Merge pull request #2842 from jessica-mitchell/fix-sphinx-warnings

Fix various issues in docs that cause Sphinx warnings

doc/htmldoc/conf.py

@@ -358,10 +358,6 @@ def copy_example_file(src):
 copy_example_file("examples/Potjans_2014/raster_plot.png")
 copy_example_file("examples/Potjans_2014/microcircuit.png")
 copy_example_file("examples/hpc_benchmark_connectivity.svg")
-copyfile(
-    os.path.join(pynest_dir, "examples/Potjans_2014/README.rst"),
-    "examples/README.rst",
-)
 
 
 def patch_documentation(patch_url):

doc/htmldoc/developer_space/workflows/documentation_workflow/user_documentation_workflow.rst

@@ -104,7 +104,7 @@ commands.
 
 3. Build the docs:
 
-.. code-black:: bash
+.. code-block:: bash
 
    sphinx-build . ../_build/html -b html
 

doc/htmldoc/examples/index.rst

@@ -237,6 +237,7 @@ PyNEST examples
 .. toctree::
    :hidden:
 
+   running_notebooks
    ../auto_examples/sudoku/index
    ../auto_examples/pong/index
    ../auto_examples/spatial/index
@@ -284,6 +285,8 @@ PyNEST examples
    ../auto_examples/brunel_siegert_nest
    ../auto_examples/brunel_exp_multisynapse_nest
    ../auto_examples/brunel_alpha_evolution_strategies
+   ../auto_examples/sonata_example/index
+   ../auto_examples/sonata_example/sonata_network
    ../auto_examples/spatial/conncomp
    ../auto_examples/spatial/conncon_sources
    ../auto_examples/spatial/conncon_targets

doc/htmldoc/faqs/faqs.rst

@@ -86,4 +86,6 @@ Connections
        nest.Connect(n, n[:1], sync_spec={'model'='exc_dist_syn'})
        nest.Simulate(10)
 
+.. _faqs_precise_neurons:
+
 .. include:: qa-precise-spike-times.rst

doc/htmldoc/faqs/qa-precise-spike-times.rst

@@ -1,5 +1,3 @@
-.. _faqs_precise_neurons:
-
 Questions and answers about precise neurons
 -------------------------------------------
 

doc/htmldoc/hpc/slurm_script.rst

@@ -116,7 +116,7 @@ trying to increase the speed of the simulation.
    How many nodes do you need for your simulations?
    This depends on how much memory is available for each node.
 
-   For example: The :ref:`microcircuit model <toc_microcircuit>` requires around 16 GB of memory and the `multi-area-model <https://github.com/INM-6/multi-area-model>`_ requires 1.4 TB.
+   For example: The :doc:`microcircuit model <../auto_examples/Potjans_2014/index>` requires around 16 GB of memory and the `multi-area-model <https://github.com/INM-6/multi-area-model>`_ requires 1.4 TB.
    If a node has 128 GB of memory then one node is more than sufficient for the microcircuit model but the multi-area model
    will need 12 nodes to run.
 

doc/htmldoc/hpc/threading.rst

@@ -22,7 +22,7 @@ For a detailed investigation, we recommend reading Kurth et al. 2022 [1]_.
 .. _pinning_threads:
 
 Pinning threads
---------------
+---------------
 
 Pinning threads allows you to control the distribution of threads across available cores on your system, and is particularly
 useful in high performance computing (HPC) systems.

doc/htmldoc/installation/admin.rst

@@ -6,7 +6,7 @@ Administrator installation instructions
 If you need to deploy NEST on a machine
 
 
-*  Check out our guides to :ref:`optimizing NEST for HPC systems <hpc_index>`
+*  Check out our guides to :ref:`optimizing NEST for HPC systems <optimize_performance>`
 
