diff --git a/doc/htmldoc/connect_nest/using_nest_with_music.rst b/doc/htmldoc/connect_nest/using_nest_with_music.rst
index 09bc75e9a0..cc89b298cb 100644
--- a/doc/htmldoc/connect_nest/using_nest_with_music.rst
+++ b/doc/htmldoc/connect_nest/using_nest_with_music.rst
@@ -7,7 +7,7 @@ Introduction
------------
NEST supports the `MUSIC interface
-`__, a standard by
+`__, a standard by
the INCF, which allows the transmission of data between applications at
runtime [1]_. It can be used to couple NEST with other simulators, with
applications for stimulus generation and data analysis and visualization
@@ -28,7 +28,7 @@ Reference
.. [1] Djurfeldt M, et al. 2010. Run-time interoperability between neuronal
simulators based on the MUSIC framework. Neuroinformatics, 8.
`doi:10.1007/s12021-010-9064-z*
- `__.
+ `_.
Sending and receiving spike events
----------------------------------
@@ -384,4 +384,3 @@ which yields the following output:
Nov 23 11:33:28 SimulationManager::run [Info]:
Simulation finished.
(array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]),)
-
diff --git a/doc/htmldoc/developer_space/guidelines/coding_guidelines_check.rst b/doc/htmldoc/developer_space/guidelines/coding_guidelines_check.rst
index 4672a879e5..7381d5682c 100644
--- a/doc/htmldoc/developer_space/guidelines/coding_guidelines_check.rst
+++ b/doc/htmldoc/developer_space/guidelines/coding_guidelines_check.rst
@@ -76,7 +76,7 @@ Our ``clang-format`` configuration is specified in the
``clang-format`` is run automatically with ``pre-commit``.
We supply the
-`build_support/format_all_c_c++_files.sh `_
+`build_support/format_all_c_c++_files.sh `_
shell script to run ``clang-format`` manually:
.. code-block:: bash
diff --git a/doc/htmldoc/developer_space/guidelines/coding_guidelines_cpp.rst b/doc/htmldoc/developer_space/guidelines/coding_guidelines_cpp.rst
index f8ce4360ef..83460ab19c 100644
--- a/doc/htmldoc/developer_space/guidelines/coding_guidelines_cpp.rst
+++ b/doc/htmldoc/developer_space/guidelines/coding_guidelines_cpp.rst
@@ -83,7 +83,7 @@ Coding style
In the following the coding style guidelines are explained by example and some
parts are adopted from `Google C++ Style
-Guide `_.
+Guide `_.
The #define guard
~~~~~~~~~~~~~~~~~
diff --git a/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst b/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst
index ba2d6a4ef1..c686881982 100644
--- a/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst
+++ b/doc/htmldoc/developer_space/guidelines/styleguide/styleguide.rst
@@ -267,7 +267,7 @@ Roles look like this ``:role-name:`content```.
We will only cover a few examples here. You can find more information at the following links:
-* `reStructuredText User Documentation `_
+* `reStructuredText User Documentation `_
* `reStructuredText Primer `_
diff --git a/doc/htmldoc/developer_space/workflows/development_workflow.rst b/doc/htmldoc/developer_space/workflows/development_workflow.rst
index 7a0e32c619..d0d6a1ad8d 100644
--- a/doc/htmldoc/developer_space/workflows/development_workflow.rst
+++ b/doc/htmldoc/developer_space/workflows/development_workflow.rst
@@ -197,7 +197,7 @@ It is extremely important to work on the latest available source code. If you
work on old code, it is possible that in the meantime, someone else has
already made more changes to the same files that you have also edited. This
will result in `merge conflicts
-`_
+`_
and resolving these is extra work for both the development team and you. It
also muddles up the ``commit history`` of the source code.
@@ -326,7 +326,8 @@ Creating a pull request
When you feel your work is finished, you can create a pull request (PR). GitHub
has a nice help page that outlines the process for
-`submitting pull requests `_.
+`submitting pull requests
+`_.
Please check out our :ref:`coding style guidelines ` and
:ref:`code review guidelines ` prior to submitting it.
diff --git a/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst b/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst
index d8d40f612f..1563c37539 100644
--- a/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst
+++ b/doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst
@@ -243,7 +243,7 @@ Read the Docs
NEST documentation is hosted on Read the Docs. If you would like to view the documentation
on Read the Docs, you can set up your own account and link it with your Github account.
-See `this guide `_
+See `this guide `_
for more information.
.. toctree::
diff --git a/doc/htmldoc/developer_space/workflows/nest_with_ides.rst b/doc/htmldoc/developer_space/workflows/nest_with_ides.rst
index 9665021a82..de10e2d08a 100644
--- a/doc/htmldoc/developer_space/workflows/nest_with_ides.rst
+++ b/doc/htmldoc/developer_space/workflows/nest_with_ides.rst
@@ -276,7 +276,7 @@ We present two ways to install the rest: MacPorts and Homebrew. For both version
Homebrew
^^^^^^^^
-1. Follow the install instructions for Homebrew (`short `_) or `long `_)
+1. Follow the install instructions for Homebrew (`short `_) or `long `_)
2. Open up the Terminal and execute the following lines:
.. code-block:: sh
@@ -430,8 +430,8 @@ Setting up the CMake configuration in CLion has the following advantages:
.. note::
`CLion `_ is a commercial product. It is *your responsibility* to ensure that you have a valid
- license permitting you to use CLion (or any software product) for your work on the
- NEST Simulator.
