoMVPA functions <modindex>` we start loading a single NIFTI image of an anatomical scan.
+Using some basic :ref:`CoSMoMVPA functions <matindex>` we start loading a single NIFTI image of an anatomical scan.
 Use the function :ref:`cosmo_fmri_dataset` to load the nifti file of the brain of subject s01 (``brain.nii``) and assign the result to a struct 'ds'. What is contained in this struct?
 
 Make a histogram of all voxels, and a second histogram of the non-zero voxels of the brain. There are two 'bumps' - what do they represent?

diff --git a/doc/source/ex_searchlight.rst b/doc/source/ex_searchlight.rst
@@ -1,8 +1,6 @@
 .. #   For CoSMoMVPA's license terms and conditions, see   #
    #   the COPYING file distributed with CoSMoMVPA         #
 
-.. ex_searchlight
-
 Write a searchlight function that computes a generic dataset measure
 ====================================================================
 

diff --git a/doc/source/get_started.rst b/doc/source/get_started.rst
@@ -50,9 +50,9 @@ Next steps
 Once you are ready:
 
 - run the :ref:`demos <contents_demo.rst>`.
-- look at the :ref:`runnable examples <modindex_run>` and the associated `Matlab outputs`_.
+- look at the :ref:`runnable examples <matindex_run>` and the associated `Matlab outputs`_.
 - try the :ref:`exercises <ex_toc>`.
-- explore the :ref:`CoSMoMVPA functions <modindex>`.
+- explore the :ref:`CoSMoMVPA functions <matindex>`.
 
 Some examples of analyses that can be run with CoSMoMVPA_:
 

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -44,7 +44,7 @@ CoSMoMVPA
 .. image:: _static/icon_download.png
    :target: download.html
 .. image:: _static/icon_modules.png
-   :target: modindex.html
+   :target: matindex.html
 .. image:: _static/icon_documentation.png
    :target: documentation.html
 .. image:: _static/icon_exercises.png
@@ -71,8 +71,8 @@ CoSMoMVPA
 Indices and tables
 ==================
 
-* :ref:`genindex`
-* :ref:`modindex`
+* :ref:`documentation`
+* :ref:`matindex`
 * :ref:`search`
 
 .. include:: links.txt

diff --git a/doc/source/prni2016.rst b/doc/source/prni2016.rst
@@ -27,12 +27,12 @@ Contents
 .. toctree::
     :maxdepth: 1
 
-    modindex
-    modindex_hdr
-    modindex_skl
+    matindex
+    matindex_hdr
+    matindex_skl
 
-    modindex_run
-    modindex_skl_run
+    matindex_run
+    matindex_skl_run
 
 Matlab outputs: matlab_pb_toc_
 
@@ -42,14 +42,14 @@ Miscellaneous
 .. toctree::
     :maxdepth: 1
 
-    modindex_test
-    modindex_demo
+    matindex_test
+    matindex_demo
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
-* :ref:`modindex`
+* :ref:`matindex`
 * :ref:`search`
 
 .. _matlab_pb_toc: _static/publish/index.html

diff --git a/doc/source/rhul2016.rst b/doc/source/rhul2016.rst
@@ -24,12 +24,12 @@ Contents
 .. toctree::
     :maxdepth: 1
 
-    modindex
-    modindex_hdr
-    modindex_skl
+    matindex
+    matindex_hdr
+    matindex_skl
 
-    modindex_run
-    modindex_skl_run
+    matindex_run
+    matindex_skl_run
 
 Matlab outputs: matlab_pb_toc_
 
@@ -39,14 +39,14 @@ Miscellaneous
 .. toctree::
     :maxdepth: 1
 
-    modindex_test
-    modindex_demo
+    matindex_test
+    matindex_demo
 
 Indices and tables
 ==================
 
 * :ref:`genindex`
-* :ref:`modindex`
+* :ref:`matindex`
 * :ref:`search`
 
 .. _matlab_pb_toc: _static/publish/index.html