 Configure HPC systems
 ~~~~~~~~~~~~~~~~~~~~~

doc/htmldoc/model_details/HillTononiModels.ipynb

@@ -74,7 +74,7 @@
     "The repolarizing current is active during, and only during the refractory period:\n",
     "\\begin{equation}\n",
     "g_{\\text{spike}} = \\begin{cases}  1  & \\text{neuron is refractory}\\\\\n",
-    " 0 & \\text{else} \\end{cases}\n",
+    "0 & \\text{else} \\end{cases}\n",
     "\\end{equation}\n",
     "\n",
     "During the refractory period, the neuron cannot fire new spikes, but all state variables evolve freely, nothing is clamped. \n",
@@ -147,7 +147,7 @@
     "N_T &= 2 \\\\\n",
     "m_T^{\\infty}(V) &=  \\frac{1}{1+\\exp\\left(-\\frac{V+59\\text{mV}}{6.2\\text{mV}}\\right)}\\\\\n",
     "\\tau_{m,T}(V) &= 0.13\\text{ms} \n",
-    "  + \\frac{0.22\\text{ms}}{\\exp\\left(-\\frac{V  + 132\\text{mV}}{16.7\\text{mV}}\\right) + \\exp\\left(\\frac{V +  16.8\\text{mV}}{18.2\\text{mV}}\\right)} \\\\ \n",
+    "+ \\frac{0.22\\text{ms}}{\\exp\\left(-\\frac{V  + 132\\text{mV}}{16.7\\text{mV}}\\right) + \\exp\\left(\\frac{V +  16.8\\text{mV}}{18.2\\text{mV}}\\right)} \\\\ \n",
     "h_T^{\\infty}(V) &=  \\frac{1}{1+\\exp\\left(\\frac{V+83\\text{mV}}{4\\text{mV}}\\right)}\\\\\n",
     "\\tau_{h,T}(V) &= 8.2\\text{ms} +  \\frac{56.6\\text{ms} +  0.27\\text{ms} \\exp\\left(\\frac{V   + 115.2\\text{mV}}{5\\text{mV}}\\right)}{1 +   \\exp\\left(\\frac{V  + 86\\text{mV}}{3.2\\text{mV}}\\right)}\n",
     "\\end{align}\n",
@@ -201,30 +201,30 @@
     "##### Equations in paper\n",
     "\n",
     "\\begin{align}\n",
-    " dD/dt &= D_{\\text{influx}} - D(1-D_{\\text{eq}})/\\tau_D \\\\\n",
-    " D_{\\text{influx}} &= 1/\\{1+ \\exp[-(V-D_{\\theta})/\\sigma_D]\\} \\\\\n",
-    " m_{DK}^{\\infty} &= 1/1 + (d_{1/2}D)^{3.5}\n",
+    "dD/dt &= D_{\\text{influx}} - D(1-D_{\\text{eq}})/\\tau_D \\\\\n",
+    "D_{\\text{influx}} &= 1/\\{1+ \\exp[-(V-D_{\\theta})/\\sigma_D]\\} \\\\\n",
+    "m_{DK}^{\\infty} &= 1/1 + (d_{1/2}D)^{3.5}\n",
     "\\end{align}\n",
     "\n",
     "There are several problems with these equations.\n",
     "\n",
     "In the steady state the first equation becomes\n",
     "\\begin{equation}\n",
-    " 0 = - D(1-D_{\\text{eq}})/\\tau_D \n",
-    " \\end{equation}\n",
-    " with solution\n",
-    " \\begin{equation}\n",
-    " D = 0\n",
+    "0 = - D(1-D_{\\text{eq}})/\\tau_D \n",
+    "\\end{equation}\n",
+    "with solution\n",
+    "\\begin{equation}\n",
+    "D = 0\n",
     "\\end{equation}\n",
     "This contradicts both the statement [HT05, p. 1679] that $D\\to D_{\\text{eq}}$ in this case, and the requirement that $D>0$ to avoid a singluarity in the equation for $m_{DK}^{\\infty}$. The most plausible correction is\n",
     "\\begin{equation}\n",
-    " dD/dt = D_{\\text{influx}} - (D-D_{\\text{eq}})/\\tau_D \n",
+    "dD/dt = D_{\\text{influx}} - (D-D_{\\text{eq}})/\\tau_D \n",
     "\\end{equation}\n",
     "\n",
     "The third equation appears incorrect and logic as well as Wang et al, *J Neurophysiol* 89:3279–3293, 2003, Eq 9, cited in [HT05, p 1679], indicate that the correct equation is\n",
     "\n",