+ license permitting you to use CLion (or any software product) for your work on the
+ NEST Simulator.
Setting up the project
~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/htmldoc/faqs/faqs.rst b/doc/htmldoc/faqs/faqs.rst
index 98bab8305e..ecded7b112 100644
--- a/doc/htmldoc/faqs/faqs.rst
+++ b/doc/htmldoc/faqs/faqs.rst
@@ -11,7 +11,7 @@ Installation
known issue in some :hxt_ref:`MPI` implementations. A solution is to add
--with-debug="-DMPICH\_IGNORE\_CXX\_SEEK" to the configure command
line. More details about this problem can be found
- `here `__
+ `here `__
2. **Configure warns that Makefile.in seems to ignore the --datarootdir
setting and the installation fails because of permission errors**
diff --git a/doc/htmldoc/faqs/qa-precise-spike-times.rst b/doc/htmldoc/faqs/qa-precise-spike-times.rst
index 64163149de..6a4b0ae641 100644
--- a/doc/htmldoc/faqs/qa-precise-spike-times.rst
+++ b/doc/htmldoc/faqs/qa-precise-spike-times.rst
@@ -29,7 +29,7 @@ Questions and answers about precise neurons
models relevant to Computational Neuroscience the dynamics of the single
neuron is not. Examples are integrate-and-fire models with linear
:hxt_ref:`subthreshold dynamics` and the AdEx model considered in `Hanuschkin
- (2010) `__. In these cases
+ (2010) `__. In these cases
it is possible to study the accuracy of a solution of the single neuron
dynamics.
@@ -61,7 +61,7 @@ Questions and answers about precise neurons
A: Although the networks dynamics is chaotic, in some cases mesoscopic
measures of network activity can be affected by the quality of the
single neuron solver. For example, `Hansel et al.
- (1998) `__ showed that a
+ (1998) `__ showed that a
measure of network synchrony exhibits a considerable error if the single
neuron dynamics is integrated using a grid-constrained algorithm.
Without confidence in the precision of the single neuron solver we
diff --git a/doc/htmldoc/installation/admin.rst b/doc/htmldoc/installation/admin.rst
deleted file mode 100644
index c95367944e..0000000000
--- a/doc/htmldoc/installation/admin.rst
+++ /dev/null
@@ -1,26 +0,0 @@
-.. _admin_install:
-
-Administrator installation instructions
----------------------------------------
-
-If you need to deploy NEST on a machine
-
-
-* Check out our guides to :ref:`optimizing NEST for HPC systems `
-
-Configure HPC systems
-~~~~~~~~~~~~~~~~~~~~~
-
-Here are some :ref:`configuration options ` that may be useful on supercomputers and large clusters.
-
-Docker install
-~~~~~~~~~~~~~~
-
-Check out the :ref:`docker installation instructions `.
-
-
-See the `nest-docker README `_ to find out more.
-
-
-
-
diff --git a/doc/htmldoc/installation/cmake_options.rst b/doc/htmldoc/installation/cmake_options.rst
index 8e919d627a..d4b8bd0f56 100644
--- a/doc/htmldoc/installation/cmake_options.rst
+++ b/doc/htmldoc/installation/cmake_options.rst
@@ -40,6 +40,29 @@ NEST allows for several configuration options for custom builds:
.. _modelset_config:
+Minimal configuration
+~~~~~~~~~~~~~~~~~~~~~~
+
+
+NEST can be compiled without any external packages; such a configuration may be useful for initial porting to a new supercomputer.
+However, this implies several restrictions:
+
+- Some neuron and synapse models will not be available, as they depend on ODE solvers from the GNU Scientific Library.
+- The Python extension will not be available
+- Multi-threading and parallel computing facilities will be disabled.
+
+To configure NEST for compilation without external packages, use the following command::
+
+ cmake -DCMAKE_INSTALL_PREFIX:PATH= \
+ -Dwith-python=OFF \
+ -Dwith-gsl=OFF \
+ -Dwith-readline=OFF \
+ -Dwith-ltdl=OFF \
+ -Dwith-openmp=OFF \
+
+
+See the :ref:`CMake Options ` to further adjust settings for your system.
+
Select built-in models
~~~~~~~~~~~~~~~~~~~~~~
@@ -104,7 +127,7 @@ Build documentation
If either documentation build is toggled to `ON`, you can then run ``make docs`` if you only want to
build the docs.
-See also the :ref:`documentation workflow ` for user facing and technical docs.
+See also the :ref:`documentation workflow ` for user-facing and technical docs.
