Merge remote-tracking branch 'upstream/master' into sli_tests_to_py_aeif_cond_beta_multisynapse

Author: C.A.P. Linssen

.github/workflows/nestbuildmatrix.yml

@@ -527,7 +527,7 @@ jobs:
           - "boost, optimize, warning"
           - "openmp, python, gsl, ltdl, boost, optimize, warning"
           - "mpi, python, gsl, ltdl, boost, optimize, warning"
-          - "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning"
+          - "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, music"
 
     steps:
       - name: Harden Runner
@@ -678,6 +678,7 @@ jobs:
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
               -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
               -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
+              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
               ..
 
       - name: "Add GCC problem matcher"
@@ -757,7 +758,7 @@ 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: |
@@ -806,6 +807,7 @@ jobs:
               -Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' || 'OFF' }} \
               -Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' || 'OFF' }} \
               -Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' || 'OFF' }} \
+              -Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' || 'OFF' }} \
               ..
 
       - name: "Add GCC problem matcher"

VERSION

@@ -1 +1 @@
-3.6.0-post0.dev0
+3.7.0-post0.dev0

doc/htmldoc/devices/index.rst

@@ -3,6 +3,21 @@
 All about devices in NEST
 =========================
 
+.. grid:: 1 1 2 2
+    :gutter: 1
+
+    .. grid-item-card::  Stimulate the network
+       :class-title: sd-d-flex-row sd-align-minor-center
+       :link: stimuate_network
+       :link-type: ref
+
+    .. grid-item-card:: Get data from simulation
+       :class-title: sd-d-flex-row sd-align-minor-center
+       :link: record_simulations
+       :link-type: ref
+
+
+
 .. toctree::
   :maxdepth: 1
   :glob:

doc/htmldoc/devices/record_from_simulations.rst

@@ -38,15 +38,39 @@ Recording devices can fundamentally be subdivided into two groups:
   neuron (not the neuron to the sampler), and that the neuron must
   support the particular type of sampling.
 
+.. _recording_backends:
 
-Recorders for every-day situations
-----------------------------------
+What values can I record?
+-------------------------
+
+This depends on neuron or synapse model specified.
+
+You can get a list of properties that you can record using the ``recordables`` property.
+
+        ::
+
+         >>> nest.GetDefaults("iaf_cond_alpha")["recordables"]
+         ["g_ex", "g_in", "t_ref_remaining", "V_m"]
+
+
+Recorders available in NEST
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- :doc:`/models/multimeter`
+
+
+- :doc:`/models/spike_recorder`
+
+
+- :doc:`/models/weight_recorder`
+
+Check out the following examples to see how the recorders are used:
+
+- :doc:`/auto_examples/recording_demo`
+- :doc:`/auto_examples/multimeter_file`
+- :doc:`/auto_examples/urbanczik_synapse_example` uses all 3 recorders.
 
-- :doc:`../models/multimeter`
-- :doc:`../models/spike_recorder`
-- :doc:`../models/weight_recorder`
 
-.. _recording_backends:
 
 Where does data end up?
 -----------------------
@@ -55,10 +79,6 @@ After a recording device has collected or sampled data, the data is
 handed to a dedicated *recording backend*, set for each recorder.
 These are responsible for how the data are processed.
 
-Theoretically, recording backends are completely free in what they do
-with the data. The ones included in NEST can collect data in memory,
-display it on the terminal, or write it to files.
-
 To specify the recording backend for a given recording device, the
 property ``record_to`` of the latter has to be set to the name of the
 recording backend to be used. This can either happen already in the
@@ -67,13 +87,33 @@ call to :py:func:`.Create` or by using :py:func:`.SetStatus` on the model instan
 
 ::
 
- sr = nest.Create('spike_recorder', params={'record_to': 'ascii'})
+ sr = nest.Create("spike_recorder", params={"record_to": "memory"})
 
 Storing data in memory using the `memory` backend is the default for
 all recording devices as this does not require any additional setup of
 data paths or filesystem permissions and allows a convenient readout
 of data by the user after simulation.
 
