nest · stinebuu · Nov 10, 2020 · Mar 26, 2020 · Mar 26, 2020 · Mar 26, 2020
diff --git a/doc/README.rst b/doc/README.rst
@@ -1,5 +1,7 @@
+:orphan:
+
 The doc folder
-===============
+==============
 
 The documentation for NEST is contained in this folder. We are currently working
 on improving the documentation and making updates. However, if you notice

diff --git a/doc/citing-nest.rst b/doc/citing-nest.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Cite NEST
 =========
 

diff --git a/doc/connection-generator-interface.rst b/doc/connection-generator-interface.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 The Connection Generator Interface
 ==================================
 

diff --git a/doc/contribute/mailing_list_guidelines.rst b/doc/contribute/mailing_list_guidelines.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Guidelines for contributing to the mailing list
 =================================================
 

diff --git a/doc/contribute/templates_styleguides/example_template.rst b/doc/contribute/templates_styleguides/example_template.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 PyNEST example template
 ==========================
 

diff --git a/doc/contribute/templates_styleguides/pyapi_template.rst b/doc/contribute/templates_styleguides/pyapi_template.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 PyNEST API template
 =====================
 

diff --git a/doc/contribute/templates_styleguides/vim_support_sli.rst b/doc/contribute/templates_styleguides/vim_support_sli.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Vim support for SLI files
 =========================
 
@@ -14,4 +16,4 @@ Then add the following lines to your ``~/.vimrc`` file to use it:
 
     " sli
     au BufRead,BufNewFile *.sli set filetype=sli
-    au FileType sli setl foldenable foldmethod=syntax
+    au FileType sli setl foldenable foldmethod=syntax
diff --git a/doc/examples/index.rst b/doc/examples/index.rst
@@ -46,7 +46,6 @@ PyNEST examples
    :maxdepth: 1
    :caption: Random balanced network examples
 
-   ../auto_examples/brunel_alpha_numpy
    ../auto_examples/brunel_alpha_nest
    ../auto_examples/brunel_delta_nest
    ../auto_examples/brunel_siegert_nest
@@ -76,7 +75,6 @@ PyNEST examples
    :caption: Connection set algebra examples
 
    ../auto_examples/csa_example
-   ../auto_examples/csa_topology_example
 
 .. toctree::
    :maxdepth: 1

diff --git a/doc/faqs/index.rst b/doc/faqs/index.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Frequently Asked Questions
 ==========================
 

diff --git a/doc/features.rst b/doc/features.rst
diff --git a/doc/glossary.rst b/doc/glossary.rst
@@ -57,6 +57,8 @@ Common abbreviations in NEST
    virtual process
 
 Physical units and variable names used for NEST parameters
+:orphan:
+
 -------------------------------------------------------------
 
 .. note::

diff --git a/doc/guides/connection_management.rst b/doc/guides/connection_management.rst
@@ -381,8 +381,7 @@ Topological Connections
 
 If the connect functions above are not sufficient, the topology provides
 more sophisticated functions. For example, it is possible to create
-receptive field structures and much more! See :doc:`Topological
-Connections <topology/index>` for more information.
+receptive field structures and much more! See :doc:`spatial/index` for more information.
 
 .. _receptor-types:
 

diff --git a/doc/guides/index.rst b/doc/guides/index.rst
@@ -26,11 +26,10 @@ Here you can find details on a variety of topics in NEST.
     using_nest_with_music
 
 
-.. toctree::
-   :maxdepth: 1
-   :caption: Model Details
+Model Details
+-------------
 
-   aeif_models_implementation
-   HillTononiModels
-   IAF_neurons_singularity
-   noise_generator
+* :download:`aeif_models_implementation.ipynb <aeif_models_implementation.ipynb>`
+* :download:`HillTononiModels.ipynb <HillTononiModels.ipynb>`
+* :download:`IAF_neurons_singularity.ipynb <IAF_neurons_singularity.ipynb>`
+* :download:`noise_generator.ipynb <noise_generator.ipynb>`
diff --git a/doc/guides/nest2_to_nest3/nest2_to_nest3_detailed_transition_guide.rst b/doc/guides/nest2_to_nest3/nest2_to_nest3_detailed_transition_guide.rst
@@ -423,7 +423,7 @@ The logic module contains logical expressions between nest.Parameter's.
 .. _distr_param:
 
 :green:`spatial_distributions`
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 The spatial_distributions module contains random distributions that take a spatial
 parameter as input and applies the distribution on the parameter. They are used
 for spatially distributed nodes.

diff --git a/doc/guides/nest2_to_nest3/nest2_to_nest3_overview.rst b/doc/guides/nest2_to_nest3/nest2_to_nest3_overview.rst
@@ -394,7 +394,7 @@ as NodeCollections.
 