External libraries
@@ -180,7 +203,7 @@ Generic build configuration
| ``-Dwith-intel-compiler-flags=[OFF|]``| User defined flags for the Intel compiler |
| | [default='-fp-model strict']. Separate multiple flags by ';'. |
+------------------------------------------------------+------------------------------------------------------------------+
-| ``-Dwith-cpp-std=[]`` | C++ standard to use for compilation [default='c++11']. |
+| ``-Dwith-cpp-std=[]`` | C++ standard to use for compilation [default='c++17']. |
+------------------------------------------------------+------------------------------------------------------------------+
| ``-Dwith-libraries=[OFF|]`` | Link additional libraries [default=OFF]. Give full path. Separate|
| | multiple libraries by ';'. |
diff --git a/doc/htmldoc/installation/hpc_install.rst b/doc/htmldoc/installation/hpc_install.rst
deleted file mode 100644
index 0a926fcd43..0000000000
--- a/doc/htmldoc/installation/hpc_install.rst
+++ /dev/null
@@ -1,61 +0,0 @@
-.. _hpc_install:
-
-High Performance Computer Systems Installation
-================================================
-
-How you want to install NEST on a supercomputer or cluster will depend on your needs
-and how the system is set up.
-
-
-
-Source install
----------------
-
-See our full guide to installing :ref:`NEST from source `, which allows you to control
-the configuration options.
-
-
-Minimal configuration
-~~~~~~~~~~~~~~~~~~~~~~
-
-
-NEST can be compiled without any external packages; such a configuration may be useful for initial porting to a new supercomputer.
-However, this implies several restrictions:
-
-- Some neuron and synapse models will not be available, as they depend on ODE solvers from the GNU Scientific Library.
-- The Python extension will not be available
-- Multi-threading and parallel computing facilities will be disabled.
-
-To configure NEST for compilation without external packages, use the following command::
-
- cmake -DCMAKE_INSTALL_PREFIX:PATH= \
- -Dwith-python=OFF \
- -Dwith-gsl=OFF \
- -Dwith-readline=OFF \
- -Dwith-ltdl=OFF \
- -Dwith-openmp=OFF \
-
-
-See the :ref:`CMake Options ` to further adjust settings for your system.
-
-
-NEST docker
------------
-
-Alternatively, you can set up the pre-built :ref:`NEST docker container ` that contains
-everything you need for NEST, as well as options like NEST server, Jupyterlab, or :doc:`NEST Desktop `.
-Our docker container also comes with :doc:`NESTML `.
-
-Connect to remote machine - NEST Server
----------------------------------------
-
-NEST Server can be deployed on a remote machine such as a workstation or cluster, and users
-can access the NEST simulation engine through the RESTful API on their laptops.
-
-See the :ref:`guide to NEST server ` to learn more.
-
-
-.. seealso::
-
-
- Check out our guides to :ref:`optimizing NEST for HPC systems `
diff --git a/doc/htmldoc/installation/index.rst b/doc/htmldoc/installation/index.rst
index b785ff2adc..7d7a2fb94a 100644
--- a/doc/htmldoc/installation/index.rst
+++ b/doc/htmldoc/installation/index.rst
@@ -4,54 +4,80 @@ Install NEST
============
-.. grid:: 3
+.. grid:: 2
:gutter: 1
.. grid-item-card:: |user| Install a pre-built NEST package using
:class-title: sd-d-flex-row sd-align-minor-center
+ :columns: 4
* :ref:`Docker (cross-platform) `
(Includes NESTML)
* :ref:`conda-forge (Linux/macOS) `
* :ref:`Ubuntu PPA (Linux) `
* :ref:`Homebrew (macOS) `
- * :ref:`Options for Windows users `
+ * :ref:`Options for Windows users `
.. grid-item-card:: |dev| Source install
:class-title: sd-d-flex-row sd-align-minor-center
+ :columns: 4
If you want to do development with NEST
* :ref:`dev_install`
- .. grid-item-card:: |admin| HPC install
+ .. grid-item-card:: |launch| Try NEST installation-free
:class-title: sd-d-flex-row sd-align-minor-center
+ :columns: 4
- If you are working with HPC systems
+ With the JupyterHub service from EBRAINS, you can
+ try out NEST (and many other tools) directly in your browser.
- * :ref:`Install NEST for supercomputers and clusters `
+ .. rst-class:: imgbutton
+
+ .. image:: https://nest-simulator.org/TryItOnEBRAINS.png
+ :target: https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator-examples&urlpath=lab%2Ftree%2Fnest-simulator-examples%2Fnotebooks%2Fnotebooks%2Fone_neuron.ipynb&branch=main
+
+
+ * For more info see :ref:`our guide to running Jupyter notebooks on EBRAINS `
+
+Install related tools
+~~~~~~~~~~~~~~~~~~~~~
+
+.. grid:: 2
+ :gutter: 1
.. grid-item-card:: |desktop|
:class-title: sd-d-flex-row sd-align-minor-center
+ :columns: 4
A graphical user interface, ideal for learning and teaching concepts
regarding neural networks in classrooms and workshops.
