Merge remote-tracking branch 'origin/master' into resolution_to_timestep

pynestml/cocos/co_co_nest_random_functions_legally_used.py

@@ -0,0 +1,73 @@
+# -*- coding: utf-8 -*-
+#
+# co_co_nest_random_functions_legally_used.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 pynestml.cocos.co_co import CoCo
+from pynestml.meta_model.ast_model import ASTModel
+from pynestml.meta_model.ast_node import ASTNode
+from pynestml.meta_model.ast_on_condition_block import ASTOnConditionBlock
+from pynestml.meta_model.ast_on_receive_block import ASTOnReceiveBlock
+from pynestml.meta_model.ast_update_block import ASTUpdateBlock
+from pynestml.symbols.predefined_functions import PredefinedFunctions
+from pynestml.utils.logger import LoggingLevel, Logger
+from pynestml.utils.messages import Messages
+from pynestml.visitors.ast_visitor import ASTVisitor
+
+
+class CoCoNestRandomFunctionsLegallyUsed(CoCo):
+    """
+    This CoCo ensure that the random functions are used only in the ``update``, ``onReceive``, and ``onCondition`` blocks.
+    This CoCo is only checked for the NEST Simulator target.
+    """
+
+    @classmethod
+    def check_co_co(cls, node: ASTNode):
+        """
+        Checks the coco.
+        :param node: a single node (typically, a neuron or synapse)
+        """
+        visitor = CoCoNestRandomFunctionsLegallyUsedVisitor()
+        visitor.neuron = node
+        node.accept(visitor)
+
+
+class CoCoNestRandomFunctionsLegallyUsedVisitor(ASTVisitor):
+    def visit_function_call(self, node):
+        """
+        Visits a function call
+        :param node: a function call
+        """
+        function_name = node.get_name()
+        if function_name == PredefinedFunctions.RANDOM_NORMAL or function_name == PredefinedFunctions.RANDOM_UNIFORM \
+                or function_name == PredefinedFunctions.RANDOM_POISSON:
+            parent = node
+            while parent:
+                parent = parent.get_parent()
+
+                if isinstance(parent, ASTUpdateBlock) or isinstance(parent, ASTOnReceiveBlock) \
+                        or isinstance(parent, ASTOnConditionBlock):
+                    # the random function is correctly defined, hence return
+                    return
+
+                if isinstance(parent, ASTModel):
+                    # the random function is defined in other blocks (parameters, state, internals). Hence, an error.
+                    code, message = Messages.get_random_functions_legally_used(function_name)
+                    Logger.log_message(node=self.neuron, code=code, message=message, error_position=node.get_source_position(),
+                                       log_level=LoggingLevel.ERROR)

pynestml/cocos/co_cos_manager.py

@@ -28,7 +28,6 @@
 from pynestml.cocos.co_co_cm_synapse_model import CoCoCmSynapseModel
 from pynestml.cocos.co_co_convolve_has_correct_parameter import CoCoConvolveHasCorrectParameter
 from pynestml.cocos.co_co_convolve_cond_correctly_built import CoCoConvolveCondCorrectlyBuilt
-from pynestml.cocos.co_co_convolve_has_correct_parameter import CoCoConvolveHasCorrectParameter
 from pynestml.cocos.co_co_correct_numerator_of_unit import CoCoCorrectNumeratorOfUnit
 from pynestml.cocos.co_co_correct_order_in_equation import CoCoCorrectOrderInEquation
 from pynestml.cocos.co_co_each_block_defined_at_most_once import CoCoEachBlockDefinedAtMostOnce
@@ -49,6 +48,7 @@
 from pynestml.cocos.co_co_invariant_is_boolean import CoCoInvariantIsBoolean
 from pynestml.cocos.co_co_kernel_type import CoCoKernelType
 from pynestml.cocos.co_co_model_name_unique import CoCoModelNameUnique
+from pynestml.cocos.co_co_nest_random_functions_legally_used import CoCoNestRandomFunctionsLegallyUsed
 from pynestml.cocos.co_co_no_kernels_except_in_convolve import CoCoNoKernelsExceptInConvolve
 from pynestml.cocos.co_co_no_nest_name_space_collision import CoCoNoNestNameSpaceCollision
 from pynestml.cocos.co_co_no_duplicate_compilation_unit_names import CoCoNoDuplicateCompilationUnitNames
@@ -418,6 +418,14 @@ def check_input_port_size_type(cls, model: ASTModel):
         """
         CoCoVectorInputPortsCorrectSizeType.check_co_co(model)
 