     "\\begin{equation}\n",
-    " m_{DK}^{\\infty} = 1/(1 + (d_{1/2} / D)^{3.5})\n",
+    "m_{DK}^{\\infty} = 1/(1 + (d_{1/2} / D)^{3.5})\n",
     "\\end{equation}\n",
     "\n",
     "\n",
@@ -235,10 +235,10 @@
     "\n",
     "\\begin{align}\n",
     "I_{DK} &= - g_{\\text{peak},DK} m_{DK}(V,t) (V - E_{DK})\\\\\n",
-    " m_{DK} &= \\frac{1}{1 + \\left(\\frac{d_{1/2}}{D}\\right)^{3.5}}\\\\\n",
-    " \\frac{dD}{dt} &= D_{\\text{influx}}(V) - \\frac{D-D_{\\text{eq}}}{\\tau_D} = \\frac{D_{\\infty}(V)-D}{\\tau_D} \\\\\n",
-    " D_{\\infty}(V) &= \\tau_D D_{\\text{influx}}(V) + {D_{\\text{eq}}}\\\\\n",
-    " D_{\\text{influx}} &= \\frac{D_{\\text{influx,peak}}}{1+ \\exp\\left(-\\frac{V-D_{\\theta}}{\\sigma_D}\\right)} \n",
+    "m_{DK} &= \\frac{1}{1 + \\left(\\frac{d_{1/2}}{D}\\right)^{3.5}}\\\\\n",
+    "\\frac{dD}{dt} &= D_{\\text{influx}}(V) - \\frac{D-D_{\\text{eq}}}{\\tau_D} = \\frac{D_{\\infty}(V)-D}{\\tau_D} \\\\\n",
+    "D_{\\infty}(V) &= \\tau_D D_{\\text{influx}}(V) + {D_{\\text{eq}}}\\\\\n",
+    "D_{\\text{influx}} &= \\frac{D_{\\text{influx,peak}}}{1+ \\exp\\left(-\\frac{V-D_{\\theta}}{\\sigma_D}\\right)} \n",
     "\\end{align}\n",
     "\n",
     "with \n",
@@ -281,10 +281,10 @@
     "The conductance change due to a single input spike at time $t=0$ through a channel of type $X$ is given by (see below for exceptions)\n",
     "\n",
     "\\begin{align}\n",
-    "    \\bar{g}_X(t) &= g_X(t)\\\\\n",
-    "    g_X(t) &= g_{\\text{peak}, X}\\frac{\\exp(-t/\\tau_1) - \\exp(-t/\\tau_2)}{\n",
-    "                 \\exp(-t_{\\text{peak}}/\\tau_1) - \\exp(-t_{\\text{peak}}/\\tau_2)} \\Theta(t)\\\\\n",
-    "     t_{\\text{peak}} &= \\frac{\\tau_2 \\tau_1}{\\tau_2 - \\tau_1} \\ln\\frac{ \\tau_2}{\\tau_1}\n",
+    "\\bar{g}_X(t) &= g_X(t)\\\\\n",
+    "g_X(t) &= g_{\\text{peak}, X}\\frac{\\exp(-t/\\tau_1) - \\exp(-t/\\tau_2)}{\n",
+    "\\exp(-t_{\\text{peak}}/\\tau_1) - \\exp(-t_{\\text{peak}}/\\tau_2)} \\Theta(t)\\\\\n",
+    "t_{\\text{peak}} &= \\frac{\\tau_2 \\tau_1}{\\tau_2 - \\tau_1} \\ln\\frac{ \\tau_2}{\\tau_1}\n",
     "\\end{align} \n",
     "\n",
     "where $t_{\\text{peak}}$ is the time of the conductance maximum and $\\tau_1$ and $\\tau_2$ are synaptic rise- and decay-time, respectively; $\\Theta(t)$ is the Heaviside step function. The equation is integrated using exact integration in Synthesis; in NEST, it is included in the ODE-system integrated using the Runge-Kutta-Fehlberg 4(5) solver from GSL.\n",
@@ -306,11 +306,11 @@
     "The voltage-dependent gating $m(V, t)$ is defined as follows (based on textual description, Vargas-Caballero and Robinson *J Neurophysiol* 89:2778–2783, 2003, [doi:10.1152/jn.01038.2002](http://dx.doi.org/10.1152/jn.01038.2002), and code inspection):\n",
     "\n",
     "\\begin{align}\n",
-    "     m(V, t) &= a(V) m_{\\text{fast}}^*(V, t) + ( 1 - a(V) ) m_{\\text{slow}}^*(V, t)\\\\\n",
-    "     a(V)    &= 0.51 - 0.0028 V \\\\\n",
-    "     m^{\\infty}(V) &= \\frac{1}{ 1 + \\exp\\left( -S_{\\text{act}} ( V - V_{\\text{act}} ) \\right) } \\\\\n",
-    "     m_X^*(V, t) &= \\min(m^{\\infty}(V), m_X(V, t))\\\\\n",
