fix bug when strictly_synaptic_vars are specified as code generator options (#1246)

Co-authored-by: C.A.P. Linssen <[email protected]>

Author: clinssen

doc/running/running_nest.rst

@@ -23,7 +23,7 @@ At the start of a timestep, the value is the one "just before" the update due to
 Event-based updating of synapses
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The synapse is allowed to contain an ``update`` block. Statements in the ``update`` block are executed whenever the internal state of the synapse is updated from one timepoint to the next; these updates are typically triggered by incoming spikes. The NESTML ``resolution()`` function will return the time that has elapsed since the last event was handled.
+The synapse is allowed to contain an ``update`` block. Statements in the ``update`` block are executed whenever the internal state of the synapse is updated from one timepoint to the next; these updates are typically triggered by incoming spikes. The NESTML ``timestep()`` function will return the time that has elapsed since the last event was handled.
 
 Synapses in NEST are not allowed to have any nonlinear time-based internal dynamics (ODEs). This is due to the fact that synapses are, unlike nodes, not updated on a regular time grid. Linear ODEs are allowed, because they admit an analytical solution, which can be updated in a single step from the previous event time to the current event time. However, nonlinear dynamics are not allowed because they would require a numeric solver evaluating the dynamics on a regular time grid.
 
@@ -214,7 +214,11 @@ In synapse models, precisely two spike event attributes are supported: a synapti
 Generating code for plastic synapses
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-When NESTML is invoked to generate code for plastic synapses, the code generator needs to know which neuron model the synapses will be connected to, so that it can generate fast C++ code for the neuron and the synapse that is mutually dependent at runtime. These pairs can be specified as a list of two-element dictionaries of the form :code:`{"neuron": "neuron_model_name", "synapse": "synapse_model_name"}`, for example:
+Synaptic and neuronal models should ideally be formulated independently of each other, so that each neuron can be combined with each synapse for maximum flexibility. When a synaptic plasticity rule (such as STDP) is formulated as a computational model, the plasticity rule is often expressed as a function of the timing of pre- and postsynaptic spikes, which are used in the dynamics of the weight update for that particular rule. Note that as each neuron is typically connected to hundreds or thousands of other neurons via synapses on its dendritic arbor, each of those synapses will observe the same postsynaptic spike times, and store and numerically integrate them in exactly the same way, causing a very large redundancy in memory and computation.
+
+To prevent this redundancy, these values should only be stored and computed once; ideally in the instances of the neuron models, where the spike timings are readily available. To achieve this, NESTML has the capability to process a synapse model as a pair together with the (postsynaptic) neuron model that it will connect to when the network is instantiated in the simulation. A list of these (neuron, synapse) pairs can be provided as code generator options when invoking the NESTML toolchain to generate code. During code generation, state variables that depend only on postsynaptic spike timing are then automatically identified and moved from the NESTML synapse model into the neuron model by the toolchain. In the generated code, at the points where the respective variables are used by the synapse (for instance, where they are used in calculating the change in synaptic strength), the variable references are replaced by function calls into the postsynaptic neuron instance. All parameters that are only used by these postsynaptic dynamics (for instance, time constants) are also moved to reduce the memory requirements for the synapse. Detecting and moving the state, parameters, and dynamics (ODEs) from synapse to neuron is carried out fully autonomously. We refer to this feature as the "co-generation" of neuron and synapse. It enables flexibility and separation of concerns in the model formalisations without compromising on performance.
+
+When NESTML is invoked to generate code for plastic synapses, the (neuron, synapse) pairs can be specified as a list of two-element dictionaries of the form :code:`{"neuron": "neuron_model_name", "synapse": "synapse_model_name"}`, for example:
 
 .. code-block:: python
 
@@ -236,6 +240,8 @@ Additionally, if the synapse requires it, specify the ``"post_ports"`` entry to
 
 This specifies that the neuron ``iaf_psc_exp_dend`` has to be generated paired with the synapse ``third_factor_stdp``, and that the input ports ``post_spikes`` and ``I_post_dend`` in the synapse are to be connected to the postsynaptic partner. For the ``I_post_dend`` input port, the corresponding variable in the (postsynaptic) neuron is called ``I_dend``.
 
+To prevent the NESTML code generator from moving specific variables from synapse into postsynaptic neuron, the code generation option ``strictly_synaptic_vars`` may be used (see https://nestml.readthedocs.io/en/latest/pynestml.transformers.html#pynestml.transformers.synapse_post_neuron_transformer.SynapsePostNeuronTransformer).
+
 Simulation of volume-transmitted neuromodulation in NEST can be done using "volume transmitter" devices [5]_. These are event-based and should correspond to a "spike" type input port in NESTML. The code generator options keyword ``"vt_ports"`` can be used here.
 
 .. code-block:: python

pynestml/transformers/synapse_post_neuron_transformer.py

@@ -294,7 +294,7 @@ def transform_neuron_synapse_pair_(self, neuron: ASTModel, synapse: ASTModel):
         strictly_synaptic_vars = ["t"]      # "seed" this with the predefined variable t
 
         if self.option_exists("strictly_synaptic_vars") and removesuffix(synapse.get_name(), FrontendConfiguration.suffix) in self.get_option("strictly_synaptic_vars").keys() and self.get_option("strictly_synaptic_vars")[removesuffix(synapse.get_name(), FrontendConfiguration.suffix)]:
-            strictly_synaptic_vars.append(self.get_option("strictly_synaptic_vars")[removesuffix(synapse.get_name(), FrontendConfiguration.suffix)])
+            strictly_synaptic_vars.extend(self.get_option("strictly_synaptic_vars")[removesuffix(synapse.get_name(), FrontendConfiguration.suffix)])
 
         if self.option_exists("delay_variable") and removesuffix(synapse.get_name(), FrontendConfiguration.suffix) in self.get_option("delay_variable").keys() and self.get_option("delay_variable")[removesuffix(synapse.get_name(), FrontendConfiguration.suffix)]:
             strictly_synaptic_vars.append(self.get_option("delay_variable")[removesuffix(synapse.get_name(), FrontendConfiguration.suffix)])