+    @classmethod
+    def check_co_co_nest_random_functions_legally_used(cls, model: ASTModel):
+        """
+        Checks if the random number functions are used only in the update block.
+        :param model: a single model object.
+        """
+        CoCoNestRandomFunctionsLegallyUsed.check_co_co(model)
+
     @classmethod
     def post_symbol_table_builder_checks(cls, model: ASTModel, after_ast_rewrite: bool = False):
         """

pynestml/codegeneration/nest_code_generator.py

@@ -28,6 +28,7 @@
 import pynestml
 
 from pynestml.cocos.co_co_nest_synapse_delay_not_assigned_to import CoCoNESTSynapseDelayNotAssignedTo
+from pynestml.cocos.co_cos_manager import CoCosManager
 from pynestml.codegeneration.code_generator import CodeGenerator
 from pynestml.codegeneration.code_generator_utils import CodeGeneratorUtils
 from pynestml.codegeneration.nest_assignments_helper import NestAssignmentsHelper
@@ -172,21 +173,30 @@ def __init__(self, options: Optional[Mapping[str, Any]] = None):
         self.setup_printers()
 
     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)
+        for model in neurons + synapses:
+            # Check if the random number functions are used in the right blocks
+            CoCosManager.check_co_co_nest_random_functions_legally_used(model)
+
+            if Logger.has_errors(model):
+                raise Exception("Error(s) occurred during code generation")
+
+        if self.get_option("neuron_synapse_pairs"):
+            for model in synapses:
+                synapse_name_stripped = removesuffix(removesuffix(model.name.split("_with_")[0], "_"),
+                                                     FrontendConfiguration.suffix)
+                # special case for NEST delay variable (state or parameter)
+                assert synapse_name_stripped in self.get_option("delay_variable").keys(), "Please specify a delay variable for synapse '" + synapse_name_stripped + "' in the code generator options (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
+                assert ASTUtils.get_variable_by_name(model, self.get_option("delay_variable")[synapse_name_stripped]), "Delay variable '" + self.get_option("delay_variable")[synapse_name_stripped] + "' not found in synapse '" + synapse_name_stripped + "' (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
 
-            # special case for NEST delay variable (state or parameter)
-            assert synapse_name_stripped in self.get_option("delay_variable").keys(), "Please specify a delay variable for synapse '" + synapse_name_stripped + "' in the code generator options (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
-            assert ASTUtils.get_variable_by_name(synapse, self.get_option("delay_variable")[synapse_name_stripped]), "Delay variable '" + self.get_option("delay_variable")[synapse_name_stripped] + "' not found in synapse '" + synapse_name_stripped + "' (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
+                # special case for NEST weight variable (state or parameter)
+                assert synapse_name_stripped in self.get_option("weight_variable").keys(), "Please specify a weight variable for synapse '" + synapse_name_stripped + "' in the code generator options (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
+                assert ASTUtils.get_variable_by_name(model, self.get_option("weight_variable")[synapse_name_stripped]), "Weight variable '" + self.get_option("weight_variable")[synapse_name_stripped] + "' not found in synapse '" + synapse_name_stripped + "' (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
 
