Merging master

models/cm_tree.cpp

@@ -50,7 +50,6 @@ Compartment::Compartment( const long compartment_index, const long parent_index
   compartment_currents = CompartmentCurrents( v_comp );
 }
 
-nest::Compartment::Compartment( const long compartment_index,
 Compartment::Compartment( const long compartment_index,
   const long parent_index,
   const DictionaryDatum& compartment_params )

models/eprop_learning_signal_connection_bsshslm_2020.h

@@ -152,7 +152,7 @@ class eprop_learning_signal_connection_bsshslm_2020 : public Connection< targeti
 
   //! Check if the target accepts the event and receptor type requested by the sender.
   void
-  check_connection( Node& s, Node& t, size_t receptor_type, const CommonPropertiesType& )
+  check_connection( Node& s, Node& t, size_t receptor_type, const synindex, const CommonPropertiesType& )
   {
     LearningSignalConnectionEvent ge;
 

models/eprop_synapse_bsshslm_2020.h

@@ -257,7 +257,7 @@ class eprop_synapse_bsshslm_2020 : public Connection< targetidentifierT >
   //! Move assignment operator
   eprop_synapse_bsshslm_2020& operator=( eprop_synapse_bsshslm_2020&& );
 
-  using ConnectionBase::get_delay;
+  using ConnectionBase::get_delay_ms;
   using ConnectionBase::get_delay_steps;
   using ConnectionBase::get_rport;
   using ConnectionBase::get_target;
@@ -295,7 +295,8 @@ class eprop_synapse_bsshslm_2020 : public Connection< targetidentifierT >
    *
    * @note This sets the optimizer_ member.
    */
-  void check_connection( Node& s, Node& t, size_t receptor_type, const CommonPropertiesType& cp );
+  void
+  check_connection( Node& s, Node& t, size_t receptor_type, const synindex syn_id, const CommonPropertiesType& cp );
 
   //! Set the synaptic weight to the provided value.
   void
@@ -470,6 +471,7 @@ inline void
 eprop_synapse_bsshslm_2020< targetidentifierT >::check_connection( Node& s,
   Node& t,
   size_t receptor_type,
+  const synindex syn_id,
   const CommonPropertiesType& cp )
 {
   // When we get here, delay has been set so we can check it.
@@ -479,7 +481,7 @@ eprop_synapse_bsshslm_2020< targetidentifierT >::check_connection( Node& s,
   }
 
   ConnTestDummyNode dummy_target;
-  ConnectionBase::check_connection_( dummy_target, s, t, receptor_type );
+  ConnectionBase::check_connection_( dummy_target, s, t, syn_id, receptor_type );
 
   t.register_eprop_connection();
 

nestkernel/connector_model.h

@@ -158,11 +158,13 @@ class GenericConnectorModel : public ConnectorModel
 
   ConnectionT default_connection_;
   size_t receptor_type_;
+  synindex syn_id_;
 
 public:
   GenericConnectorModel( const std::string name )
     : ConnectorModel( name, ConnectionT::properties )
     , receptor_type_( 0 )
+    , syn_id_( invalid_synindex )
   {
   }
 
@@ -171,6 +173,7 @@ class GenericConnectorModel : public ConnectorModel
     , cp_( cm.cp_ )
     , default_connection_( cm.default_connection_ )
     , receptor_type_( cm.receptor_type_ )
+    , syn_id_( cm.syn_id_ )
   {
   }
 
@@ -215,8 +218,7 @@ class GenericConnectorModel : public ConnectorModel
 
 private:
   void used_default_delay();
-
-}; // GenericConnectorModel
+};
 
 } // namespace nest
 

nestkernel/connector_model_impl.h

@@ -54,7 +54,7 @@ namespace nest
 // double get_default_delay(const GenericConnectorModel<ConnectionT> &cm)
 // {
 //   //std::cout << "standard implementation of get_default_delay" << std::endl;
-//   return cm.get_default_connection().get_delay();
+//   return cm.get_default_connection().get_delay_ms();
 // }
 
 
@@ -63,6 +63,7 @@ ConnectorModel*
 GenericConnectorModel< ConnectionT >::clone( std::string name, synindex syn_id ) const
 {
   ConnectorModel* new_cm = new GenericConnectorModel( *this, name ); // calls copy construtor
+  new_cm->set_syn_id( syn_id );
 
   const bool is_primary = new_cm->has_property( ConnectionModelProperties::IS_PRIMARY );
   if ( not is_primary )
@@ -201,7 +202,14 @@ template < typename ConnectionT >
 size_t
 GenericConnectorModel< ConnectionT >::get_syn_id() const
 {
-  return default_connection_.get_syn_id();
+  return syn_id_;
+}
+
+template < typename ConnectionT >
+void
+GenericConnectorModel< ConnectionT >::set_syn_id( synindex syn_id )
+{
+  syn_id_ = syn_id;
 }
 
 template < typename ConnectionT >

nestkernel/model_manager_impl.h

@@ -101,6 +101,7 @@ ModelManager::register_specific_connection_model_( const std::string& name )
 #pragma omp parallel
   {
     ConnectorModel* conn_model = new GenericConnectorModel< CompleteConnectionT >( name );
+    conn_model->set_syn_id( new_syn_id );
     if ( not conn_model->has_property( ConnectionModelProperties::IS_PRIMARY ) )
     {
       conn_model->get_secondary_event()->add_syn_id( new_syn_id );

pynest/nest/lib/hl_api_connections.py

@@ -264,7 +264,8 @@ def Connect(pre, post, conn_spec=None, syn_spec=None, return_synapsecollection=F
         else:
             syn_param_values = None
 
