Merge branch 'master' of github.com:nest/nest-simulator into amat-par…

…am-update

.github/workflows/nestbuildmatrix.yml

@@ -707,6 +707,8 @@ jobs:
           echo "backend : svg" > $HOME/.matplotlib/matplotlibrc
 
       - name: "Run NEST testsuite"
+        env:
+          DO_TESTS_SKIP_TEST_REQUIRING_MANY_CORES: ${{ contains(matrix.use, 'mpi') && contains(matrix.use, 'openmp') }}
         run: |
           pwd
           cd "$NEST_VPATH"
@@ -719,9 +721,8 @@ jobs:
         with:
           name: "build-logs-${{ matrix.os }}-${{ matrix.cpp_compiler }}-${{ matrix.use }}"
           path: |
-            install_manifest.txt
-            **.log
-            build/reports/**
+            build/install_manifest.txt
+            build/test_report_*/
 
   build_macos:
     if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
@@ -758,7 +759,7 @@ jobs:
       - name: "Set up Python 3.x"
         uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
         with:
-          python-version: 3.9
+          python-version: 3.12
 
       - name: "Install MacOS system dependencies"
         run: |
@@ -848,6 +849,5 @@ jobs:
         with:
           name: "${{ matrix.NEST_BUILD_TYPE }}-build-logs-${{ matrix.os }}-${{ matrix.cpp_compiler }}"
           path: |
-            install_manifest.txt
-            **.log
-            build/reports/**
+            build/install_manifest.txt
+            build/test_report_*/

README.md

@@ -3,7 +3,7 @@
 [![Documentation](https://img.shields.io/readthedocs/nest-simulator?logo=readthedocs&logo=Read%20the%20Docs&label=Documentation)](https://nest-simulator.org/documentation)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2218/badge)](https://bestpractices.coreinfrastructure.org/projects/2218)
 [![License](http://img.shields.io/:license-GPLv2+-green.svg)](http://www.gnu.org/licenses/gpl-2.0.html)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8069926.svg)](https://doi.org/10.5281/zenodo.8069926)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10834751.svg)](https://doi.org/10.5281/zenodo.10834751)
 
 [![Latest release](https://img.shields.io/github/release/nest/nest-simulator.svg?color=brightgreen&label=latest%20release)](https://github.com/nest/nest-simulator/releases)
 [![GitHub contributors](https://img.shields.io/github/contributors/nest/nest-simulator?logo=github)](https://github.com/nest/nest-simulator)

doc/htmldoc/connect_nest/nest_server.rst

@@ -79,9 +79,9 @@ consideration, each of the restrictions can be disabled by setting a correspondi
 * ``NEST_SERVER_DISABLE_AUTH``: By default, the NEST Server requires a NESTServerAuth tokens. Setting this variable to
   ``1`` disables this restriction. A token is automatically created and printed to the console by NEST Server upon
   start-up. If needed, a custom token can be set using the environment variable  ``NEST_SERVER_ACCESS_TOKEN``
-* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see `CORS
-  <https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS>`_). Other hosts can be explicitly allowed by supplying them
-  in the form `http://host_or_ip:*`` to this variable (By default: http://localhost:*).
+* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see
+  `CORS <https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS>`_). Other hosts can be explicitly allowed by supplying them
+  in the form http://host_or_ip:\* to this variable (By default: http://localhost:\*).
 * ``NEST_SERVER_ENABLE_EXEC_CALL``: By default, NEST Server only allows calls to its PyNEST-like API. If the use-case
   requires the execution of scripts via the ``/exec`` route, this variable can be set to ``1``. PLEASE BE AWARE THAT
   THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION.

doc/htmldoc/devices/index.rst

@@ -8,7 +8,7 @@ All about devices in NEST
 
     .. grid-item-card::  Stimulate the network
        :class-title: sd-d-flex-row sd-align-minor-center
-       :link: stimuate_network
+       :link: stimulate_network
        :link-type: ref
 
     .. grid-item-card:: Get data from simulation

doc/htmldoc/get-started_index.rst

@@ -232,8 +232,6 @@ More topics
 .. toctree::
    :hidden:
 
