nest · jessica-mitchell · Jan 26, 2024 · Jan 22, 2024 · Jan 22, 2024 · Jan 23, 2024
diff --git a/doc/htmldoc/connect_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst
@@ -104,7 +104,8 @@ a corresponding environment variable.
 * ``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.
 * ``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.
 * ``NEST_SERVER_DISABLE_RESTRICTION``: By default, NEST Server runs all code passed to the ``/exec`` route through RestrictedPython to sanitize it. To disable this mechanism, this variable can be set to ``1``. For increased security, code passed in this way only allows explictly whitelisted modules to be imported. To import modules, the variable ``NEST_SERVER_MODULES`` can be set to a standard Python import line like this:
-       ``NEST_SERVER_MODULES='import nest; import scipy as sp; from numpy import random'``
+  ``NEST_SERVER_MODULES='import nest; import scipy as sp; from numpy import random'``
+
 Run NEST Server
 ~~~~~~~~~~~~~~~
 

diff --git a/doc/htmldoc/developer_space/cppcomments.rst b/doc/htmldoc/developer_space/cppcomments.rst
@@ -6,6 +6,7 @@ There are two types of code comments for C++ files: doxygen style and C++ style
 * Doxygen styled comments are used for describing things like the purpose of the function, which parameters it accepts, and what output it generates.
 * Use Doxygen style comments in the header (``.h``)  files. Avoid using them in ``.cpp`` files.
 * Do not duplicate code in comments.
+
 ..  Include the variable name in functions in header file to match cpp file.
 
 
@@ -14,7 +15,7 @@ Generate HTML from doxygen comments
 
 To generate HTML output of the doxgyen comments,
 
-in the build directory, 
+in the build directory,
 
 run ``cmake`` with developer documentation on::
 

diff --git a/doc/htmldoc/developer_space/guidelines/coding_guidelines_cpp.rst b/doc/htmldoc/developer_space/guidelines/coding_guidelines_cpp.rst
@@ -14,7 +14,7 @@ on their own.
 
 .. seealso::
 
-    Before you make a pull request :ref:`see how to check your code <check_code>`  to ensure its compliant with our guidelines.
+    Before you make a pull request :ref:`see which developer tools are required <required_dev_tools>`  to ensure its compliant with our guidelines.
 
 C++ language features
 ---------------------
@@ -303,7 +303,7 @@ line.
 
 Control structures (``if``, ``while``, ``for``, ...) have a single space after the
 keyword. The parenthesis around the tests
-have a space after the opening and before the closing parenthesis. 
+have a space after the opening and before the closing parenthesis.
 The case labels in ``switch`` statements are not indented.
 
 .. code::
@@ -328,7 +328,7 @@ The case labels in ``switch`` statements are not indented.
 Binary operators (`+`, `-`, `*`, `||`, `&`, ...) are surrounded by one space, e.g.
 ``a + b``.
 
-Unary operators have no space between operator and operand, e.g. ``-a``. 
+Unary operators have no space between operator and operand, e.g. ``-a``.
 Do not use the negation operator `!` since it can easily be
 overseen. Instead use ``not``, e.g. ``not vec.empty()``.
 
@@ -673,5 +673,3 @@ And the corresponding ``stopwatch.cpp``:
       return os;
     }
     }
-
-
diff --git a/doc/htmldoc/examples/index.rst b/doc/htmldoc/examples/index.rst
@@ -327,6 +327,7 @@ PyNEST examples
    ../auto_examples/csa_example
    ../auto_examples/csa_spatial_example
    ../auto_examples/hpc_benchmark
+   ../auto_examples/astrocytes/index
    ../auto_examples/astrocytes/astrocyte_single
    ../auto_examples/astrocytes/astrocyte_interaction
    ../auto_examples/astrocytes/astrocyte_small_network

diff --git a/doc/htmldoc/get-started_index.rst b/doc/htmldoc/get-started_index.rst
@@ -7,7 +7,7 @@ Tutorials and examples
 
    tutorials/index
    PyNEST example scripts <examples/index>
-
+   understand_index
 
 .. grid:: 1 1 2 2
     :gutter: 1
@@ -24,5 +24,5 @@ Tutorials and examples
 
 
 
-.. |nav| image:: static/img/GPS-Settings-256_nest.svg 
+.. |nav| image:: static/img/GPS-Settings-256_nest.svg
 .. |example| image::  static/img/Documents-02-256_nest.svg
diff --git a/doc/htmldoc/ref_material/pynest_api/nest.lib.hl_api_models.rst b/doc/htmldoc/ref_material/pynest_api/nest.lib.hl_api_models.rst
@@ -2,23 +2,25 @@ Models module
 =============
 
 .. automodule:: nest.lib.hl_api_models
-   :members:
+   :members: CopyModel, GetDefaults, SetDefaults
    :undoc-members:
    :show-inheritance:
 
 
 
 
+.. admonition:: Deprecated function
 
-.. autofunction:: Models(mtype="all", sel=None)
+    ``ConnectionRules`` deprecated since 3.3.
 
+    Use :py:obj:`~.NestModule.connection_rules` instead.
 
-   Deprecated since 3.3.
+.. autofunction:: ConnectionRules
 
-   Use :py:obj:`~.NestModule.node_models` or :py:obj:`~.NestModule.synapse_models` instead.
+.. admonition:: Deprecated function
 
-.. autofunction:: ConnectionRules
+     ``Models`` deprecated since 3.3.
 
-   Deprecated since 3.3.
+     Use :py:obj:`~.NestModule.node_models` or :py:obj:`~.NestModule.synapse_models` instead.
 
-   Use :py:obj:`~.NestModule.connection_rules` instead.
+.. autofunction:: Models(mtype="all", sel=None)
diff --git a/doc/htmldoc/ref_material/pynest_api/nest.lib.hl_api_spatial.rst b/doc/htmldoc/ref_material/pynest_api/nest.lib.hl_api_spatial.rst
@@ -1,6 +1,6 @@
 Spatial module
 ==============
- 
+
 
 Functions related to spatially-structured networks.
 
@@ -9,8 +9,6 @@ Functions related to spatially-structured networks.
    See our in depth guide to :ref:`spatial_networks` for details.
 
 
-Query functions for spatial layers
-----------------------------------
 
 Syntax:
 ~~~~~~~
@@ -19,26 +17,10 @@ Syntax:
 
