ensure compatibility with NESTML custom as well as NEST built-in synaptic plasticity models

Author: C.A.P. Linssen

pynestml/codegeneration/nest_code_generator.py

@@ -169,6 +169,7 @@ def __init__(self, options: Optional[Mapping[str, Any]] = None):
     def run_nest_target_specific_cocos(self, neurons: Sequence[ASTModel], synapses: Sequence[ASTModel]):
         for synapse in synapses:
             synapse_name_stripped = removesuffix(removesuffix(synapse.name.split("_with_")[0], "_"), FrontendConfiguration.suffix)
+            assert synapse_name_stripped in self.get_option("delay_variable").keys(), "Please specify a ``delay_variable`` for the synapse '" + synapse_name_stripped + "'"
             delay_variable = self.get_option("delay_variable")[synapse_name_stripped]
             CoCoNESTSynapseDelayNotAssignedTo.check_co_co(delay_variable, synapse)
             if Logger.has_errors(synapse):

tests/nest_tests/resources/iaf_psc_exp_nonlineardendrite_alternate.nestml renamed to tests/nest_tests/resources/iaf_psc_exp_nonlineardendrite_neuron.nestml

@@ -1,4 +1,29 @@
-neuron iaf_psc_exp_nonlineardendrite:
+"""
+iaf_psc_exp_nonlineardendrite_alternate.nestml
+##############################################
+
+
+Copyright statement
++++++++++++++++++++
+
+This file is part of NEST.
+
+Copyright (C) 2004 The NEST Initiative
+
+NEST is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 2 of the License, or
+(at your option) any later version.
+
+NEST is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+"""
+model iaf_psc_exp_nonlineardendrite_neuron:
 
   state:
     V_m mV = 0mV     # membrane potential in mV
@@ -8,7 +33,6 @@ neuron iaf_psc_exp_nonlineardendrite:
     ref_counts integer = 0
 
   equations:
-
     # exponential shaped postsynaptic current kernel
     kernel I_kernel1 = exp(-1/tau_syn1*t)
 

tests/nest_tests/resources/stdsp_synapse_no_permanence.nestml renamed to tests/nest_tests/resources/stdsp_no_permanence_synapse.nestml

@@ -1,12 +1,36 @@
+"""
+stdsp_no_permanence_synapse.nestml
+##################################
 
-synapse stdsp_synapse_no_permanence:
+
+Copyright statement
++++++++++++++++++++
+
+This file is part of NEST.
+
+Copyright (C) 2004 The NEST Initiative
+
+NEST is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 2 of the License, or
+(at your option) any later version.
+
+NEST is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+"""
+model stdsp_no_permanence_synapse:
 
   state:
-    w real = 1.  @nest::weight
-    t_last_pre_spike ms = -1ms
+    w real = 1
+    t_last_pre_spike ms = -1 ms
 
   parameters:
-    d ms = 2.0 ms  @nest::delay # !!! cannot have a variable called "delay"
+    d ms = 2.0 ms
     lambda real = .01
     lambda_minus real = .01
     tau_tr_pre ms = 20 ms
@@ -54,5 +78,7 @@ synapse stdsp_synapse_no_permanence:
     w = max(Wmin, w_)
 
     # deliver spike to postsynaptic partner
-    deliver_spike(w, d)
+    emit_spike(w, d)
 
+  update:
+    integrate_odes()

tests/nest_tests/test_built_in_and_nestml_plastic_synapse.py

@@ -35,17 +35,16 @@
 class TestBuiltInAndNESTMLPlasticSynapse:
     r"""Test that synaptic plasticity works with both a NEST built-in plastic synapse and a NESTML custom plastic synapse attached to the same neuron."""
 
-    neuron_model = "iaf_psc_exp_nonlineardendrite"
-    synapse_model = "stdsp_synapse_no_permanence"
+    neuron_model = "iaf_psc_exp_nonlineardendrite_neuron"
+    synapse_model = "stdsp_no_permanence_synapse"
 
     def setup_nest(self):
-        files = [f"{TestBuiltInAndNESTMLPlasticSynapse.neuron_model}_alternate.nestml",
+        files = [f"{TestBuiltInAndNESTMLPlasticSynapse.neuron_model}.nestml",
                  f"{TestBuiltInAndNESTMLPlasticSynapse.synapse_model}.nestml"]
         input_path = [os.path.realpath(os.path.join(os.path.dirname(__file__), "resources", s)) for s in files]
 
         generate_nest_target(
             input_path=input_path,
-            target_path="module",
             logging_level="DEBUG",
             module_name=f"nestml_{TestBuiltInAndNESTMLPlasticSynapse.neuron_model}_{TestBuiltInAndNESTMLPlasticSynapse.synapse_model}_module",
             suffix="_nestml",
@@ -57,12 +56,11 @@ def setup_nest(self):
                         "post_ports": ["post_spikes", ["z_post", "z"]],
                     }
                 ],
-            },
+                "delay_variable": {"stdsp_no_permanence_synapse": "d"},
+                "weight_variable": {"stdsp_no_permanence_synapse": "w"}
+            }
         )
 
-        # install custom neuron models
-        nest.Install(f"nestml_{TestBuiltInAndNESTMLPlasticSynapse.neuron_model}_{TestBuiltInAndNESTMLPlasticSynapse.synapse_model}_module")
-
     def _test_plasticity(self, neuron_model, synapse_model):
 
         print("testing plasticity for synapse mode " + str(synapse_model))
@@ -73,6 +71,7 @@ def _test_plasticity(self, neuron_model, synapse_model):
         initial_weight = 123.
 
         nest.ResetKernel()
+        nest.Install(f"nestml_{TestBuiltInAndNESTMLPlasticSynapse.neuron_model}_{TestBuiltInAndNESTMLPlasticSynapse.synapse_model}_module")
 
         # create pre and post neurons
         pre_neuron = nest.Create(neuron_model)