-   understand_index
-
 .. |nav| image:: static/img/GPS-Settings-256_nest.svg
 .. |script| image:: static/img/script_white.svg
       :scale: 20%

doc/htmldoc/index.rst

@@ -1,29 +1,35 @@
-Welcome to the NEST Simulator documentation
-===========================================
-
-
+Welcome to the NEST Simulator documentation!
+============================================
 
 
 .. grid::
+  :gutter: 2
 
   .. grid-item::
 
-    NEST is used in computational neuroscience to model and study behavior of large networks of neurons.
+     .. grid:: 1 1 1 1
+       :gutter: 2
 
-    The models describe single neuron and synapse behavior and their connections.
-    Different mechanisms of plasticity can be used to investigate artificial learning
-    and help to shed light on the fundamental principles of how the brain works.
+       .. grid-item::
+
+          NEST is used in computational neuroscience to model and study behavior of large networks of neurons.
 
-    NEST offers convenient and efficient commands to define and connect large networks,
-    ranging from algorithmically determined connections to data-driven connectivity.
-    Create connections between neurons using numerous synapse models from STDP to gap junctions.
+          The models describe single neuron and synapse behavior and their connections.
+          Different mechanisms of plasticity can be used to investigate learning
+          and help to shed light on the fundamental principles of how the brain works.
 
-    .. button-ref:: tutorials_guides
-       :ref-type: ref
-       :shadow:
-       :color: primary
+          NEST offers convenient and efficient commands to define and connect large networks,
+          ranging from algorithmically determined connections to data-driven connectivity.
+          Create connections between neurons using numerous synapse models from STDP to gap junctions.
 
-       Start exploring NEST
+       .. grid-item::
+
+          .. button-ref:: tutorials_guides
+             :ref-type: ref
+             :shadow:
+             :color: primary
+
+             Start exploring NEST
 
   .. grid-item::
 
@@ -47,7 +53,7 @@ Welcome to the NEST Simulator documentation
                 .. figure:: static/img/astrocyte_interaction.png
 
 
-                  Investigate neuron and astrocyte interactions
+                  Inspect neuron and astrocyte interactions
 
 
                 .. figure:: static/img/hpc_benchmark_connectivity.svg
@@ -58,7 +64,7 @@ Welcome to the NEST Simulator documentation
                 .. figure:: static/img/pong_sim.gif
 
 
-                  Play PONG with NEST
+                  Simulate a game of PONG with NEST
 
                 .. figure:: static/img/gapjunctions.png
 
@@ -76,6 +82,36 @@ Welcome to the NEST Simulator documentation
              Discover all our examples!
 
 
+How NEST works --- The Big Picture
+----------------------------------
+
+.. grid::
+
+    .. grid-item::
+
+        .. raw:: html
+
+           <object data="_static/img/excalidraw_nestconcept_horiz.svg" type="image/svg+xml"></object>
+
+
+.. grid::
+
+    .. grid-item::
+
+
+        A NEST simulation is created with input from :doc:`stimulation devices </models/index_generator>`,
+        :doc:`neuron models </models/index_neuron>`, and :doc:`synapse models </models/index_synapse>`,
+        along with  :ref:`connection rules <connectivity_concepts>`.
+        You can choose what data to record with :doc:`recording devices </models/index_recorder>`.
+        After simulation, the output is ready for analysis with NEST's built in :py:mod:`.raster_plot` and :py:mod:`.voltage_trace`
+        modules or external tools such as :doc:`Elephant <elephant:index>`.
+
+
+        You can find these components in NEST or you can implement your own custom
+        models and extend NEST's functionalities using :doc:`NESTML <nestml:index>` and the :doc:`NEST extension module <extmod:index>`, respectively.
+        Check out our wide-ranging list of :doc:`network model <examples/index>` examples.
+
+
 .. toctree::
    :caption: USAGE
    :hidden:

doc/htmldoc/related_projects.rst

@@ -90,10 +90,10 @@ real-time operation.
 TheVirtualBrain (TVB)
 ---------------------
 
-:ref:`TVB <tvb:top_basic>` is a framework for the simulation of the dynamics of large-scale brain networks with
+:ref:`TVB <tvb:index>` is a framework for the simulation of the dynamics of large-scale brain networks with
 biologically realistic connectivity.
 