    nest.Distance(nodes[1], nodes[2])
 
-.. automodule:: nest.lib.hl_api_spatial
-   :members: CreateMask, Displacement, Distance, DumpLayerConnections, DumpLayerNodes, FindCenterElement, FindNearestElement, GetPosition, GetTargetNodes, GetSourceNodes, GetTargetPositions, GetSourcePositions, SelectNodesByMask
-   :undoc-members:
-   :show-inheritance:
-
-Visualization functions
------------------------
-
-Syntax:
-~~~~~~~
-
 .. code-block:: Python
 
     nest.PlotLayer(layer, fig, nodecolor, nodesize)
 
-.. automodule:: nest.lib.hl_api_spatial
-   :members: PlotLayer, PlotSources, PlotTargets, PlotProbabilityParameter
-   :undoc-members:
-   :show-inheritance:
-
-
-
 
+.. automodule:: nest.lib.hl_api_spatial
+   :members:
diff --git a/doc/htmldoc/ref_material/pynest_api/nest.lib.hl_api_types.rst b/doc/htmldoc/ref_material/pynest_api/nest.lib.hl_api_types.rst
@@ -7,8 +7,3 @@ Accessing and setting node and parameter types in NEST.
    :members:
    :undoc-members:
    :show-inheritance:
-
-.. automodule:: nest.lib.hl_api_info
-   :members: get_argv, GetStatus, SetStatus
-   :undoc-members:
-   :show-inheritance:
diff --git a/doc/htmldoc/whats_new/index.rst b/doc/htmldoc/whats_new/index.rst
@@ -21,11 +21,11 @@ the new versions.
    :hidden:
    :glob:
 