-        connect_arrays(pre, post, weights, delays, axonal_delays, synapse_model, reduced_processed_syn_spec.keys(), syn_param_values)
+        connect_arrays(pre, post, weights, delays, axonal_delays, synapse_model, reduced_processed_syn_spec.keys(),
+                       syn_param_values)
 
         return
 

testsuite/pytests/test_stdp_pl_synapse_hom.py

@@ -36,7 +36,6 @@
     except Exception:
         DEBUG_PLOTS = False
 
-
 # Defined here so we can use it in init_params() and in parametrization
 RESOLUTION = 0.1  # [ms]
 
@@ -96,9 +95,9 @@ def do_nest_simulation_and_compare_to_reproduced_weight(self, fname_snip):
         assert len(weight_by_nest) > 0
 
         difference_matrix = (
-            t_weight_by_nest[t_weight_by_nest < self.simulation_duration].reshape(1, -1)
-            + self.axonal_delay
-            - t_weight_reproduced_independently.reshape(-1, 1)
+                t_weight_by_nest[t_weight_by_nest < self.simulation_duration].reshape(1, -1)
+                + self.axonal_delay
+                - t_weight_reproduced_independently.reshape(-1, 1)
         )
         pre_spike_reproduced_indices = np.abs(difference_matrix).argmin(axis=0)
         time_differences = np.diagonal(difference_matrix[pre_spike_reproduced_indices])
@@ -218,7 +217,7 @@ def facilitate(w, Kplus):
 
         def depress(w, Kminus):
             new_weight = (
-                w - self.synapse_common_properties["alpha"] * self.synapse_common_properties["lambda"] * w * Kminus
+                    w - self.synapse_common_properties["alpha"] * self.synapse_common_properties["lambda"] * w * Kminus
             )
             return new_weight if new_weight > 0.0 else 0.0
 
@@ -294,7 +293,7 @@ def depress(w, Kminus):
                         # if time when next pre-synaptic spike is being communicated is before post-synaptic spike
                         # occurs, a correction will be required in NEST
                         if (
-                            t_next_pre_spike - RESOLUTION - self.axonal_delay + self.min_delay
+                                t_next_pre_spike - RESOLUTION - self.axonal_delay + self.min_delay
                         ) // self.min_delay * self.min_delay < t_next_post_spike:
                             allowed_to_deviate.append(True)
                         else:
@@ -307,15 +306,15 @@ def depress(w, Kminus):
                         # if the next post-synaptic spike occurs after the pre-synaptic is being communicated, but
                         # before the pre-synaptic spike arrives at the synapse, a correction will be required in NEST
                         if (
-                            abs(t_next_post_spike - t_next_pre_spike) < eps
-                            and (t_next_pre_spike - RESOLUTION - self.axonal_delay + self.min_delay)
-                            // self.min_delay
-                            * self.min_delay
-                            < t_next_post_spike - self.dendritic_delay
+                                abs(t_next_post_spike - t_next_pre_spike) < eps
+                                and (t_next_pre_spike - RESOLUTION - self.axonal_delay + self.min_delay)
+                                // self.min_delay
+                                * self.min_delay
+                                < t_next_post_spike - self.dendritic_delay
                         ):
                             pass
                         elif (
-                            t_next_pre_spike - RESOLUTION - self.axonal_delay + self.min_delay
+                                t_next_pre_spike - RESOLUTION - self.axonal_delay + self.min_delay
                         ) // self.min_delay * self.min_delay < t_last_post_spike:
                             allowed_to_deviate.append(True)
                         else:
@@ -349,16 +348,16 @@ def depress(w, Kminus):
         return np.array(t_log), np.array(w_log), Kplus_log, Kminus_log, np.array(allowed_to_deviate)
 
     def plot_weight_evolution(
-        self,
-        pre_spikes,
-        post_spikes,
-        t_log,
-        w_log,
-        Kpre_log=None,
-        Kpost_log=None,
-        pre_indices=slice(-1),
-        fname_snip="",
-        title_snip="",
+            self,
+            pre_spikes,
+            post_spikes,
+            t_log,
+            w_log,
+            Kpre_log=None,
+            Kpost_log=None,
+            pre_indices=slice(-1),
+            fname_snip="",
+            title_snip="",
     ):
         if not DEBUG_PLOTS:  # make pylint happy if no matplotlib
             return
@@ -396,7 +395,8 @@ def plot_weight_evolution(
         fig.savefig("./tmp/nest_stdp_pl_synapse_hom_test" + fname_snip + ".png", dpi=300)
         plt.close(fig)
 
-    @pytest.mark.parametrize(["dend_delay", "ax_delay"], ((1.0, 0.0), (0.5, 0.5), (0.0, 1.0), (RESOLUTION, 0.0), (0.0, RESOLUTION)))
+    @pytest.mark.parametrize(["dend_delay", "ax_delay"],
+                             ((1.0, 0.0), (0.5, 0.5), (0.0, 1.0), (RESOLUTION, 0.0), (0.0, RESOLUTION)))
     @pytest.mark.parametrize("model", ("iaf_psc_alpha",))
     @pytest.mark.parametrize("min_delay", (1.0, 0.4, RESOLUTION))
     @pytest.mark.parametrize("max_delay", (1.0, 3.0))