-* :ref:`Get started with TVB <tvb:tutorial_0_gettingstarted>`
+* :ref:`Get started with TVB <tvb:tutorial_0_GettingStarted>`
 
 ConnPlotter
 -----------

doc/htmldoc/static/css/custom.css

@@ -115,6 +115,20 @@ section#kernel-attributes-nest-nestmodule dd {
 	padding-bottom: 20px !important;
   box-shadow: 3px 3px var(--nest-orange) !important;
 }
+
+
+.center {
+
+  text-align: center;
+  font-style: italic;
+}
+/* Provide a specific height to the svg object on index page
+ * Reason: Safari does not interpret percentages or max-content
+ * correctly
+ * there is an additional @media setting for <768px screens*/
+section#welcome-to-the-nest-simulator-documentation  object {
+  height: 400px;
+}
 /*************************************************************
  * Rules for  mermaid diagrams
  *************************************************************/
@@ -141,12 +155,6 @@ figure.align-default {
 	outline-style: groove;
 }
 
-.center {
-
-  text-align: center;
-  font-style: italic;
-}
-
 /**************************************************************************************
  * Rules for carousel
  * ***********************************************************************************/
@@ -212,10 +220,11 @@ div[role="main"] .md-source {
 	border-radius: 5px;
 }
 /* Add padding around buttons on index page */
-#welcome-to-the-nest-simulator-documentation [data-md-color-primary="orange"] .md-typeset a {
+#welcome-to-the-nest-simulator-documentation [data-md-color-primary="orange"] .sd-button {
    padding: 6px;
 }
 
+
 .md-typeset details {
    background-color: white;
 }
@@ -347,6 +356,11 @@ nav.md-nav.md-nav--secondary label.md-nav__title:after{
   font-weight: bold;
   display: flex;
   align-items: center;
+
+}
+
+#welcome-to-the-nest-simulator-documentation .sd-row-cols-lg-1 > *{
+width: 85%;
 }
 
 #pynest-examples img.sd-card-img-top {
@@ -975,7 +989,11 @@ This is for the larger monitors and possibly full screen viewers.
 @media only screen and (min-width: 1240px) {
 #hero h1{ font-size:2em;}
 }
-
+@media only screen and (max-width: 768px) {
+ section#welcome-to-the-nest-simulator-documentation  object {
+  height: 200px;
+ }
+}
 /*
 RETINA (2x RESOLUTION DEVICES)
 This applies to the retina iPhone (4s) and iPad (2,3) along with

doc/htmldoc/synapses/synapse_specification.rst

@@ -65,7 +65,7 @@ Array parameters
 
 Array parameters can be used with the rules ``one_to_one``, ``all_to_all``,
 ``fixed_total_number``, ``fixed_indegree``, and ``fixed_outdegree``.
-For details on connection rules, see :ref:`connectivity_concept`.
+For details on connection rules, see :ref:`connectivity_concepts`.
 The arrays can be specified as NumPy arrays or Python
 lists. As with the scalar parameters, all parameters have to be
 specified as arrays of the correct type.

lib/sli/nest-init.sli

@@ -488,9 +488,14 @@ def
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-% add conversion from NodeCollection
-/cva [/nodecollectiontype]
-  /cva_g load
+% add new functions to trie if it exists, else create new
+/cva dup lookup not
+{
+  trie
+} if
+  [/connectiontype] /cva_C load addtotrie
+  [/nodecollectiontype] { /all cva_g_l } addtotrie
+  [/nodecollectiontype /literaltype] /cva_g_l load addtotrie
 def
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -1426,8 +1431,6 @@ def
 [/integertype /integertype] /TimeCommunicationAlltoallv_i_i load addtotrie
 def
 
-/cva [/connectiontype] /cva_C load def
-
 /abort
 {
   statusdict /exitcodes get /userabort get

libnestutil/CMakeLists.txt

@@ -27,6 +27,7 @@ set( nestutil_sources
     lockptr.h
     logging_event.h logging_event.cpp
     logging.h
+    nest_types.h
     numerics.h numerics.cpp
     regula_falsi.h
     sort.h