Change model registration for NEST target (#1002)

* Change the way models are registered in NEST * adjust compartmental_model_test.py to take into account the new initialization paradigm introduced in NEST 3.6 Co-authored-by: WillemWybo <willem.a.m.wybo@gmail.com>
nest · Apr 4, 2024 · ca6e490 · ca6e490
1 parent 4e02bf3
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diff --git a/doc/tutorials/active_dendrite/nestml_active_dendrite_tutorial.ipynb b/doc/tutorials/active_dendrite/nestml_active_dendrite_tutorial.ipynb
diff --git a/doc/tutorials/izhikevich/nestml_izhikevich_tutorial.ipynb b/doc/tutorials/izhikevich/nestml_izhikevich_tutorial.ipynb
diff --git a/doc/tutorials/ornstein_uhlenbeck_noise/nestml_ou_noise_tutorial.ipynb b/doc/tutorials/ornstein_uhlenbeck_noise/nestml_ou_noise_tutorial.ipynb
diff --git a/doc/tutorials/spike_frequency_adaptation/nestml_spike_frequency_adaptation_tutorial.ipynb b/doc/tutorials/spike_frequency_adaptation/nestml_spike_frequency_adaptation_tutorial.ipynb
diff --git a/doc/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.ipynb b/doc/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.ipynb
diff --git a/doc/tutorials/stdp_windows/stdp_windows.ipynb b/doc/tutorials/stdp_windows/stdp_windows.ipynb
diff --git a/doc/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.ipynb b/doc/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.ipynb
diff --git a/pynestml/codegeneration/nest_builder.py b/pynestml/codegeneration/nest_builder.py
@@ -41,7 +41,6 @@ def __add_library_to_sli(lib_path):
         lib_path = os.path.abspath(lib_path)
 
     system = platform.system()
-    lib_key = ""
 
     if system == "Linux":
         lib_key = "LD_LIBRARY_PATH"
@@ -51,8 +50,7 @@ def __add_library_to_sli(lib_path):
     if lib_key in os.environ:
         current = os.environ[lib_key].split(os.pathsep)
         if lib_path not in current:
-            current.append(lib_path)
-            os.environ[lib_key] += os.pathsep.join(current)
+            os.environ[lib_key] = os.pathsep.join([os.environ[lib_key], lib_path])
     else:
         os.environ[lib_key] = lib_path
 

diff --git a/pynestml/codegeneration/nest_code_generator.py b/pynestml/codegeneration/nest_code_generator.py
@@ -248,6 +248,9 @@ def _get_module_namespace(self, neurons: List[ASTNeuron], synapses: List[ASTSyna
                      "synapses": synapses,
                      "moduleName": FrontendConfiguration.get_module_name(),
                      "now": datetime.datetime.utcnow()}
+        # NEST version
+        if self.option_exists("nest_version"):
+            namespace["nest_version"] = self.get_option("nest_version")
         return namespace
 
     def analyse_transform_neurons(self, neurons: List[ASTNeuron]) -> None:

diff --git a/pynestml/codegeneration/nest_code_generator_utils.py b/pynestml/codegeneration/nest_code_generator_utils.py
@@ -18,7 +18,6 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
-
 from typing import List, Optional
 
 import re
@@ -63,12 +62,12 @@ def print_symbol_origin(cls, variable_symbol: VariableSymbol, variable: ASTVaria
     def generate_code_for(cls,
                           nestml_neuron_model: str,
                           nestml_synapse_model: Optional[str] = None,
+                          module_name: Optional[str] = None,
+                          target_path: str = "target",
                           post_ports: Optional[List[str]] = None,
                           mod_ports: Optional[List[str]] = None,
-                          uniq_id: Optional[str] = None,
                           logging_level: str = "WARNING"):
         """Generate code for a given neuron and synapse model, passed as a string.
-        NEST cannot yet unload or reload modules. This function implements a workaround using UUIDs to generate unique names.
         The neuron and synapse models can be passed directly as strings in NESTML syntax, or as filenames, in which case the NESTML model is loaded from the given filename.
 