- :doc:`NEST Desktop documentation ` :octicon:`link-external`
+ * :doc:`NEST Desktop documentation ` :octicon:`link-external`
- :ref:`Install docker container with NEST + NEST Desktop `
+ * :ref:`Install docker container with NEST + NEST Desktop `
.. grid-item-card:: |nestml|
:class-title: sd-d-flex-row sd-align-minor-center
+ :columns: 4
Install the NEST modeling language to create and customize models
- :doc:`NESTML documentation ` :octicon:`link-external`
+ * :doc:`NESTML documentation ` :octicon:`link-external`
+
+ * :ref:`Install docker container for NEST + NESTML `
+
+
+ .. grid-item-card:: |hpc| Configure HPC systems
+ :class-title: sd-d-flex-row sd-align-minor-center
+ :columns: 4
- :ref:`Install docker container for NEST + NESTML `
+ Find out how to set up and optimize HPC systems for NEST
+ * :ref:`optimize_performance`
@@ -66,14 +92,14 @@ If installation didn't work, see the :ref:`troubleshooting section ` or the :ref:`High Performance Computing ` instructions to
+:ref:`CMake Options ` instructions to
further adjust settings for your system.
* If not already installed on your system, the following packages are recommended.
@@ -95,6 +95,3 @@ sourcing the script:
.. code-block:: sh
source /bin/nest_vars.sh
-
-
-
diff --git a/doc/htmldoc/installation/user.rst b/doc/htmldoc/installation/user.rst
index da135c21c1..0cc8532bfe 100644
--- a/doc/htmldoc/installation/user.rst
+++ b/doc/htmldoc/installation/user.rst
@@ -89,7 +89,7 @@ Options for Windows users |windows|
------------------------------------
Please note that NEST does not officially support Windows. Members of our community have had success
-using NEST on Windows with the `Windows Subsystem for Linux `_.
+using NEST on Windows with the `Windows Subsystem for Linux `_.
You can also try our :ref:`docker container `.
.. |linux| image:: ../static/img/linux.png
diff --git a/doc/htmldoc/model_details/HillTononiModels.ipynb b/doc/htmldoc/model_details/HillTononiModels.ipynb
index 074836d444..a2e39c532d 100644
--- a/doc/htmldoc/model_details/HillTononiModels.ipynb
+++ b/doc/htmldoc/model_details/HillTononiModels.ipynb
@@ -1,5 +1,5 @@
{
- "cells": [
+ "cells": [
{
"cell_type": "markdown",
"metadata": {},
@@ -10,7 +10,7 @@
"\n",
"## Background\n",
"\n",
- "This notebook describes the neuron and synapse model proposed by Hill and Tononi in *J Neurophysiol* 93:1671-1698, 2005 ([doi:10.1152/jn.00915.2004](http://dx.doi.org/doi:10.1152/jn.00915.2004)) and their implementation in NEST. The notebook also contains some tests.\n",
+ "This notebook describes the neuron and synapse model proposed by Hill and Tononi in *J Neurophysiol* 93:1671-1698, 2005 ([doi:10.1152/jn.00915.2004](https://doi.org/doi:10.1152/jn.00915.2004)) and their implementation in NEST. The notebook also contains some tests.\n",
"\n",
"This description is based on the original publication and publications cited therein, an analysis of the source code of the original Synthesis implementation kindly provided by Sean Hill, and plausibility arguments.\n",
"\n",
diff --git a/doc/htmldoc/model_details/aeif_models_implementation.ipynb b/doc/htmldoc/model_details/aeif_models_implementation.ipynb
index 38f1bce242..68cf2651a7 100644
--- a/doc/htmldoc/model_details/aeif_models_implementation.ipynb
+++ b/doc/htmldoc/model_details/aeif_models_implementation.ipynb
@@ -1,5 +1,5 @@
{
- "cells": [
+ "cells": [
{
"cell_type": "markdown",
"metadata": {},
@@ -48,15 +48,14 @@
"\n",
"The reference solution is implemented using the LSODAR solver which is described and compared in the following references:\n",
"\n",
- "* http://www.radford.edu/~thompson/RP/eventlocation.pdf (papers citing this one)\n",
- "* http://www.sciencedirect.com/science/article/pii/S0377042712000684\n",
- "* http://www.radford.edu/~thompson/RP/rootfinding.pdf\n",
- "* https://computation.llnl.gov/casc/nsde/pubs/u88007.pdf\n",
- "* http://www.cs.ucsb.edu/~cse/Files/SCE000136.pdf\n",
- "* http://www.sciencedirect.com/science/article/pii/0377042789903348\n",
- "* http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.455.2976&rep=rep1&type=pdf\n",
- "* https://theses.lib.vt.edu/theses/available/etd-12092002-105032/unrestricted/etd.pdf"
- ]
+
+ "* Shampine LF, and Thompson S. (2000). Event location for ordinary differential equations. Computers and Mathematics with Applications, 39(5–6), 43–54. https://doi.org/10.1016/S0898-1221(00)00045-6 \n",
+ "* Thompson S (1987). A collection of test problems for ordinary differential equation solvers which have provisions for rootfinding (ORNL/TM-9912, 6111421; p. ORNL/TM-9912, 6111421). https://doi.org/10.2172/6111421 \n",
+ "* Dieci L, and Lopez L (2012). A survey of numerical methods for IVPs of ODEs with discontinuous right-hand side. Journal of Computational and Applied Mathematics, 236(16), 3967–3991. https://doi.org/10.1016/j.cam.2012.02.011 \n",
+ "* Hindmarsh, AC (1983). ODEPACK, a systematized collection of ODE solvers. In R. S. Stepleman & others (Eds.), Scientific computing (Vol. 1, pp. 55–64). North-Holland. https://computing.llnl.gov/sites/default/files/u88007.pdf \n",
+ "* Petzold L. (1983). Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations. SIAM Journal on Scientific and Statistical Computing, 4(1), 136–148. https://doi.org/10.1137/0904010 \n",
+ "* Kahaner DK, Lawkins WF, and Thompson S. (1989). On the use of rootfinding ODE software for the solution of a common problem in nonlinear dynamical systems. Journal of Computational and Applied Mathematics, 28, 219–230. https://doi.org/10.1016/0377-0427(89)90334-8 \n"
+ ]
},
{
"cell_type": "markdown",
diff --git a/doc/htmldoc/neurons/exact-integration.rst b/doc/htmldoc/neurons/exact-integration.rst
index cd282325d8..0980d968b0 100644
--- a/doc/htmldoc/neurons/exact-integration.rst
+++ b/doc/htmldoc/neurons/exact-integration.rst
@@ -208,7 +208,7 @@ Every matrix entry is calculated twice. For inhibitory postsynaptic inputs (with
The update is performed `here `_. The first multiplication evolves the external input. The others are the multiplication of the matrix :math:`e^{Ah}` with :math:`y` (for inhibitory and excitatory inputs).
