Align documentation of connection management with connectivity concepts publication

doc/htmldoc/installation/cmake_options.rst

@@ -262,7 +262,7 @@ follwing switch for the invocation of ``cmake``. It expects either
     -Dwith-libneurosim=[OFF|ON|</path/to/libneurosim>]
 
 For details on how to use the Connection Generator Interface, see the
-:ref:`guide on connection management <conn_builder_conngen>`.
+:ref:`guide on connection generation <connection_generator>`.
 
 .. _compile_with_python:
 

doc/htmldoc/nest_behavior/running_simulations.rst

@@ -129,7 +129,7 @@ NEST also has some models that determine the precise time of the
 threshold crossing during the interval. Please see the documentation on
 :ref:`precise spike time neurons <sim_precise_spike_times>`
 for details about neuron update in continuous time and the
-:ref:`documentation on connection management <connection_management>`
+:ref:`documentation on the connectivty concept  <connectivity_concept>`
 for how to set the delay when creating synapses.
 
 .. _stepped_simulations:

doc/htmldoc/networks/spatially_structured_networks.rst

@@ -1317,7 +1317,7 @@ The following table presents some query functions provided by NEST.
 +---------------------------------+-----------------------------------------------------+
 | ``nest.GetConnections()``       | Retrieve connections (all or for a given            |
 |                                 | source or target); see also                         |
-|                                 | http://www.nest-simulator.org/connection_management.|
+|                                 | :ref:`connectivity_concept`.                        |
 +---------------------------------+-----------------------------------------------------+
 | ``nest.GetNodes()``             | Returns a NodeCollection of all elements with given |
 |                                 | properties.                                         |

doc/htmldoc/static/css/custom.css

@@ -1,4 +1,4 @@
-/* 
+/*
  * Customize css to define NEST specific colors, style and format
  *
    primary styles, for custom index.html and layout.html pages (see templates/ folder)
@@ -8,7 +8,7 @@
 
    Sphinx theme: sphinx-material
    https://bashtage.github.io/sphinx-material/index.html
-   Sphinx material theme properties use 'md' in variable names 
+   Sphinx material theme properties use 'md' in variable names
    Extesion for grid / cards in reStructured Text see sphinx-design
    https://sphinx-design.readthedocs.io/
    Sphinx design properties use the sd in variable names
@@ -123,9 +123,14 @@ figure.align-default {
 	outline-style: groove;
 }
 
+.center {
+
+  text-align: center;
+  font-style: italic;
+}
 
 /**************************************************************************************
- Settings for overriding material design theme 
+ Settings for overriding material design theme
  Setting nest colors to override sphinx material "orange" and other default colors
 
 **************************************************************************************/
@@ -140,7 +145,7 @@ figure.align-default {
    font-weight: 600;
 }
 .md-typeset h1[id]:before,
-.md-typeset h2[id]:before, 
+.md-typeset h2[id]:before,
 .md-typeset h3[id]:before,
 .md-typeset h4[id]:before {
    margin-top: -3.4rem;
@@ -199,7 +204,7 @@ div[role="main"] .md-source {
 div.sd-card-title.sd-font-weight-bold.sd-d-flex-row.docutils a.reference.internal img {
  margin-right: 2em;
  margin-bottom: 0.5em;
- 
+
 }
 
 .md-typeset .admonition, .md-typeset .admonition.tip {
@@ -228,7 +233,7 @@ div.sd-card-title.sd-font-weight-bold.sd-d-flex-row.docutils a.reference.interna
 }
 .md-typeset .admonition.warning {
    border-left-color: #be1717;
-} 
+}
 .md-typeset .admonition.warning > .admonition-title {
    background-color: #be1717;
 }

doc/htmldoc/synapses/connection_generator.rst

@@ -0,0 +1,53 @@
+.. _connection_generator:
+
+Connection generator interface
+------------------------------
+
+.. admonition:: Availability
+
+   This connection rule is only available if NEST was compiled with
+   :ref:`support for libneurosim <compile_with_libneurosim>`.
+
+To allow the generation of connectivity by means of an external
+library, NEST supports the Connection Generator Interface [2]_. For
+more details on this interface, see the git repository of `libneurosim
+<https://github.com/INCF/libneurosim>`_.
+
+In contrast to the other rules for creating connections, this rule
+relies on a Connection Generator object to describe the connectivity
+pattern in a library-specific way. The Connection Generator is handed
+to :py:func:`.Connect` under the key ``cg`` of the connection specification
+dictionary and evaluated internally. If the Connection Generator
+provides values for connection weights and delays, their respective
+indices can be specified under the key ``params_map``. Alternatively,
+all synapse parameters can be specified using the synapse
+specification argument to ``Connect()``.
+
+The following listing shows an example for using CSA (`Connection Set Algebra <https://github.com/INCF/csa>`_ [1]_) in NEST via the Connection
+generator interface and randomly connects 10% of the neurons from
+``A`` to the neurons in ``B``, each connection having a weight of
+10000.0 pA and a delay of 1.0 ms:
+
+.. code-block:: python
+
+   A = nest.Create('iaf_psc_alpha', 100)
+   B = nest.Create('iaf_psc_alpha', 100)
+
+   # Create the Connection Generator object
+   import csa
+   cg = csa.cset(csa.random(0.1), 10000.0, 1.0)
+
+   # Map weight and delay indices to values from cg
+   params_map = {'weight': 0, 'delay': 1}
+
+   conn_spec = {'rule': 'conngen', 'cg': cg, 'params_map': params_map}
+   nest.Connect(A, B, conn_spec)
+
+
+References
+----------
+.. [1] Djurfeldt M. The Connection-set Algebra—A Novel Formalism for the Representation of Connectivity Structure in Neuronal Network Models. Neuroinformatics. 2012; 10: 287–304. https://doi.org/10.1007/s12021-012-9146-1
+.. [2] Djurfeldt M, Davison AP and Eppler JM (2014). Efficient generation of
+       connectivity in neuronal networks from simulator-independent
+       descriptions. Front. Neuroinform.
+       https://doi.org/10.3389/fninf.2014.00043