         Returns
@@ -81,59 +80,52 @@ def generate_code_for(cls,
         # generate temporary install directory
         install_path = tempfile.mkdtemp(prefix="nestml_target_")
 
-        # generate unique ID
-        if uniq_id is None:
-            uniq_id = str(uuid.uuid4().hex)
-
         # read neuron model from file?
-        if not "\n" in nestml_neuron_model and ".nestml" in nestml_neuron_model:
+        if "\n" not in nestml_neuron_model and ".nestml" in nestml_neuron_model:
             with open(nestml_neuron_model, "r") as nestml_model_file:
                 nestml_neuron_model = nestml_model_file.read()
 
         # update neuron model name inside the file
-        neuron_model_name_orig = re.findall(r"neuron\ [^:\s]*:", nestml_neuron_model)[0][7:-1]
-        neuron_model_name_uniq = neuron_model_name_orig + uniq_id
-        nestml_model = re.sub(r"neuron\ [^:\s]*:",
-                              "neuron " + neuron_model_name_uniq + ":", nestml_neuron_model)
-        neuron_uniq_fn = neuron_model_name_uniq + ".nestml"
-        with open(neuron_uniq_fn, "w") as f:
-            print(nestml_model, file=f)
+        neuron_model_name = re.findall(r"neuron [^:\s]*:", nestml_neuron_model)[0][7:-1]
+        neuron_fn = neuron_model_name + ".nestml"
+        with open(neuron_fn, "w") as f:
+            print(nestml_neuron_model, file=f)
+
+        input_fns = [neuron_fn]
+        codegen_opts = {"neuron_parent_class": "StructuralPlasticityNode",
+                        "neuron_parent_class_include": "structural_plasticity_node.h"}
+        mangled_neuron_name = neuron_model_name + "_nestml"
 
         if nestml_synapse_model:
             # read synapse model from file?
-            if not "\n" in nestml_synapse_model and ".nestml" in nestml_synapse_model:
+            if "\n" not in nestml_synapse_model and ".nestml" in nestml_synapse_model:
                 with open(nestml_synapse_model, "r") as nestml_model_file:
                     nestml_synapse_model = nestml_model_file.read()
 
             # update synapse model name inside the file
-            synapse_model_name_orig = re.findall(r"synapse\ [^:\s]*:", nestml_synapse_model)[0][8:-1]
-            synapse_model_name_uniq = synapse_model_name_orig + uniq_id
-            nestml_model = re.sub(r"synapse\ [^:\s]*:",
-                                  "synapse " + synapse_model_name_uniq + ":", nestml_synapse_model)
-            synapse_uniq_fn = synapse_model_name_uniq + ".nestml"
-            with open(synapse_uniq_fn, "w") as f:
-                print(nestml_model, file=f)
-
-        # generate the code for neuron and optionally synapse
-        module_name = "nestml_" + uniq_id + "_module"
-        input_fns = [neuron_uniq_fn]
-        codegen_opts = {"neuron_parent_class": "StructuralPlasticityNode",
-                        "neuron_parent_class_include": "structural_plasticity_node.h"}
-
-        mangled_neuron_name = neuron_model_name_uniq + "_nestml"
-        if nestml_synapse_model:
-            input_fns += [synapse_uniq_fn]
-            codegen_opts["neuron_synapse_pairs"] = [{"neuron": neuron_model_name_uniq,
-                                                     "synapse": synapse_model_name_uniq,
+            synapse_model_name = re.findall(r"synapse [^:\s]*:", nestml_synapse_model)[0][8:-1]
+            synapse_fn = synapse_model_name + ".nestml"
+            with open(synapse_fn, "w") as f:
+                print(nestml_synapse_model, file=f)
+
+            input_fns += [synapse_fn]
+            codegen_opts["neuron_synapse_pairs"] = [{"neuron": neuron_model_name,
+                                                     "synapse": synapse_model_name,
                                                      "post_ports": post_ports,
                                                      "vt_ports": mod_ports}]
-            mangled_neuron_name = neuron_model_name_uniq + "_nestml__with_" + synapse_model_name_uniq + "_nestml"
-            mangled_synapse_name = synapse_model_name_uniq + "_nestml__with_" + neuron_model_name_uniq + "_nestml"
+            mangled_neuron_name = neuron_model_name + "_nestml__with_" + synapse_model_name + "_nestml"
+            mangled_synapse_name = synapse_model_name + "_nestml__with_" + neuron_model_name + "_nestml"
+
+        if not module_name:
+            # generate unique ID
+            uniq_id = str(uuid.uuid4().hex)
+            module_name = "nestml_" + uniq_id + "_module"
 