-If synaptic and membrane time constants become very close, :math:`\tau_m\approx \tau_{syn}`, the matrix :math:`e^{Ah}` becomes numerically unstable. NEST handles this gracefully as described in the `IAF Integration Singularity notebook `_.
+If synaptic and membrane time constants become very close, :math:`\tau_m\approx \tau_{syn}`, the matrix :math:`e^{Ah}` becomes numerically unstable. NEST handles this gracefully as described in the `IAF Integration Singularity notebook <../model_details/IAF_Integration_Singularity.ipynb>`_.
For more information see [1]_.
diff --git a/doc/htmldoc/neurons/simulations_with_precise_spike_times.rst b/doc/htmldoc/neurons/simulations_with_precise_spike_times.rst
index ad981d040c..574da67b2b 100644
--- a/doc/htmldoc/neurons/simulations_with_precise_spike_times.rst
+++ b/doc/htmldoc/neurons/simulations_with_precise_spike_times.rst
@@ -15,7 +15,7 @@ neurons can propagate their state variables for an entire *h*-step
without interruption by incoming spikes. This enables faster simulations
of neurons with linear sub-threshold dynamics as a precomputed
propagator matrix for a time step of fixed size *h* can be employed
-(`Rotter & Diesmann, 1999 `__).
+(`Rotter & Diesmann, 1999 `__).
Neurons buffer the incoming spikes until they become due, where spikes
can be lumped together provided that the corresponding synapses have the
@@ -79,25 +79,24 @@ integrate-and-fire neuron model with alpha-shaped postsynaptic
current that employ precise spike times; The grid-constrained
counterpart is ``iaf_psc_alpha``. The neuron models have been developed
in the context of `Morrison et al.
-(2007) `__. As the model
+(2007) `__. As the model
employ interpolation in order to determine the precise location of an
outgoing spike, the achieved precision depends on the simulation
resolution *h*. The models differ in the way they process incoming
spikes, which also affects the attained precision (see `Morrison et al.
-(2007) `__ for details).
+(2007) `__ for details).
``iaf_psc_exp_ps`` is an integrate-and-fire neuron model with
exponentially shaped postsynaptic currents that employs precise spike
times; its grid-constrained counterpart is ``iaf_psc_exp``. It has been
developed in the context of `Hanuschkin et al.
-(2010) `__, which is a
+(2010) `__, which is a
continuation of the work presented in `Morrison et al.
-(2007) `__. As the neuron
+(2007) `__. As the neuron
model employs an iterative search in order to determine the precise
location of an outgoing spike, the achieved precision does not depend on
the simulation resolution h. The model can also be used through the
-`PyNN
-interface `__.
+:doc:`PyNN interface `.
Questions and answers about precise neurons
-------------------------------------------
@@ -106,5 +105,3 @@ During the review process of the above mentioned papers, we came up with
a list of questions and answers pertaining to the implementation and
usage of precise spiking neurons. This list can be found
:ref:`here `.