+For example, you can use the ``events`` property to get the data output from the `memory` backend
+from any of the recorders:
+
+::
+
+   >>> spike_recorder.get("events")
+   {"senders": array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
+   "times": array([ 2.1,  4.4,  6.7,  8.9, 11.1, 13.3, 15.5, 17.7, 19.9, 22.1, 24.3, 26.5, 28.7])}
+
+Additional properties can be set, depending on the recorder and recording backend used.
+
+For example:
+
+::
+
+   mm = nest.Create( "multimeter",
+      params={"interval": 0.1, "record_from": ["V_m", "g_ex", "g_in"], "record_to": "ascii", "label": "my_multimeter"},
+      )
+
+
 Each recording backend may provide a specific set of parameters
 (explained in the backend documentation below) that will be included
 in the model status dictionary once the backend is set. This means
@@ -97,7 +137,7 @@ kernel attribute ``recording_backends``.
 ::
 
    >>> print(nest.recording_backends)
-   ('ascii', 'memory', 'mpi', 'screen', 'sionlib')
+   ("ascii", "memory", "mpi", "screen", "sionlib")
 
 If a recording backend has global properties (i.e., parameters shared
 by all enrolled recording devices), those can be inspected with
@@ -106,17 +146,17 @@ by all enrolled recording devices), those can be inspected with
 ::
 
    >>> nest.GetDefaults("sionlib")
-   {'buffer_size': 1024,
-    'filename': '',
-    'sion_chunksize': 262144,
-    'sion_collective': False,
-    'sion_n_files': 1}
+   {"buffer_size": 1024,
+    "filename": "",
+    "sion_chunksize": 262144,
+    "sion_collective": False,
+    "sion_n_files": 1}
 
 Such global parameters can be set using :py:func:`.SetDefaults`
 
 ::
 
-   >>> nest.SetDefaults('sionlib', {'buffer_size': 512})
+   >>> nest.SetDefaults("sionlib", {"buffer_size": 512})
 
 Built-in backends
 -----------------
@@ -126,8 +166,8 @@ NEST. Please note that the availability of some of them depends on the
 compile-time configuration for NEST. See the backend documentation for
 details.
 
-- :doc:`../models/recording_backend_memory`
-- :doc:`../models/recording_backend_ascii`
-- :doc:`../models/recording_backend_screen`
-- :doc:`../models/recording_backend_sionlib`
-- :doc:`../models/recording_backend_mpi`
+.. include:: ../models/recording_backend_memory.rst
+.. include:: ../models/recording_backend_ascii.rst
+.. include:: ../models/recording_backend_screen.rst
+.. include:: ../models/recording_backend_sionlib.rst
+.. include:: ../models/recording_backend_mpi.rst

doc/htmldoc/examples/index.rst

@@ -80,31 +80,31 @@ PyNEST examples
 
            * :doc:`../auto_examples/Potjans_2014/index`
 
+
+
+    .. grid-item-card:: EI clustered network (Rostami et al)
+           :img-top: ../static/img/pynest/EI_clustered_network_schematic.png
+
+           :doc:`../auto_examples/EI_clustered_network/index`
+
+
+
+.. grid:: 1 1 2 3
+
     .. grid-item-card:: GLIF (from Allen institute)
            :img-top: ../static/img/pynest/glif_cond.png
 
            * :doc:`../auto_examples/glif_cond_neuron`
            * :doc:`../auto_examples/glif_psc_neuron`
            * :doc:`../auto_examples/glif_psc_double_alpha_neuron`
 
-
-
-.. grid:: 1 1 2 3
-
     .. grid-item-card:: Compartmental neurons
            :img-top: ../static/img/pynest/dendritic_synapse_conductances.png
 
            * :doc:`../auto_examples/compartmental_model/receptors_and_current`
            * :doc:`../auto_examples/compartmental_model/two_comps`
 
 
-    .. grid-item-card:: Rate neurons
-           :img-top: ../static/img/pynest/rate_neuron.png
-
-           * :doc:`../auto_examples/lin_rate_ipn_network`
-           * :doc:`../auto_examples/rate_neuron_dm`
-
-
 