-    "      \\frac{\\text{d}m_X}{\\text{d}t} &= \\frac{m^{\\infty}(V) - m_X }{ \\tau_{\\text{Mg}, X}}\n",
+    "m(V, t) &= a(V) m_{\\text{fast}}^*(V, t) + ( 1 - a(V) ) m_{\\text{slow}}^*(V, t)\\\\\n",
+    "a(V)    &= 0.51 - 0.0028 V \\\\\n",
+    "m^{\\infty}(V) &= \\frac{1}{ 1 + \\exp\\left( -S_{\\text{act}} ( V - V_{\\text{act}} ) \\right) } \\\\\n",
+    "m_X^*(V, t) &= \\min(m^{\\infty}(V), m_X(V, t))\\\\\n",
+    "\\frac{\\text{d}m_X}{\\text{d}t} &= \\frac{m^{\\infty}(V) - m_X }{ \\tau_{\\text{Mg}, X}}\n",
     "\\end{align} \n",
     "\n",
     "where $X$ is \"slow\" or \"fast\". $a(V)$ expresses voltage-dependent weighting between slow and fast unblocking, $m^{\\infty}(V)$ the steady-state value of the proportion of unblocked NMDA-channels, the minimum condition in $m_X^*(V,t)$ the instantaneous blocking and the differential equation for $m_X(V,t)$ the unblocking dynamics.\n",
@@ -1004,7 +1004,7 @@
     "I_T &= g_{\\text{peak}, T} m_T^2(V, t) h_T(V,t) (V-E_T) \\\\\n",
     "m_T^{\\infty}(V) &=  \\frac{1}{1+\\exp\\left(-\\frac{V+59\\text{mV}}{6.2\\text{mV}}\\right)}\\\\\n",
     "\\tau_{m,T}(V) &= 0.13\\text{ms} \n",
-    "  + \\frac{0.22\\text{ms}}{\\exp\\left(-\\frac{V  + 132\\text{mV}}{16.7\\text{mV}}\\right) + \\exp\\left(\\frac{V +  16.8\\text{mV}}{18.2\\text{mV}}\\right)} \\\\ \n",
+    "+ \\frac{0.22\\text{ms}}{\\exp\\left(-\\frac{V  + 132\\text{mV}}{16.7\\text{mV}}\\right) + \\exp\\left(\\frac{V +  16.8\\text{mV}}{18.2\\text{mV}}\\right)} \\\\ \n",
     "h_T^{\\infty}(V) &=  \\frac{1}{1+\\exp\\left(\\frac{V+83\\text{mV}}{4\\text{mV}}\\right)}\\\\\n",
     "\\tau_{h,T}(V) &= 8.2\\text{ms} +  \\frac{56.6\\text{ms} +  0.27\\text{ms} \\exp\\left(\\frac{V   + 115.2\\text{mV}}{5\\text{mV}}\\right)}{1 +   \\exp\\left(\\frac{V  + 86\\text{mV}}{3.2\\text{mV}}\\right)}\n",
     "\\end{align}"
@@ -1248,10 +1248,10 @@
     "\n",
     "\\begin{align}\n",
     "I_{DK} &= - g_{\\text{peak},DK} m_{DK}(V,t) (V - E_{DK})\\\\\n",
-    " m_{DK} &= \\frac{1}{1 + \\left(\\frac{d_{1/2}}{D}\\right)^{3.5}}\\\\\n",
-    " \\frac{dD}{dt} &= D_{\\text{influx}}(V) - \\frac{D-D_{\\text{eq}}}{\\tau_D} = \\frac{D_{\\infty}(V)-D}{\\tau_D} \\\\\n",
-    " D_{\\infty}(V) &= \\tau_D D_{\\text{influx}}(V) + {D_{\\text{eq}}}\\\\\n",
-    " D_{\\text{influx}} &= \\frac{D_{\\text{influx,peak}}}{1+ \\exp\\left(-\\frac{V-D_{\\theta}}{\\sigma_D}\\right)} \n",
+    "m_{DK} &= \\frac{1}{1 + \\left(\\frac{d_{1/2}}{D}\\right)^{3.5}}\\\\\n",
+    "\\frac{dD}{dt} &= D_{\\text{influx}}(V) - \\frac{D-D_{\\text{eq}}}{\\tau_D} = \\frac{D_{\\infty}(V)-D}{\\tau_D} \\\\\n",
+    "D_{\\infty}(V) &= \\tau_D D_{\\text{influx}}(V) + {D_{\\text{eq}}}\\\\\n",
+    "D_{\\text{influx}} &= \\frac{D_{\\text{influx,peak}}}{1+ \\exp\\left(-\\frac{V-D_{\\theta}}{\\sigma_D}\\right)} \n",
     "\\end{align}\n",
     "\n",
     "with \n",
@@ -1363,8 +1363,8 @@
    "metadata": {},
    "source": [
     "- Note that current in steady state is \n",
-    "    - $\\approx 0$ for $V < -40$mV\n",
-    "    - $\\sim -(V-E_{DK})$ for $V> -30$mV"
+    "- $\\approx 0$ for $V < -40$mV\n",
+    "- $\\sim -(V-E_{DK})$ for $V> -30$mV"