-            # special case for NEST weight variable (state or parameter)
-            assert synapse_name_stripped in self.get_option("weight_variable").keys(), "Please specify a weight variable for synapse '" + synapse_name_stripped + "' in the code generator options (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
-            assert ASTUtils.get_variable_by_name(synapse, self.get_option("weight_variable")[synapse_name_stripped]), "Weight variable '" + self.get_option("weight_variable")[synapse_name_stripped] + "' not found in synapse '" + synapse_name_stripped + "' (see https://nestml.readthedocs.io/en/latest/running/running_nest.html#dendritic-delay-and-synaptic-weight)"
+                if self.option_exists("delay_variable") and synapse_name_stripped in self.get_option("delay_variable").keys():
+                    delay_variable = self.get_option("delay_variable")[synapse_name_stripped]
+                    CoCoNESTSynapseDelayNotAssignedTo.check_co_co(delay_variable, model)
 
-            if self.option_exists("delay_variable") and synapse_name_stripped in self.get_option("delay_variable").keys():
-                delay_variable = self.get_option("delay_variable")[synapse_name_stripped]
-                CoCoNESTSynapseDelayNotAssignedTo.check_co_co(delay_variable, synapse)
-                if Logger.has_errors(synapse):
+                if Logger.has_errors(model):
                     raise Exception("Error(s) occurred during code generation")
 
     def setup_printers(self):

pynestml/frontend/pynestml_frontend.py

@@ -464,19 +464,22 @@ def process():
         Flag indicating whether errors occurred during processing
     """
 
-    # initialize and set options for transformers, code generator and builder
-    codegen_and_builder_opts = FrontendConfiguration.get_codegen_opts()
-
-    transformers, codegen_and_builder_opts = transformers_from_target_name(FrontendConfiguration.get_target_platform(),
-                                                                           options=codegen_and_builder_opts)
+    # initialise model transformers
+    transformers, unused_opts_transformer = transformers_from_target_name(FrontendConfiguration.get_target_platform(),
+                                                                          options=FrontendConfiguration.get_codegen_opts())
 
+    # initialise code generator
     code_generator = code_generator_from_target_name(FrontendConfiguration.get_target_platform())
-    codegen_and_builder_opts = code_generator.set_options(codegen_and_builder_opts)
+    unused_opts_codegen = code_generator.set_options(FrontendConfiguration.get_codegen_opts())
 
-    _builder, codegen_and_builder_opts = builder_from_target_name(FrontendConfiguration.get_target_platform(), options=codegen_and_builder_opts)
+    # initialise builder
+    _builder, unused_opts_builder = builder_from_target_name(FrontendConfiguration.get_target_platform(),
+                                                             options=FrontendConfiguration.get_codegen_opts())
 
-    if len(codegen_and_builder_opts) > 0:
-        raise CodeGeneratorOptionsException("The code generator option(s) \"" + ", ".join(codegen_and_builder_opts.keys()) + "\" do not exist.")
+    # check for unused codegen options
+    for opt_key in FrontendConfiguration.get_codegen_opts().keys():
+        if opt_key in unused_opts_transformer.keys() and opt_key in unused_opts_codegen.keys() and opt_key in unused_opts_builder.keys():
+            raise CodeGeneratorOptionsException("The code generator option \"" + opt_key + "\" does not exist.")
 
     models, errors_occurred = get_parsed_models()
 

pynestml/utils/messages.py

@@ -133,6 +133,7 @@ class MessageCode(Enum):
     NON_CONSTANT_EXPONENT = 111
     RESOLUTION_FUNC_USED = 112
     TIMESTEP_FUNCTION_LEGALLY_USED = 113
+    RANDOM_FUNCTIONS_LEGALLY_USED = 113
     EXPONENT_MUST_BE_INTEGER = 114
 
 
@@ -1386,3 +1387,8 @@ def get_non_constant_exponent(cls) -> Tuple[MessageCode, str]:
         message = "Cannot calculate value of exponent. Must be a constant value!"
 