+   v3.7/*
    v3.6/*
    v3.5/*
    v3.4/*
    v3.3/*
    v3.2/*
    v3.1/*
    v3.0/*
-
diff --git a/models/glif_psc_double_alpha.h b/models/glif_psc_double_alpha.h
@@ -56,7 +56,7 @@ The relative peak current of the slow component is given as ``amp_slow``, at
 .. math::
 
     I_\text{syn} = \text{alpha_function} \left( \tau_\text{syn} = \tau_\text{syn, fast} \right) + \text{amp_slow} \cdot
-\text{alpha_function} \left( \tau_\text{syn} = \tau_\text{syn, slow} \right).
+    \text{alpha_function} \left( \tau_\text{syn} = \tau_\text{syn, slow} \right).
 
 Therefore if ``amp_slow`` is not 0, the peak current of the total synaptic current is larger
 than the specified weight. By default, ``glif_psc_double_alpha`` has a single synapse that

diff --git a/models/ignore_and_fire.h b/models/ignore_and_fire.h
@@ -66,8 +66,8 @@ irrespective of the network size and structure.
    The model can easily be extended and equipped with any arbitrary input processing (such as calculating input
    currents with alpha-function shaped PSC kernels or updating the gating variables in the Hodgkin-Huxley model) or
    (after-) spike generation dynamics to make it more similar and comparable to other non-ignorant neuron models. In
-such extended ignore_and_fire models, the spike emission process would still be decoupled from the intrinsic neuron
-dynamics.
+   such extended ignore_and_fire models, the spike emission process would still be decoupled from the intrinsic neuron
+   dynamics.
 
 Parameters
 ++++++++++

diff --git a/pynest/examples/glif_psc_double_alpha_neuron.py b/pynest/examples/glif_psc_double_alpha_neuron.py
@@ -21,8 +21,8 @@
 
 """
 Current-based generalized leaky integrate and fire (GLIF) neuron with double alpha \
-synaptic function example
-------------------------------------------------------------------------
+synaptic function
+-------------------------------------------------------------------------------------------------------------
 
 Simple example of how to use the ``glif_psc_double_alpha`` neuron model that illustrates
 differences from the ``glif_psc`` neuron model.

diff --git a/pynest/nest/lib/hl_api_models.py b/pynest/nest/lib/hl_api_models.py
@@ -42,10 +42,10 @@
 ]
 
 
-@deprecated("nest.node_models or nest.synapse_models")
 @check_stack
+@deprecated("nest.node_models or nest.synapse_models")
 def Models(mtype="all", sel=None):
-    """Return a tuple of neuron, device, or synapse model names.
+    r"""Return a tuple of neuron, device, or synapse model names.
 
     Parameters
     ----------
@@ -68,7 +68,7 @@ def Models(mtype="all", sel=None):
     Notes
     -----
     - Synapse model names ending in ``_hpc`` require less memory because of
-      thread-local indices for target neuron IDs and fixed ``rport``s of 0.
+      thread-local indices for target neuron IDs and fixed ``rport``\s of 0.
     - Synapse model names ending in ``_lbl`` allow to assign an integer label
       (``synapse_label``) to each individual synapse, at the cost of increased
       memory requirements.
@@ -94,8 +94,8 @@ def Models(mtype="all", sel=None):
     return tuple(models)
 
 
-@deprecated("nest.connection_rules")
 @check_stack
+@deprecated("nest.connection_rules")
 def ConnectionRules():
     """Return a tuple of all available connection rules, sorted by name.
 

diff --git a/pynest/nest/lib/hl_api_simulation.py b/pynest/nest/lib/hl_api_simulation.py
@@ -207,7 +207,7 @@ def ResetKernel():
 def SetKernelStatus(params):
     """Set parameters for the simulation kernel.
 
-    See the documentation of :ref:`sec:kernel_attributes` for a valid
+    See the documentation of :ref:`sec_kernel_attributes` for a valid
     list of params.
 
     Parameters