         generate_nest_target(input_path=input_fns,
                              install_path=install_path,
                              logging_level=logging_level,
                              module_name=module_name,
+                             target_path=target_path,
                              suffix="_nestml",
                              codegen_opts=codegen_opts)
 

diff --git a/pynestml/codegeneration/nest_compartmental_code_generator.py b/pynestml/codegeneration/nest_compartmental_code_generator.py
@@ -235,6 +235,7 @@ def _get_module_namespace(self, neurons: List[ASTNeuron]) -> Dict:
         :return: a context dictionary for rendering templates
         """
         namespace = {"neurons": neurons,
+                     "nest_version": self.get_option("nest_version"),
                      "moduleName": FrontendConfiguration.get_module_name(),
                      "now": datetime.datetime.utcnow()}
 

diff --git a/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronClass.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronClass.jinja2
@@ -57,6 +57,7 @@ along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 // Includes from nestkernel:
 #include "exceptions.h"
 #include "kernel_manager.h"
+#include "nest_impl.h"
 #include "universal_data_logger_impl.h"
 
 // Includes from sli:
@@ -68,6 +69,15 @@ along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
 #include "{{neuronName}}.h"
 
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2")
+        or nest_version.startswith("v3.3") or nest_version.startswith("v3.4") or nest_version.startswith("v3.5") or nest_version.startswith("v3.6")) %}
+void
+register_{{ neuronName }}( const std::string& name )
+{
+  nest::register_node_model< {{ neuronName }} >( name );
+}
+{%- endif %}
+
 // ---------------------------------------------------------------------------
 //   Recordables map
 // ---------------------------------------------------------------------------

diff --git a/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronHeader.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronHeader.jinja2
@@ -209,6 +209,13 @@ size_t access_counter )
 
   Receives: {% if has_spike_input %}Spike, {% endif %}{% if has_continuous_input %}Current,{% endif %} DataLoggingRequest
 */
+
+// Register the neuron model
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2")
+        or nest_version.startswith("v3.3") or nest_version.startswith("v3.4") or nest_version.startswith("v3.5") or nest_version.startswith("v3.6")) %}
+void register_{{ neuronName }}( const std::string& name );
+{%- endif %}
+
 class {{neuronName}} : public nest::{{neuron_parent_class}}
 {
 public:

diff --git a/pynestml/codegeneration/resources_nest/point_neuron/common/SynapseHeader.h.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/common/SynapseHeader.h.jinja2
@@ -82,6 +82,11 @@ along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace nest
 {
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2")
+        or nest_version.startswith("v3.3") or nest_version.startswith("v3.4") or nest_version.startswith("v3.5") or nest_version.startswith("v3.6")) %}
+// Register the synapse model
+void register_{{ synapseName }}( const std::string& name );
+{%- endif %}
 
 namespace {{names_namespace}}
 {
@@ -218,7 +223,6 @@ public:
 {%- endif %}
 };
 
-
 template < typename targetidentifierT >
 class {{synapseName}} : public Connection< targetidentifierT >
 {
@@ -654,8 +658,13 @@ public:
   }
 
 {%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+{%-   if not (nest_version.startswith("v3.5") or nest_version.startswith("v3.6")) %}
+  bool
+  send( Event& e, const size_t tid, const {{synapseName}}CommonSynapseProperties& cp )
+{%-   else %}
   void
   send( Event& e, const size_t tid, const {{synapseName}}CommonSynapseProperties& cp )
+{%-   endif %}
 {%- else %}
   void
   send( Event& e, const thread tid, const {{synapseName}}CommonSynapseProperties& cp )
@@ -845,6 +854,11 @@ public:
     **/
 
     t_lastspike_ = __t_spike;
+
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2")
+        or nest_version.startswith("v3.3") or nest_version.startswith("v3.4") or nest_version.startswith("v3.5") or nest_version.startswith("v3.6")) %}
+    return true;
+{%- endif %}
   }
 
   void get_status( DictionaryDatum& d ) const;
@@ -860,6 +874,15 @@ public:
 {%- endif %}
 };
 
