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/contribute/mailing_list_guidelines.rst b/doc/contribute/mailing_list_guidelines.rst
@@ -1,5 +1,7 @@
+:orphan:
+
 Guidelines for contributing to the mailing list
-=================================================
+===============================================
 
 To ensure community members provide accurate and quick responses to questions on the mailing list,
 please follow the guidelines below:
@@ -40,4 +42,3 @@ knowledge and experience to those seeking advice.
 `Access the mailing list here <https://www.nest-initiative.org/mailinglist/>`_
 ------------------------------------------------------------------------------------
 
-
diff --git a/doc/contribute/templates_styleguides/example_template.rst b/doc/contribute/templates_styleguides/example_template.rst
@@ -1,5 +1,7 @@
+:orphan:
+
 PyNEST example template
-==========================
+=======================
 
 
 .. literalinclude:: pynest_example_template.py
diff --git a/doc/contribute/templates_styleguides/pyapi_template.rst b/doc/contribute/templates_styleguides/pyapi_template.rst
@@ -1,4 +1,6 @@
+:orphan:
+
 PyNEST API template
-=====================
+===================
 
 .. literalinclude:: pynest_api_template.py
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

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
@@ -135,4 +135,4 @@ Supported platforms
 By support we mean that we regularly test and use NEST on recent
 versions of these systems and that NEST therefore should work on those
 systems. It should not be construed as any warranty that NEST will run
-on any particular system.
+on any particular system.
diff --git a/doc/glossary.rst b/doc/glossary.rst
@@ -1,8 +1,10 @@
+:orphan:
+
 Glossary
-==============
+========
 
 Common abbreviations in NEST
-------------------------------
+----------------------------
 .. glossary::
 
  iaf
@@ -57,7 +59,7 @@ Common abbreviations in NEST
    virtual process
 
 Physical units and variable names used for NEST parameters
--------------------------------------------------------------
+----------------------------------------------------------
 
 .. note::
 
@@ -141,4 +143,3 @@ Physical units and variable names used for NEST parameters
    Potassium reversal potential in mV.
 
 
-
diff --git a/doc/guides/conngen_interface.rst b/doc/guides/conngen_interface.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 The Connection Generator Interface
 ==================================
 

diff --git a/doc/guides/index.rst b/doc/guides/index.rst
@@ -31,4 +31,4 @@ Here you can find details on a variety of topics in NEST.
     :maxdepth: 1
     :caption: Model Details
 
-    exact-integration
+    exact-integration
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
@@ -427,7 +427,7 @@ 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
@@ -1468,8 +1468,6 @@ All details about the new infrastructure can be found in the guide on
 What's removed?
 ---------------
 
-.. subnet_rm::
-
 Subnets
 ~~~~~~~
 
@@ -1502,8 +1500,6 @@ prints ID ranges and model names of the nodes in the network.
   |                                              |                                       |
   +----------------------------------------------+---------------------------------------+
 
-.. model_rm::
-
 Models
 ~~~~~~
 
@@ -1527,8 +1523,6 @@ 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
@@ -208,7 +208,7 @@ 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
 
@@ -332,7 +332,6 @@ these instructions.**
 
    linux_install
    mac_install
-   conda_install
    hpc_install
    livemedia
    install_options
diff --git a/doc/sli_docs/an-introduction-to-sli.rst b/doc/sli_docs/an-introduction-to-sli.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 An Introduction to SLI
 ======================
 

diff --git a/doc/sli_docs/first-steps.rst b/doc/sli_docs/first-steps.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 First Steps
 ===========
 

diff --git a/doc/sli_docs/neural-simulations.rst b/doc/sli_docs/neural-simulations.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Neural simulations
 ==================
 

diff --git a/doc/sli_docs/objects-and-data-types.rst b/doc/sli_docs/objects-and-data-types.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Objects and data types
 ======================
 

diff --git a/doc/sli_docs/programming-in-sli.rst b/doc/sli_docs/programming-in-sli.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Programming in SLI
 ==================
 

diff --git a/doc/sli_docs/using-files-and-keyboard-input.rst b/doc/sli_docs/using-files-and-keyboard-input.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Using files and keyboard input
 ==============================
 

diff --git a/doc/tutorials/music_tutorial/music_tutorial_parrot.rst b/doc/tutorials/music_tutorial/music_tutorial_parrot.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 Those parrot neurons, or why you never connect devices to each other
 --------------------------------------------------------------------
 

diff --git a/doc/tutorials/music_tutorial/music_tutorial_setlatency.rst b/doc/tutorials/music_tutorial/music_tutorial_setlatency.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 The SetAcceptableLatency command
 --------------------------------
 

diff --git a/doc/tutorials/music_tutorial/music_tutorial_sli.rst b/doc/tutorials/music_tutorial/music_tutorial_sli.rst
@@ -1,3 +1,5 @@
+:orphan:
+
 MUSIC with SLI
 ==============
 

diff --git a/doc/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst b/doc/tutorials/pynest_tutorial/part_4_spatially_structured_networks.rst
@@ -375,8 +375,7 @@ was built correctly:
 
 It may also be useful to look at the ``.spatial`` property of the
 NodeCollection, which describes the spatial properties. Other useful
-functions that may be of help are listed in :doc:`<../../ref_material/nest2_vs_3>`
-Section 4.1 *Query functions*.
+functions that may be of help are listed in the :doc:`../../guides/nest2_to_nest3/nest2_to_nest3_detailed_transition_guide`.
 
 >>>  ex_pop.spatial
      {'center': (0.0, 0.0),

diff --git a/pynest/examples/glif_cond_neuron.py b/pynest/examples/glif_cond_neuron.py
@@ -21,7 +21,7 @@
 
 """
 Conductance-based generalized leaky integrate and fire (GLIF) neuron example
---------------------------------
+----------------------------------------------------------------------------
 
 Simple example of how to use the ``glif_cond`` neuron model for
 five different levels of GLIF neurons.

diff --git a/pynest/examples/glif_psc_neuron.py b/pynest/examples/glif_psc_neuron.py
@@ -21,7 +21,7 @@
 
 """
 Current-based generalized leaky integrate and fire (GLIF) neuron example
---------------------------------
+------------------------------------------------------------------------
 
 Simple example of how to use the ``glif_psc`` neuron model for
 five different levels of GLIF neurons.

diff --git a/pynest/examples/spatial/connex_ew.py b/pynest/examples/spatial/connex_ew.py
@@ -21,6 +21,7 @@
 
 """
 NEST spatial example
+--------------------
 
 Create two populations of iaf_psc_alpha neurons on a 30x30 grid with edge_wrap,
 connect with circular mask, flat probability,

diff --git a/pynest/examples/spatial/hill_tononi_Vp.py b/pynest/examples/spatial/hill_tononi_Vp.py
@@ -461,7 +461,7 @@ def nop(s=None, block=None):
 
 ##############################################################################
 # Synapse models
-# =-------------
+# --------------
 #
 # Actual synapse dynamics, e.g., properties such as the synaptic time
 # course, time constants, reversal potentials, are properties of
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,7 +21,7 @@ @@
     """
     Conductance-based generalized leaky integrate and fire (GLIF) neuron example
-    --------------------------------
+    ----------------------------------------------------------------------------
     Simple example of how to use the ``glif_cond`` neuron model for
     five different levels of GLIF neurons.
@@ Expand Down @@