     .. grid-item-card:: GIF (from Gerstner lab)
            :img-top: ../static/img/pynest/gif_pop.png
@@ -116,6 +116,13 @@ PyNEST examples
 
 .. grid:: 1 1 2 3
 
+    .. grid-item-card:: Rate neurons
+           :img-top: ../static/img/pynest/rate_neuron.png
+
+           * :doc:`../auto_examples/lin_rate_ipn_network`
+           * :doc:`../auto_examples/rate_neuron_dm`
+
+
     .. grid-item-card:: Hodgkin-Huxley
            :img-top: ../static/img/pynest/hh_phase.png
 
@@ -127,14 +134,14 @@ PyNEST examples
 
            * :doc:`../auto_examples/BrodyHopfield`
 
+.. grid:: 1 1 2 3
+
     .. grid-item-card:: Brette and Gerstner
            :img-top: ../static/img/pynest/brette_gerstner2c.png
 
            * :doc:`../auto_examples/brette_gerstner_fig_2c`
            * :doc:`../auto_examples/brette_gerstner_fig_3d`
 
-.. grid:: 1 1 2 3
-
 
     .. grid-item-card:: Precise spiking
            :img-top: ../static/img/pynest/precisespiking.png
@@ -146,11 +153,6 @@ PyNEST examples
 
            * :doc:`../auto_examples/CampbellSiegert`
 
-    .. grid-item-card:: SONATA network
-           :img-top: ../static/img/300_pointneurons.png
-
-           * :doc:`../auto_examples/sonata_example/sonata_network`
-
 
 .. grid:: 1 1 2 3
 
@@ -242,6 +244,11 @@ PyNEST examples
 
 .. grid:: 1 1 2 3
 
+    .. grid-item-card:: SONATA network
+           :img-top: ../static/img/300_pointneurons.png
+
+           * :doc:`../auto_examples/sonata_example/sonata_network`
+
     .. grid-item-card:: HPC benchmark
            :img-top: ../static/img/nest_logo-faded.png
 
@@ -342,6 +349,7 @@ PyNEST examples
    ../auto_examples/astrocytes/astrocyte_interaction
    ../auto_examples/astrocytes/astrocyte_small_network
    ../auto_examples/astrocytes/astrocyte_brunel
+   ../auto_examples/EI_clustered_network/index
    ../auto_examples/eprop_plasticity/index
 
 .. toctree::

doc/htmldoc/get-started_index.rst

@@ -61,9 +61,10 @@ Next steps: Create your own network model
 
          |random| Connect neurons, synapses, and devices
          ^^^
-
-         * :ref:`connection_management`: A guide to building connections in NEST
+         * :ref:`connectivity_concepts`: A guide to define network connectivity in NEST
          * :ref:`spatial_networks`: A deep dive into building 2D and 3D networks
+         * :ref:`connection_generator`: Using an external library for generating connections
+         * :ref:`synapse_spec`: Details on parameterizing synapses
 
     .. grid-item-card::
          :class-header: sd-d-flex-row sd-align-minor-center sd-bg-info sd-text-white

doc/htmldoc/hpc/parallel_computing.rst

@@ -161,7 +161,7 @@ Spikes between neurons and devices
 Synaptic plasticity models
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-For synapse models supporting plasticity, synapse dynamics in the
+For synapse models supporting :hxt_ref:`plasticity`, synapse dynamics in the
 ``Connection`` object are always handled by the virtual process of the
 `target node`.
 

doc/htmldoc/installation/cmake_options.rst

@@ -313,7 +313,7 @@ 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 concepts  <connectivity_concepts>`
 for how to set the delay when creating synapses.
 
 .. _stepped_simulations:

doc/htmldoc/networks/spatially_structured_networks.rst

@@ -1339,7 +1339,7 @@ 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_concepts`.                       |
 +---------------------------------+-----------------------------------------------------+
 | ``nest.GetNodes()``             | Returns a NodeCollection of all elements with given |
 |                                 | properties.                                         |