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2")
+        or nest_version.startswith("v3.3") or nest_version.startswith("v3.4") or nest_version.startswith("v3.5") or nest_version.startswith("v3.6")) %}
+void
+register_{{ synapseName }}( const std::string& name )
+{
+  nest::register_connection_model< {{ synapseName }} >( name );
+}
+{%- endif %}
+
 {%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
 template < typename targetidentifierT >
 constexpr ConnectionModelProperties {{synapseName}}< targetidentifierT >::properties;

diff --git a/pynestml/codegeneration/resources_nest/point_neuron/setup/@MODULE_NAME@.cpp.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/setup/@MODULE_NAME@.cpp.jinja2
@@ -19,120 +19,11 @@
 *  along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 *
 */#}
-{%- if tracing %}/* generated by {{self._TemplateReference__context.name}} */ {% endif %}
-/*
-*  {{moduleName}}.cpp
-*
-*  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/>.
-*
-*  {{now}}
-*/
-
-// Includes from nestkernel:
-#include "connection_manager_impl.h"
-#include "connector_model_impl.h"
-#include "dynamicloader.h"
-#include "exceptions.h"
-#include "genericmodel_impl.h"
-#include "kernel_manager.h"
-#include "model.h"
-#include "model_manager_impl.h"
-#include "nestmodule.h"
-#include "target_identifier.h"
-
-// Includes from sli:
-#include "booldatum.h"
-#include "integerdatum.h"
-#include "sliexceptions.h"
-#include "tokenarray.h"
-
-// include headers with your own stuff
-#include "{{moduleName}}.h"
-
-{% for neuron in neurons %}
-#include "{{neuron.get_name()}}.h"
-{% endfor %}
-{% for synapse in synapses %}
-#include "{{synapse.get_name()}}.h"
-{% endfor %}
-// -- Interface to dynamic module loader ---------------------------------------
-
-/*
-* There are three scenarios, in which MyModule can be loaded by NEST:
-*
-* 1) When loading your module with `Install`, the dynamic module loader must
-* be able to find your module. You make the module known to the loader by
-* defining an instance of your module class in global scope. (LTX_MODULE is
-* defined) This instance must have the name
-*
-* <modulename>_LTX_mod
-*
-* The dynamicloader can then load modulename and search for symbol "mod" in it.
-*
-* 2) When you link the library dynamically with NEST during compilation, a new
-* object has to be created. In the constructor the DynamicLoaderModule will
-* register your module. (LINKED_MODULE is defined)
-*
-* 3) When you link the library statically with NEST during compilation, the
-* registration will take place in the file `static_modules.h`, which is
-* generated by cmake.
-*/
-#if defined(LTX_MODULE) | defined(LINKED_MODULE)
-{{moduleName}} {{moduleName}}_LTX_mod;
-#endif
-
-// -- DynModule functions ------------------------------------------------------
 
-{{moduleName}}::{{moduleName}}()
-{
-#ifdef LINKED_MODULE
-  // register this module at the dynamic loader
-  // this is needed to allow for linking in this module at compile time
-  // all registered modules will be initialized by the main app's dynamic loader
-  nest::DynamicLoaderModule::registerLinkedModule( this );
-#endif
-}
-
-{{moduleName}}::~{{moduleName}}()
-{
-}
-
-const std::string
-{{moduleName}}::name() const
-{
-  return std::string("{{moduleName}}"); // Return name of the module
-}
-
-//-------------------------------------------------------------------------------------
-void
-{{moduleName}}::init( SLIInterpreter* i )
-{
-{%- if neurons %}
-    // register neurons
-{%-   for neuron in neurons %}
-    nest::kernel().model_manager.register_node_model<{{neuron.get_name()}}>("{{neuron.get_name()}}");
-{%-   endfor %}
+{%- if nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2")
+    or nest_version.startswith("v3.3") or nest_version.startswith("v3.4") or nest_version.startswith("v3.5") or nest_version.startswith("v3.6") %}
+{%- include "common/ModuleClass.jinja2" %}
+{%- else %}
+{%- include "common/ModuleClassMaster.jinja2"  %}
 {%- endif %}
-{%- if synapses %}
 
-    // register synapses
-{%-   for synapse in synapses %}
-    nest::register_connection_model< nest::{{synapse.get_name()}} >( "{{synapse.get_name()}}" );
-{%-   endfor %}
-{%- endif %}
-} // {{moduleName}}::init()