-
-
diff --git a/doc/htmldoc/static/css/custom.css b/doc/htmldoc/static/css/custom.css
index 5733ad92f3..611dbdbc3e 100644
--- a/doc/htmldoc/static/css/custom.css
+++ b/doc/htmldoc/static/css/custom.css
@@ -93,7 +93,28 @@ section#kernel-attributes-nest-nestmodule dd {
border: none;
border-bottom: 1px solid #ddd;
}
-
+.imgbutton {
+
+ background-color: white;
+ outline-color: lightgray !important;
+ outline-style: solid !important;
+ outline-width: 1px !important;
+ padding-right: 1px !important;
+ padding-right: 1px !important;
+ padding-top: 20px !important;
+ padding-bottom: 20px !important;
+ box-shadow: 3px 3px lightgray !important;
+}
+.imgbutton:hover {
+
+ background-color: white;
+ outline-color: var(--nest-orange) !important;
+ outline-style: solid !important;
+ outline-width: 1px !important;
+ padding-top: 20px !important;
+ padding-bottom: 20px !important;
+ box-shadow: 3px 3px var(--nest-orange) !important;
+}
/*************************************************************
* Rules for mermaid diagrams
*************************************************************/
diff --git a/doc/htmldoc/static/img/nestdesktop022023.svg b/doc/htmldoc/static/img/nestdesktop022023.svg
new file mode 100644
index 0000000000..d688ec8c2f
--- /dev/null
+++ b/doc/htmldoc/static/img/nestdesktop022023.svg
@@ -0,0 +1,120 @@
+
+
diff --git a/doc/htmldoc/static/img/nestml022023.svg b/doc/htmldoc/static/img/nestml022023.svg
new file mode 100644
index 0000000000..07b6832c5c
--- /dev/null
+++ b/doc/htmldoc/static/img/nestml022023.svg
@@ -0,0 +1,95 @@
+
+
diff --git a/doc/htmldoc/synapses/connection_management.rst b/doc/htmldoc/synapses/connection_management.rst
index 3ddffcae14..b9c782f408 100644
--- a/doc/htmldoc/synapses/connection_management.rst
+++ b/doc/htmldoc/synapses/connection_management.rst
@@ -314,6 +314,12 @@ specification to connections from ``pre`` to ``third`` nodes and
the ``'third_out'`` specification to connections from ``third`` to
``post`` nodes.
+.. admonition:
+
+ Tripartite connectivity is a new feature. Please expect some adjustments to
+ the syntax and semantics for the tripartite connectivity in the next NEST releases.
+
+
.. _tripartite_bernoulli_with_pool:
Tripartite Bernoulli with pool
diff --git a/doc/requirements.txt b/doc/requirements.txt
index b46181a4b8..e4eb2c4dc8 100644
--- a/doc/requirements.txt
+++ b/doc/requirements.txt
@@ -27,6 +27,7 @@ sphinx>=6.2.1
sphinx_autobuild>=2021.3.14
sphinx-carousel
sphinx-copybutton>=0.5.2
+sphinx-carousel
sphinx-notfound-page>=0.8.3
sphinx-design>=0.4.1
sphinx-gallery>=0.13.0
diff --git a/models/aeif_psc_delta_clopath.h b/models/aeif_psc_delta_clopath.h
index 893db047a6..e865a4e854 100644
--- a/models/aeif_psc_delta_clopath.h
+++ b/models/aeif_psc_delta_clopath.h
@@ -188,8 +188,7 @@ References
in STDP – a unified model. Frontiers in Synaptic Neuroscience. 2:25
DOI: https://doi.org/10.3389/fnsyn.2010.00025
.. [3] Voltage-based STDP synapse (Clopath et al. 2010) on ModelDB
- https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566&file=%2f
- modeldb_package%2fVoTriCode%2faEIF.m
+ https://modeldb.science/144566?tab=1
See also
++++++++
diff --git a/models/clopath_synapse.h b/models/clopath_synapse.h
index 080f73333d..0252e7f019 100644
--- a/models/clopath_synapse.h
+++ b/models/clopath_synapse.h
@@ -98,7 +98,7 @@ References
in STDP – a unified model. Frontiers in Synaptic Neuroscience 2:25.
DOI: https://doi.org/10.3389/fnsyn.2010.00025
.. [3] Voltage-based STDP synapse (Clopath et al. 2010) on ModelDB
- https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566
+ https://modeldb.science/144566?tab=1
See also
++++++++
diff --git a/models/glif_psc_double_alpha.h b/models/glif_psc_double_alpha.h
index 841a75ff5c..ce4c310acd 100644
--- a/models/glif_psc_double_alpha.h
+++ b/models/glif_psc_double_alpha.h
@@ -124,7 +124,7 @@ condition of
``tau_syn_in``, respectively, to avoid numerical instabilities.
For implementation details see the
- `IAF_neurons_singularity <../model_details/IAF_neurons_singularity.ipynb>`_ notebook.
+ `IAF Integration Singularity <../model_details/IAF_Integration_Singularity.ipynb>`_ notebook.
Parameters
++++++++++
diff --git a/models/hh_cond_beta_gap_traub.h b/models/hh_cond_beta_gap_traub.h
index 4e2ae9f5c9..c4dda9b281 100644
--- a/models/hh_cond_beta_gap_traub.h
+++ b/models/hh_cond_beta_gap_traub.h
@@ -78,24 +78,24 @@ based on a model of hippocampal pyramidal cells by Traub and Miles [1]_.
The key differences between the current model and the model in [1]_ are:
- This model is a point neuron, not a compartmental model.
-- This model includes only ``I_Na`` and ``I_K``, with simpler ``I_K`` dynamics than
+- Following [2]_, this model includes only ``I_Na`` and ``I_K``, with simpler ``I_K`` dynamics than
in [1]_, so it has only three instead of eight gating variables;
in particular, all Ca dynamics have been removed.
- Incoming spikes induce an instantaneous conductance change followed by
exponential decay instead of activation over time.
+- The model incorporates gap junctions [3]_.
For details on asynchronicity in spike and firing events with Hodgkin Huxley models
see :ref:`here `.
-See also [2]_.