    ]
   },
   {
@@ -1717,11 +1717,11 @@
     "The equations for this channel are\n",
     "\n",
     "\\begin{align}\n",
-    "    \\bar{g}_{\\text{NMDA}}(t) &= m(V, t) g_{\\text{NMDA}}(t)     m(V, t)\\\\ &= a(V) m_{\\text{fast}}^*(V, t) + ( 1 - a(V) ) m_{\\text{slow}}^*(V, t)\\\\\n",
-    "     a(V)    &= 0.51 - 0.0028 V \\\\\n",
-    "     m^{\\infty}(V) &= \\frac{1}{ 1 + \\exp\\left( -S_{\\text{act}} ( V - V_{\\text{act}} ) \\right) } \\\\\n",
-    "     m_X^*(V, t) &= \\min(m^{\\infty}(V), m_X(V, t))\\\\\n",
-    "      \\frac{\\text{d}m_X}{\\text{d}t} &= \\frac{m^{\\infty}(V) - m_X }{ \\tau_{\\text{Mg}, X}}\n",
+    "\\bar{g}_{\\text{NMDA}}(t) &= m(V, t) g_{\\text{NMDA}}(t)     m(V, t)\\\\ &= a(V) m_{\\text{fast}}^*(V, t) + ( 1 - a(V) ) m_{\\text{slow}}^*(V, t)\\\\\n",
+    "a(V)    &= 0.51 - 0.0028 V \\\\\n",
+    "m^{\\infty}(V) &= \\frac{1}{ 1 + \\exp\\left( -S_{\\text{act}} ( V - V_{\\text{act}} ) \\right) } \\\\\n",
+    "m_X^*(V, t) &= \\min(m^{\\infty}(V), m_X(V, t))\\\\\n",
+    "\\frac{\\text{d}m_X}{\\text{d}t} &= \\frac{m^{\\infty}(V) - m_X }{ \\tau_{\\text{Mg}, X}}\n",
     "\\end{align} \n",
     "\n",
     "where $g_{\\text{NMDA}}(t)$ is the beta functions as for the other channels. In case of instantaneous unblocking, $m=m^{\\infty}$."

doc/htmldoc/ref_material/pynest_apis.rst

@@ -96,11 +96,11 @@ Functions related to randomization
 .. automodule:: nest.random.hl_api_random
     :members:
 
+.. _pynest_spatial:
+
 Functions related to spatial distributions
 ------------------------------------------
 
-.. _pynest_spatial:
-
 .. automodule:: nest.spatial
     :members: distance
 
@@ -123,4 +123,4 @@ Functions related to SONATA networks
 ------------------------------------
 
 .. automodule:: nest.lib.hl_api_sonata
-    :members:
+    :members:

doc/htmldoc/synapses/connection_management.rst

@@ -63,7 +63,7 @@ Have a look at the :ref:`inspecting_connections` section further down
 to get more tips on how to examine the connections in greater detail.
 
 Multapses and autapses
-~~~~~~~~~~~~~~~~~~~~~~
+----------------------
 
 In the connection specification dictionary (containing the rule name and rule-
 specific parameters), the additional switch ``allow_autapses`` (default:
@@ -324,8 +324,8 @@ Array parameters can be used with the rules ``all_to_all``,
 lists. As with the scalar parameters, all parameters have to be
 specified as arrays of the correct type.
 
-all-to-all
-^^^^^^^^^^
+rule: all-to-all
+^^^^^^^^^^^^^^^^
 
 When connecting with rule ``all_to_all``, the array parameter must
 have dimension `len(B) x len(A)`.
@@ -337,8 +337,8 @@ have dimension `len(B) x len(A)`.
     syn_spec_dict = {'weight': [[1.2, -3.5, 2.5], [0.4, -0.2, 0.7]]}
     nest.Connect(A, B, syn_spec=syn_spec_dict)
 
-fixed indegree
-^^^^^^^^^^^^^^
+rule: fixed indegree
+^^^^^^^^^^^^^^^^^^^^
 
 For rule ``fixed_indegree`` the array has to be a two-dimensional
 NumPy array or Python list with shape ``(len(B), indegree)``, where
@@ -355,8 +355,8 @@ of the identity of the source neurons.
     syn_spec_dict = {'weight': [[1.2, -3.5],[0.4, -0.2],[0.6, 2.2]]}