 .. seealso::
 
-    You can find a :doc:`full example <../examples/SynapseCollection>` in our example network page
+    You can find a :doc:`full example <../../auto_examples/synapsecollection>` in our example network page.
 
 Printing
     Printing a SynapseCollection produces a table of source and target node IDs
@@ -1368,8 +1368,6 @@ All details about the new infrastructure can be found in the guide on
 What's removed?
 ---------------
 
-.. subnet_rm::
-
 Subnets
 ~~~~~~~
 
@@ -1402,8 +1400,6 @@ prints ID ranges and model names of the nodes in the network.
   |                                              |                                       |
   +----------------------------------------------+---------------------------------------+
 
-.. model_rm::
-
 Models
 ~~~~~~
 
@@ -1427,8 +1423,6 @@ be used instead.
 Furthermore, the model `iaf_tum_2000` has been renamed to `iaf_psc_exp_htum`. iaf_psc_exp_htum is
 the exact same model as iaf_tum_2000, it has just been renamed to match NEST's naming conventions.
 
-.. function_rm::
-
 Functions
 ~~~~~~~~~
 

diff --git a/doc/guides/running_simulations.rst b/doc/guides/running_simulations.rst
@@ -113,7 +113,7 @@ end of the interval* during which the threshold was crossed.
 
 NEST also has a some models that determine the precise time of the
 threshold crossing during the interval. Please see the documentation on
-:doc:`precise spike time neurons <simulations_with_precise_spike_time>`
+:doc:`precise spike time neurons <simulations_with_precise_spike_times>`
 for details about neuron update in continuous time and the
 :doc:`documentation on connection management <connection_management>`
 for how to set the delay when creating synapses.

diff --git a/doc/guides/spatial/guide_spatially_structured_networks.rst b/doc/guides/spatial/guide_spatially_structured_networks.rst
@@ -299,7 +299,7 @@ To create a spatially distributed NodeCollection from a list, do the following:
     :start-after: #{ layer4b #}
     :end-before: #{ end #}
 
-.. _fig_layer4:
+.. _fig_layer4b:
 
 .. figure:: user_manual_figures/layer4b.png
    :name: fig:layer4b
@@ -339,7 +339,7 @@ the shape argument, ``shape=[nx, ny, nz]``:
     :start-after: #{ layer4_3d_b #}
     :end-before: #{ end #}
 
-.. _fig_layer4_3d:
+.. _fig_layer4_3d_b:
 
 .. figure:: user_manual_figures/layer4_3d_b.png
    :name: fig:layer4_3d_b

diff --git a/doc/guides/spatial/pynest.rst b/doc/guides/spatial/pynest.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 pynest package
 ==============
 

diff --git a/doc/installation/index.rst b/doc/installation/index.rst
@@ -127,7 +127,7 @@ provide containerized versions of NEST in several formats:
           generated, as shown below. You can then copy and paste the
           link into your browser.
 
-           .. image:: ../../_static/img/docker_link.png
+           .. image:: ../_static/img/docker_link.png
               :align: center
               :width: 1000px
 
@@ -255,10 +255,10 @@ these instructions.**
 
    linux_install
    mac_install
-   conda_install
    hpc_install
    livemedia
    install_options
+   oldvers_install
 
 
 .. note::

diff --git a/doc/installation/oldvers_install.rst b/doc/installation/oldvers_install.rst
@@ -1,13 +1,15 @@
+:orphan:
+
 
 Installation instructions for NEST 2.10 and earlier
-====================================================
+===================================================
 
 .. note:: These instructions contain only information on points that differ from
- current versions of NEST. :doc:`See the installation page for details <installation>`.
+ current versions of NEST. :doc:`See the installation page for details <index>`.
 
 The following are the basic steps to compile and install NEST from source code:
 
-*  :doc:`Download NEST <../download.rst>`
+*  :doc:`Download NEST <../download>`
 
 * Unpack the tarball::
 
@@ -33,7 +35,7 @@ with appropriate configuration options
     make install
 
 Dependencies
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 
 The `GNU readline library <http://www.gnu.org/software/readline/>`_ is recommended
 if you use NEST interactively without Python. Although most Linux distributions

diff --git a/doc/microcircuit/api_potjans/helpers.rst b/doc/microcircuit/api_potjans/helpers.rst
diff --git a/doc/microcircuit/api_potjans/modules.rst b/doc/microcircuit/api_potjans/modules.rst