change timestep adder to a transformer

Author: C.A.P. Linssen

pynestml/codegeneration/nest_code_generator.py

@@ -344,7 +344,6 @@ def analyse_neuron(self, neuron: ASTModel) -> Tuple[Dict[str, ASTAssignment], Di
             self.non_equations_state_variables[neuron.get_name()] = []
             self.non_equations_state_variables[neuron.get_name()].extend(
                 ASTUtils.all_variables_defined_in_block(neuron.get_state_blocks()))
-            ASTUtils.add_timestep_symbol(neuron)
 
             return {}, {}, [], []
 
@@ -402,7 +401,6 @@ def analyse_neuron(self, neuron: ASTModel) -> Tuple[Dict[str, ASTAssignment], Di
         ASTUtils.create_integrate_odes_combinations(neuron)
         ASTUtils.replace_variable_names_in_expressions(neuron, [analytic_solver, numeric_solver])
         ASTUtils.replace_convolution_aliasing_inlines(neuron)
-        ASTUtils.add_timestep_symbol(neuron)
 
         if self.analytic_solver[neuron.get_name()] is not None:
             neuron = ASTUtils.add_declarations_to_internals(
@@ -448,18 +446,14 @@ def analyse_synapse(self, synapse: ASTModel) -> Dict[str, ASTAssignment]:
             ASTUtils.create_initial_values_for_kernels(synapse, [analytic_solver, numeric_solver], kernels)
             ASTUtils.create_integrate_odes_combinations(synapse)
             ASTUtils.replace_variable_names_in_expressions(synapse, [analytic_solver, numeric_solver])
-            ASTUtils.add_timestep_symbol(synapse)
             self.update_symbol_table(synapse)
             spike_updates, _ = self.get_spike_update_expressions(synapse, kernel_buffers, [analytic_solver, numeric_solver], delta_factors)
 
             if not self.analytic_solver[synapse.get_name()] is None:
                 synapse = ASTUtils.add_declarations_to_internals(
                     synapse, self.analytic_solver[synapse.get_name()]["propagators"])
 
-            self.update_symbol_table(synapse)
-        else:
-            ASTUtils.add_timestep_symbol(synapse)
-            self.update_symbol_table(synapse)
+        self.update_symbol_table(synapse)
 
         ASTUtils.update_blocktype_for_common_parameters(synapse)
 

pynestml/codegeneration/nest_compartmental_code_generator.py

@@ -515,9 +515,6 @@ def analyse_neuron(self, neuron: ASTModel) -> List[ASTAssignment]:
         # conventions of ODE-toolbox
         ASTUtils.replace_convolution_aliasing_inlines(neuron)
 
-        # add variable __h to internals block
-        ASTUtils.add_timestep_symbol(neuron)
-
         # add propagator variables calculated by odetoolbox into internal blocks
         if self.analytic_solver[neuron.get_name()] is not None:
             neuron = ASTUtils.add_declarations_to_internals(

pynestml/frontend/pynestml_frontend.py

@@ -61,6 +61,12 @@ def transformers_from_target_name(target_name: str, options: Optional[Mapping[st
     if options is None:
         options = {}
 
+    if target_name.upper() in ["NEST", "PYTHON_STANDALONE", "NEST_COMPARTMENTAL", "NEST_DESKTOP"]:
+        from pynestml.transformers.add_timestep_to_internals_transformer import AddTimestepToInternalsTransformer
+
+        add_timestep_to_internals_transformer = AddTimestepToInternalsTransformer()
+        transformers.append(add_timestep_to_internals_transformer)
+
     if target_name.upper() in ["NEST", "SPINNAKER"]:
         from pynestml.transformers.illegal_variable_name_transformer import IllegalVariableNameTransformer
 

pynestml/transformers/add_timestep_to_internals_transformer.py

@@ -0,0 +1,63 @@
+# -*- coding: utf-8 -*-
+#
+# add_timestep_to_internals_transformer.py
+#
+# 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/>.
+
+from __future__ import annotations
+
+from typing import Optional, Mapping, Any, Union, Sequence
+from pynestml.meta_model.ast_model import ASTModel
+
+from pynestml.meta_model.ast_node import ASTNode
+from pynestml.transformers.transformer import Transformer
+
+
+class AddTimestepToInternalsTransformer(Transformer):
+    r"""
+    Add timestep variable to the internals block
+    """
+
+    def __init__(self, options: Optional[Mapping[str, Any]] = None):
+        super(Transformer, self).__init__(options)
+
+    def transform(self, models: Union[ASTNode, Sequence[ASTNode]]) -> Union[ASTNode, Sequence[ASTNode]]:
+        single = False
+        if isinstance(models, ASTNode):
+            single = True
+            models = [models]
+
+        for model in models:
+            self.add_timestep_symbol(model)
+
+        if single:
+            return models[0]
+
+        return models
+
+    @classmethod
+    def add_timestep_symbol(cls, model: ASTModel) -> None:
+        r"""
+        Add timestep variable to the internals block
+        """
+        from pynestml.utils.model_parser import ModelParser
+        assert model.get_initial_value(
+            "__h") is None, "\"__h\" is a reserved name, please do not use variables by this name in your NESTML file"
+        assert not "__h" in [sym.name for sym in model.get_internal_symbols(
+        )], "\"__h\" is a reserved name, please do not use variables by this name in your NESTML file"
+        model.add_to_internals_block(ModelParser.parse_declaration('__h ms = resolution()'), index=0)

pynestml/utils/ast_utils.py

@@ -2256,18 +2256,6 @@ def remove_kernel_definitions_from_equations_block(cls, model: ASTModel) -> ASTD
 
         return decl_to_remove
 
-    @classmethod
-    def add_timestep_symbol(cls, model: ASTModel) -> None:
-        """
-        Add timestep variable to the internals block
-        """
-        from pynestml.utils.model_parser import ModelParser
-        assert model.get_initial_value(
-            "__h") is None, "\"__h\" is a reserved name, please do not use variables by this name in your NESTML file"
-        assert not "__h" in [sym.name for sym in model.get_internal_symbols(
-        )], "\"__h\" is a reserved name, please do not use variables by this name in your NESTML file"
-        model.add_to_internals_block(ModelParser.parse_declaration('__h ms = resolution()'), index=0)
-
     @classmethod
     def generate_kernel_buffers(cls, model: ASTModel, equations_block: Union[ASTEquationsBlock, List[ASTEquationsBlock]]) -> Mapping[ASTKernel, ASTInputPort]:
         """