Postsynaptic currents
---------------------
Incoming spike events induce a postsynaptic change of conductance modelled by a
-beta function as outlined in [3]_ [4]_. The beta function is normalized such that an
+beta function as outlined in [4]_ [5]_. The beta function is normalized such that an
event of weight 1.0 results in a peak current of 1 nS at :math:`t = \tau_{rise,xx}`
-where xx is ex or in.
+where xx is `ex` or `in`.
Spike Detection
---------------
@@ -151,11 +151,17 @@ References
.. [1] Traub RD and Miles R (1991). Neuronal Networks of the Hippocampus.
Cambridge University Press, Cambridge UK.
-.. [2] http://modeldb.yale.edu/83319
-.. [3] Rotter S and Diesmann M (1999). Exact digital simulation of
+.. [2] Brette R, et al (2007). Simulation of networks of spiking neurons:
+ A review of tools and strategies. J Comput Neurosci, 23, 349–398
+ DOI: https://doi.org/10.1007/s10827-007-0038-6
+.. [3] Hahne J, Helias M, Kunkel S, Igarashi J, Bolten M, Frommer A,
+ and Diesmann M. (2015). A unified framework for spiking and gap-junction
+ interactions in distributed neuronal network simulations.
+ Frontiers in Neuroinformatics, 9. DOI: https://doi.org/10.3389/fninf.2015.00022
+.. [4] Rotter S and Diesmann M (1999). Exact digital simulation of
time-invariant linear systems with applications to neuronal modeling.
Biological Cybernetics 81:381 DOI: https://doi.org/10.1007/s004220050570
-.. [4] Roth A and van Rossum M (2010). Chapter 6: Modeling synapses.
+.. [5] Roth A and van Rossum M (2010). Chapter 6: Modeling synapses.
in De Schutter, Computational Modeling Methods for Neuroscientists,
MIT Press.
diff --git a/models/hh_psc_alpha_clopath.h b/models/hh_psc_alpha_clopath.h
index f7901a556e..dc47de64f9 100644
--- a/models/hh_psc_alpha_clopath.h
+++ b/models/hh_psc_alpha_clopath.h
@@ -163,9 +163,7 @@ References
DOI: https://doi.org/10.3389/fnsyn.2010.00025
.. [6] Voltage-based STDP synapse (Clopath et al. 2010) connected to a
Hodgkin-Huxley neuron on ModelDB:
- https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566&file
- =%2fmodeldb_package%2fstdp_cc.mod
-
+ https://modeldb.science/144566?tab=1
Sends
+++++
diff --git a/models/sigmoid_rate_gg_1998.h b/models/sigmoid_rate_gg_1998.h
index fcfbf52fa4..6039d9692b 100644
--- a/models/sigmoid_rate_gg_1998.h
+++ b/models/sigmoid_rate_gg_1998.h
@@ -103,7 +103,7 @@ References
.. [3] Hahne J, Helias M, Kunkel S, Igarashi J, Bolten M, Frommer A, Diesmann M
(2015). A unified framework for spiking and gap-junction interactions
in distributed neuronal network simulations. Frontiers in
- Neuroinformatics, 9:22. DOI: https://doi/org/10.3389/fninf.2015.00022
+ Neuroinformatics, 9:22. DOI: https://doi.org/10.3389/fninf.2015.00022
Sends
diff --git a/nestkernel/mpi_manager.cpp b/nestkernel/mpi_manager.cpp
index 591aecb17f..3492e33c20 100644
--- a/nestkernel/mpi_manager.cpp
+++ b/nestkernel/mpi_manager.cpp
@@ -400,7 +400,7 @@ nest::MPIManager::communicate_Allgather( std::vector< unsigned int >& send_buffe
int disp = 0;
unsigned int max_recv_count = send_buffer_size_;
bool overflow = false;
- for ( int pid = 0; pid < get_num_processes(); ++pid )
+ for ( size_t pid = 0; pid < get_num_processes(); ++pid )
{
unsigned int block_disp = pid * send_buffer_size_;
displacements[ pid ] = disp;
@@ -470,7 +470,7 @@ nest::MPIManager::communicate_Allgather( std::vector< T >& send_buffer,
int disp = 0;
unsigned int max_recv_count = send_buffer_size_;
bool overflow = false;
- for ( int pid = 0; pid < get_num_processes(); ++pid )
+ for ( size_t pid = 0; pid < get_num_processes(); ++pid )
{
unsigned int block_disp = pid * send_buffer_size_;
displacements[ pid ] = disp;
@@ -560,7 +560,7 @@ nest::MPIManager::communicate_Allgather( std::vector< OffGridSpike >& send_buffe
int disp = 0;
unsigned int max_recv_count = send_buffer_size_;
bool overflow = false;
- for ( int pid = 0; pid < get_num_processes(); ++pid )
+ for ( size_t pid = 0; pid < get_num_processes(); ++pid )
{
unsigned int block_disp = pid * send_buffer_size_;
displacements[ pid ] = disp;
@@ -604,7 +604,7 @@ nest::MPIManager::communicate( std::vector< double >& send_buffer,
communicate( n_nodes );
// Set up displacements vector.
