Merge branch 'master' into doc-getstarted

doc/htmldoc/connect_nest/using_nest_with_music.rst

@@ -7,7 +7,7 @@ Introduction
 ------------
 
 NEST supports the `MUSIC interface
-<http://software.incf.org/software/music>`__, a standard by
+<https://github.com/INCF/MUSIC>`__, 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*
- <http://www.springerlink.com/content/r6j425027lmv1251/>`__.
+ <https://link.springer.com/article/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.]),)
-

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 <https://github.com/nest/nest-simulator/blob/master/build_support/format_all_c_c++_files.sht>`_
+`build_support/format_all_c_c++_files.sh <https://github.com/nest/nest-simulator/blob/master/build_support/format_all_c_c++_files.sh>`_
 shell script to run ``clang-format`` manually:
 
 .. code-block:: bash

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 <https://google-styleguide.googlecode.com/svn/trunk/cppguide.html>`_.
+Guide <https://google.github.io/styleguide/cppguide.html>`_.
 
 The #define guard
 ~~~~~~~~~~~~~~~~~

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 <https://docutils.sourceforge.io/rst.html#id24>`_
+* `reStructuredText User Documentation <https://docutils.sourceforge.io/rst.html>`_
 
 * `reStructuredText Primer <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`_
 

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
-<https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging#Basic-Merge-Conflicts>`_
+<https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging>`_
 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 <https://help.github.com/articles/using-pull-requests/#initiating-the-pull-request>`_.
+`submitting pull requests
+<https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests#initiating-the-pull-request>`_.
 
 Please check out our :ref:`coding style guidelines <code_style_cpp>` and
 :ref:`code review guidelines <code_guidelines>` prior to submitting it.

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 <https://docs.readthedocs.io/en/stable/intro/import-guide.htmli>`_
+See `this guide <https://docs.readthedocs.io/en/stable/intro/import-guide.html>`_
 for more information.
 
 .. toctree::

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 <http://brew.sh/>`_) or `long <https://github.com/Homebrew/homebrew/blob/master/share/doc/homebrew/Installation.md#installation>`_)
+1. Follow the install instructions for Homebrew (`short <http://brew.sh/>`_) or `long <https://github.com/Homebrew/brew/blob/master/docs/Installation.md>`_)
 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 <https://www.jetbrains.com/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
 ~~~~~~~~~~~~~~~~~~~~~~

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 <http://www-unix.mcs.anl.gov/mpi/mpich/faq.htm#cxxseek>`__
+   `here <https://www.mpich.org/#cxxseek>`__
 
 2. **Configure warns that Makefile.in seems to ignore the --datarootdir
    setting and the installation fails because of permission errors**

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) <http://dx.doi.org/10.3389/fninf.2010.00113>`__. In these cases
+   (2010) <https://doi.org/10.3389/fninf.2010.00113>`__. 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) <http://dx.doi.org/10.1162/089976698300017845>`__ showed that a
+   (1998) <https://doi.org/10.1162/089976698300017845>`__ 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

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=<nest_install_dir> \
+          -Dwith-python=OFF \
+          -Dwith-gsl=OFF \
+          -Dwith-readline=OFF \
+          -Dwith-ltdl=OFF \
+          -Dwith-openmp=OFF \
+          </path/to/nest/source>
+
+See the :ref:`CMake Options <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 <doc_workflow>` for user facing and technical docs.
+See also the :ref:`documentation workflow <doc_workflow>` for user-facing and technical docs.
 
 
 External libraries
@@ -180,7 +203,7 @@ Generic build configuration
 | ``-Dwith-intel-compiler-flags=[OFF|<list;of;flags>]``| User defined flags for the Intel compiler                        |
 |                                                      | [default='-fp-model strict']. Separate multiple flags by ';'.    |
 +------------------------------------------------------+------------------------------------------------------------------+
-| ``-Dwith-cpp-std=[<C++ standard>]``                  | C++ standard to use for compilation [default='c++11'].           |
+| ``-Dwith-cpp-std=[<C++ standard>]``                  | C++ standard to use for compilation [default='c++17'].           |
 +------------------------------------------------------+------------------------------------------------------------------+
 | ``-Dwith-libraries=[OFF|<list;of;libraries>]``       | Link additional libraries [default=OFF]. Give full path. Separate|
 |                                                      | multiple libraries by ';'.                                       |

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) <docker>`
         (Includes NESTML)
       * :ref:`conda-forge (Linux/macOS) <conda_forge_install>`
       * :ref:`Ubuntu PPA (Linux) <ubuntu_install>`
       * :ref:`Homebrew (macOS) <macos_install>`
-      * :ref:`Options for Windows users <windows_install>`
+     * :ref:`Options for Windows users <windows_install>`
 
 
    .. 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 <hpc_install>`
+      .. 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 <run_jupyter>`
+
+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 <desktop:index>` :octicon:`link-external`
+      * :doc:`NEST Desktop documentation <desktop:index>` :octicon:`link-external`
 
-      :ref:`Install docker container with NEST + NEST Desktop <docker_compose>`
+      * :ref:`Install docker container with NEST + NEST Desktop <docker_compose>`
 
    .. 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 <nestml:index>` :octicon:`link-external`
+      * :doc:`NESTML documentation <nestml:index>` :octicon:`link-external`
+
+      * :ref:`Install docker container for NEST + NESTML <docker>`
+
+
+   .. 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 <docker>`
+      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 <troubleshoot
    :glob:
 
    mac_install
-   hpc_install
    livemedia
    cmake_options
    *
 
 .. |user| image:: ../static/img/020-user.svg
 .. |teacher| image:: ../static/img/014-teacher.svg
-.. |admin| image:: ../static/img/001-shuttle.svg
+.. |launch| image:: ../static/img/001-shuttle.svg
 .. |dev| image:: ../static/img/dev_orange.svg
 .. |desktop| image:: ../static/img/nestdesktop022023.svg
 .. |nestml| image:: ../static/img/nestml022023.svg
+.. |hpc| image:: ../static/img/hpc_orange128.svg

doc/htmldoc/installation/noenv_install.rst

@@ -4,7 +4,7 @@ Install from source without a virtual environment
 =================================================
 
 The following are the basic steps to compile and install NEST from source code. See the
-:ref:`CMake Options <cmake_options>` or the :ref:`High Performance Computing <hpc_install>` instructions to
+:ref:`CMake Options <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 <nest_install_dir>/bin/nest_vars.sh
-
-
-

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 <https://ubuntu.com/tutorials/install-ubuntu-on-wsl2-on-windows-11-with-gui-support#1-overview>`_.
+using NEST on Windows with the `Windows Subsystem for Linux <https://ubuntu.com/tutorials/install-ubuntu-on-wsl2-on-windows-11-with-gui-support>`_.
 You can also try our :ref:`docker container <docker_win>`.
 
 .. |linux| image:: ../static/img/linux.png