Modify jupyter notebooks

pnbabu · Mar 26, 2024 · e637704 · e637704
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Showing 6 changed files with 7,417 additions and 521 deletions.
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_windows/stdp_windows.ipynb b/doc/tutorials/stdp_windows/stdp_windows.ipynb
diff --git a/pynestml/codegeneration/nest_code_generator_utils.py b/pynestml/codegeneration/nest_code_generator_utils.py
@@ -23,7 +23,6 @@
 
 import re
 import tempfile
-import uuid
 
 from pynestml.meta_model.ast_variable import ASTVariable
 from pynestml.symbols.variable_symbol import BlockType
@@ -63,12 +62,11 @@ 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,
                           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
@@ -81,54 +79,51 @@ 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:
+        neuron_model_name = re.findall(r"neuron [^:\s]*:", nestml_neuron_model)[0][7:-1]
+        nestml_model = re.sub(r"neuron [^:\s]*:",
+                              "neuron " + neuron_model_name + ":", nestml_neuron_model)
+        neuron_fn = neuron_model_name + ".nestml"
+        with open(neuron_fn, "w") as f:
             print(nestml_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:
+            synapse_model_name = re.findall(r"synapse [^:\s]*:", nestml_synapse_model)[0][8:-1]
+            nestml_model = re.sub(r"synapse [^:\s]*:",
+                                  "synapse " + synapse_model_name + ":", nestml_synapse_model)
+            synapse_fn = synapse_model_name + ".nestml"
+            with open(synapse_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,
+            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"
+
+        # generate the code for neuron and optionally synapse
+        if module_name:
+            module_name = "nestml_" + module_name + "_module"
+        else:
+            module_name = "nestml_module"
 
         generate_nest_target(input_path=input_fns,
                              install_path=install_path,