displacements.resize( get_num_processes(), 0 );
- for ( int i = 1; i < get_num_processes(); ++i )
+ for ( size_t i = 1; i < get_num_processes(); ++i )
{
displacements.at( i ) = displacements.at( i - 1 ) + n_nodes.at( i - 1 );
}
@@ -864,7 +864,7 @@ nest::MPIManager::time_communicatev( int num_bytes, int samples )
std::vector< int > n_nodes( get_num_processes(), packet_length );
std::vector< int > displacements( get_num_processes(), 0 );
- for ( int i = 1; i < get_num_processes(); ++i )
+ for ( size_t i = 1; i < get_num_processes(); ++i )
{
displacements.at( i ) = displacements.at( i - 1 ) + n_nodes.at( i - 1 );
}
@@ -963,7 +963,7 @@ nest::MPIManager::time_communicate_alltoallv( int num_bytes, int samples )
std::vector< int > n_nodes( get_num_processes(), packet_length );
std::vector< int > displacements( get_num_processes(), 0 );
- for ( int i = 1; i < get_num_processes(); ++i )
+ for ( size_t i = 1; i < get_num_processes(); ++i )
{
displacements.at( i ) = displacements.at( i - 1 ) + n_nodes.at( i - 1 );
}
diff --git a/nestkernel/vp_manager.h b/nestkernel/vp_manager.h
index 226c389adf..c0acc819a0 100644
--- a/nestkernel/vp_manager.h
+++ b/nestkernel/vp_manager.h
@@ -203,7 +203,8 @@ inline void
nest::VPManager::assert_thread_parallel() const
{
#ifdef _OPENMP
- assert( omp_get_num_threads() == n_threads_ );
+ // omp_get_num_threads() returns int
+ assert( omp_get_num_threads() == static_cast< int >( n_threads_ ) );
#endif
}
diff --git a/pynest/examples/Potjans_2014/README.rst b/pynest/examples/Potjans_2014/README.rst
index ed00587823..d8ec2c5539 100644
--- a/pynest/examples/Potjans_2014/README.rst
+++ b/pynest/examples/Potjans_2014/README.rst
@@ -56,7 +56,7 @@ To run the simulation, simply use:
The output will be saved in the ``data`` directory.
-The code can be `parallelized `_ using OpenMP and MPI, if NEST has been built with these features.
+The code can be :ref:`parallelized ` using OpenMP and MPI, if NEST has been built with these features.
The number of threads (per MPI process) can be chosen by adjusting ``local_num_threads`` in ``sim_params.py``.
diff --git a/pynest/examples/iaf_tum_2000_short_term_depression.py b/pynest/examples/iaf_tum_2000_short_term_depression.py
index ac6ac2cc78..a68f0767ce 100644
--- a/pynest/examples/iaf_tum_2000_short_term_depression.py
+++ b/pynest/examples/iaf_tum_2000_short_term_depression.py
@@ -62,7 +62,7 @@
20,RC50:1-5. URL: https://infoscience.epfl.ch/record/183402
.. [2] Tsodyks M, Pawelzik K, Markram H (1998). Neural networks with dynamic synapses. Neural
- computation, http://dx.doi.org/10.1162/089976698300017502
+ computation, https://doi.org/10.1162/089976698300017502
See Also
~~~~~~~~
diff --git a/pynest/examples/intrinsic_currents_spiking.py b/pynest/examples/intrinsic_currents_spiking.py
index 22a69f79ed..dc9dc24293 100644
--- a/pynest/examples/intrinsic_currents_spiking.py
+++ b/pynest/examples/intrinsic_currents_spiking.py
@@ -39,7 +39,7 @@
.. [1] Hill and Tononi (2005) Modeling sleep and wakefulness in the
thalamocortical system. J Neurophysiol 93:1671
- http://dx.doi.org/10.1152/jn.00915.2004.
+ https://doi.org/10.1152/jn.00915.2004
See Also
~~~~~~~~
diff --git a/pynest/examples/sonata_example/sonata_network.py b/pynest/examples/sonata_example/sonata_network.py
index f01b7be2c7..4fb9d86c33 100644
--- a/pynest/examples/sonata_example/sonata_network.py
+++ b/pynest/examples/sonata_example/sonata_network.py
@@ -27,8 +27,8 @@
the SONATA format [1]_. The network model consists of 300 internal nodes
(explicitly simulated) and 100 external nodes (only provide inputs to the
simulated system). The SONATA files can be found in the
-`pynest/examples/300_pointneurons
-`_
+`pynest/examples/sonata_example/300_pointneurons
+`_
directory.
See the :ref:`nest_sonata` for details on the NEST support of the SONATA format.
diff --git a/pynest/nest/lib/hl_api_connections.py b/pynest/nest/lib/hl_api_connections.py
index b977c3f23b..c6f8475c1f 100644
--- a/pynest/nest/lib/hl_api_connections.py
+++ b/pynest/nest/lib/hl_api_connections.py
@@ -366,6 +366,12 @@ def TripartiteConnect(pre, post, third, conn_spec, syn_specs=None):
- any parameters specific to the selected synapse model.
+ .. admonition:
+
+ Tripartite connectivity is a new feature. Please expect some adjustments to
+ the syntax and semantics for the tripartite connectivity in the next NEST releases.
+
+
See Also
---------
:ref:`connection_management`