     nest.Connect(A, B, conn_spec_dict, syn_spec_dict)
 
-fixed outdegree
-^^^^^^^^^^^^^^^
+rule: fixed outdegree
+^^^^^^^^^^^^^^^^^^^^^
 
 For rule ``fixed_outdegree`` the array has to be a two-dimensional
 NumPy array or Python list with shape ``(len(A), outdegree)``, where
@@ -373,8 +373,8 @@ regardless of the identity of the target neuron.
     syn_spec_dict = {'weight': [[1.2, -3.5, 0.4], [-0.2, 0.6, 2.2]]}
     nest.Connect(A, B, conn_spec_dict, syn_spec_dict)
 
-fixed total number
-^^^^^^^^^^^^^^^^^^
+rule: fixed total number
+^^^^^^^^^^^^^^^^^^^^^^^^
 
 For rule ``fixed_total_number``, the array has to be same the length as the
 number of connections ``N``.
@@ -387,8 +387,8 @@ number of connections ``N``.
     syn_spec_dict = {'weight': [1.2, -3.5, 0.4, -0.2]}
     nest.Connect(A, B, conn_spec_dict, syn_spec_dict)
 
-one-to-one
-^^^^^^^^^^
+rule: one-to-one
+^^^^^^^^^^^^^^^^
 
 For rule ``one_to_one`` the array must have the same length as there
 are nodes in ``A`` and ``B``.

doc/htmldoc/whats_new/v3.4/index.rst

@@ -44,8 +44,8 @@ Extent and center for spatial layers with freely placed neurons
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Spatial layers in NEST can be created by specifying node positions in
-the call to :py:func:`.Create` using :ref:`spatial distributions
-<pynest_spatial>` from ``nest.spatial``.
+the call to :py:func:`.Create` using :ref:`spatial distributions <pynest_spatial>`
+from ``nest.spatial``.
 
 When using :py:class:`.spatial.free`, the layer's ``extent`` will be
 determined automatically based on the positions of the lower-leftmost

pynest/nest/lib/hl_api_connections.py

@@ -305,7 +305,7 @@ def Disconnect(*args, conn_spec=None, syn_spec=None):
     Parameters
     ----------
     args : SynapseCollection or NodeCollections
-        Either a collection of connections to disconnect, or pre- and postsynaptic nodes given as `NodeCollection`s
+        Either a collection of connections to disconnect, or pre- and postsynaptic nodes given as NodeCollections
     conn_spec : str or dict
         Disconnection rule when specifying pre- and postsynaptic nodes, see below
     syn_spec : str or dict

pynest/nest/lib/hl_api_nodes.py

@@ -68,6 +68,7 @@ def Create(model, n=1, params=None, positions=None):
           The single values will be applied to all nodes, while the lists will be distributed across
           the nodes. Both single values and lists can be given at the same time.
         - A list with n dictionaries, one dictionary for each node.
+
         Values may be :py:class:`.Parameter` objects. If omitted,
         the model's defaults are used.
     positions: :py:class:`.grid` or :py:class:`.free` object, optional

pynest/nest/lib/hl_api_simulation.py

@@ -189,10 +189,12 @@ def ResetKernel():
     * all network nodes
     * all connections
     * all user-defined neuron and synapse models
+
     are deleted, and
 
     * time
     * random generators
+
     are reset. The only exception is that dynamically loaded modules are not
     unloaded. This may change in a future version of NEST.