diff --git a/doc/source/cimec2014.rst b/doc/source/cimec2014.rst index 4adbc7d7..0fd15448 100644 --- 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 index feadb64b..0a1da936 100644 --- 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 index 743f3295..771e398e 100644 --- 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 `_ 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 `_ 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 index 8496c481..f28140a9 100644 --- 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 index fd427595..1adc0728 100644 --- 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 ` we start loading a single NIFTI image of an anatomical scan. +Using some basic :ref:`CoSMoMVPA functions ` 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 index 2ee96c47..3820351c 100644 --- 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 index ab1edfd3..aa126244 100644 --- 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 `. -- look at the :ref:`runnable examples ` and the associated `Matlab outputs`_. +- look at the :ref:`runnable examples ` and the associated `Matlab outputs`_. - try the :ref:`exercises `. -- explore the :ref:`CoSMoMVPA functions `. +- explore the :ref:`CoSMoMVPA functions `. Some examples of analyses that can be run with CoSMoMVPA_: diff --git a/doc/source/index.rst b/doc/source/index.rst index 9866c28b..12a053d4 100644 --- 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 index b33c6118..5c65b963 100644 --- 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 index 323708f1..771f7528 100644 --- 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