         return MessageCode.NON_CONSTANT_EXPONENT, message
+
+    @classmethod
+    def get_random_functions_legally_used(cls, name):
+        message = "The function '" + name + "' can only be used in the update, onReceive, or onCondition blocks."
+        return MessageCode.RANDOM_FUNCTIONS_LEGALLY_USED, message

tests/nest_tests/nest_random_functions_test.py

@@ -0,0 +1,57 @@
+# -*- coding: utf-8 -*-
+#
+# nest_random_functions_test.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/>.
+import os
+
+import pytest
+
+from pynestml.frontend.pynestml_frontend import generate_nest_target
+
+
+class TestNestRandomFunctions:
+    """
+    Tests that, for the NEST target, random number functions are called only in ``update``, ``onReceive``, and ``onCondition`` block
+    """
+
+    @pytest.mark.xfail(strict=True, raises=Exception)
+    def test_nest_random_function_neuron_illegal(self):
+        input_path = os.path.realpath(os.path.join(os.path.dirname(__file__),
+                                                   "resources", "random_functions_illegal_neuron.nestml"))
+        generate_nest_target(input_path=input_path,
+                             target_path="target",
+                             logging_level="INFO",
+                             suffix="_nestml")
+
+    @pytest.mark.xfail(strict=True, raises=Exception)
+    def test_nest_random_function_synapse_illegal(self):
+        input_path = [
+            os.path.realpath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "models", "neurons",
+                                          "iaf_psc_exp_neuron.nestml")),
+            os.path.realpath(os.path.join(os.path.dirname(__file__),
+                                          "resources", "random_functions_illegal_synapse.nestml"))]
+
+        generate_nest_target(input_path=input_path,
+                             target_path="target",
+                             logging_level="INFO",
+                             suffix="_nestml",
+                             codegen_opts={"neuron_synapse_pairs": [{"neuron": "iaf_psc_exp_neuron",
+                                                                     "synapse": "random_functions_illegal_synapse",
+                                                                     "post_ports": ["post_spikes"]}],
+                                           "weight_variable": {"stdp_synapse": "w"}})

tests/nest_tests/resources/random_functions_illegal_neuron.nestml

@@ -0,0 +1,46 @@
+"""
+random_functions_illegal_neuron.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 random_functions_illegal_neuron:
+    state:
+        noise real = random_normal(0,sigma_noise)
+        v mV = -15 mV
+
+    parameters:
+        rate ms**-1 = 15.5 s**-1
+        sigma_noise real = 16.
+        u real = random_uniform(0,1)
+
+    internals:
+        poisson_input integer = random_poisson(rate * resolution() * 1E-3)
+
+    update:
+        if u < 0.5:
+            noise = 0.
+        else:
+            noise = random_normal(0,sigma_noise)
+
+        v += (poisson_input + noise) * mV

tests/nest_tests/resources/random_functions_illegal_synapse.nestml

@@ -0,0 +1,73 @@
+"""
+random_functions_illegal_synapse.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 random_functions_illegal_synapse:
+    state:
+        w real = 1    # Synaptic weight
+        pre_trace real = 0.
+        post_trace real = 0.
+
+    parameters:
+        d ms = 1 ms    # Synaptic transmission delay
+        lambda real = .01
+        tau_tr_pre ms = random_normal(110 ms, 55 ms)
+        tau_tr_post ms = random_normal(5 ms, 2.5 ms)
+        alpha real = 1
+        mu_plus real = 1
+        mu_minus real = 1
+        Wmax real = 100.
+        Wmin real = 0.
+
+    equations:
+        pre_trace' = -pre_trace / tau_tr_pre
+        post_trace' = -post_trace / tau_tr_post
+
+    input:
+        pre_spikes <- spike
+        post_spikes <- spike
+
+    output:
+        spike
+
+    onReceive(post_spikes):
+        post_trace += 1
+
+        # potentiate synapse
+        w_ real = Wmax * ( w / Wmax  + (lambda * ( 1. - ( w / Wmax ) )**mu_plus * pre_trace ))
+        w = min(Wmax, w_)
+
+    onReceive(pre_spikes):
+        pre_trace += 1
+
+        # depress synapse
+        w_ real = Wmax * ( w / Wmax  - ( alpha * lambda * ( w / Wmax )**mu_minus * post_trace ))
+        w = max(Wmin, w_)
+
+        # deliver spike to postsynaptic partner
+        emit_spike(w, d)
+
+    update:
+        integrate_odes()