Merge pull request #413 from Hjorthmedh/init_redux2

Fixed init bug

snudda/init/init_config.py

@@ -62,6 +62,10 @@ def replace_network_path(self, network_path):
         print(f"Setting {network_path = }")
         self.config_data["network_path"] = network_path
 
+    def skip_item(self, item):
+
+        return isinstance(item, str) and len(item) > 0 and item[0] == '!'
+
     def substitute_json(self, putative_file, key=None, parent_file=None):
 
         if not (isinstance(putative_file, str) and putative_file.endswith(".json")):
@@ -120,14 +124,17 @@ def parse_subtree(self, config_dict, parent_file=None):
                 updated_config[key] = self.parse_subtree(value, parent_file=parent_file)
 
             elif isinstance(value, list):
-                updated_config[key] = [self.substitute_json(x, parent_file=parent_file) for x in value]
+                updated_config[key] = [self.substitute_json(x, parent_file=parent_file) for x in value if not self.skip_item(x)]
 
                 # If the first element is a dict, assume all are dict and merge them
                 if isinstance(updated_config[key][0], dict):
                     updated_config[key] = dict(ChainMap(*reversed(updated_config[key])))
 
             else:
-                updated_config[key] = self.substitute_json(value, key, parent_file=parent_file)
+                if not self.skip_item(item=value):
+                    updated_config[key] = self.substitute_json(value, key, parent_file=parent_file)
+                else:
+                    del updated_config[key]
 
         return updated_config
 

snudda/input/input.py

@@ -902,6 +902,15 @@ def make_neuron_input_parallel(self):
 
                     # If your code fails here, it might be that you are trying to override the background input
                     # frequency, but have the incorrect name of that input (check the meta.json file)
+
+                    if "conductance" not in input_inf:
+                        raise ValueError(f"No conductance specified for {input_type = }.\n"
+                                         f"Are you trying to use meta.json input, but spelled name wrong, "
+                                         f"or did you miss to specify conductance for the input?"
+                                         f"\n{neuron_id = }, {neuron_name = }, {neuron_type = }, {population_unit_id = }"
+                                         f"\n{input_inf = }"
+                                         f"\nSee examples: https://github.com/Hjorthmedh/Snudda/tree/master/examples/notebooks")
+
                     cond = input_inf["conductance"]
 
                     if "num_inputs" in input_inf:

snudda/place/place.py

@@ -447,6 +447,8 @@ def parse_config(self, config_file=None, resort_neurons=True):
                 else:
                     raise ValueError(f"You need to specify 'fraction' or 'num_neurons' for {neuron_type}")
 
+                # print(f"{neuron_type = }, {num_neurons = }")
+
                 n_types = len(neuron_data["neuron_path"])
 
                 if isinstance(num_neurons, int):
@@ -463,6 +465,8 @@ def parse_config(self, config_file=None, resort_neurons=True):
                 else:
                     n_neurons = num_neurons
 
+                # print(f"{n_neurons = }")
+
                 parameter_key_list = SnuddaPlace.replicate_str(neuron_data.get("parameter_key"),
                                                                n_neurons, f"{neuron_type} parameter_key")
                 morphology_key_list = SnuddaPlace.replicate_str(neuron_data.get("morphology_key"),
@@ -474,6 +478,8 @@ def parse_config(self, config_file=None, resort_neurons=True):
                         in zip(neuron_data["neuron_path"].items(), n_neurons,
                                parameter_key_list, morphology_key_list, modulation_key_list):
 
+                    print(f"{neuron_name = }, {num = }, {neuron_path = }")
+
                     if neuron_name.split("_")[0] != neuron_type and neuron_name != neuron_type:
                         raise ValueError(f"The keys in neuron_path must be {neuron_name}_X where X is usually a number")
 
@@ -1438,11 +1444,11 @@ def replicate_str(string, n_replicas, variable_name=None):
         # variable_name is just used to help with error message if incorrect input
 
         if string is None or isinstance(string, str):
-            rep_str = [string for x in range(np.sum(n_replicas))]
+            rep_str = [string for x in range(len(n_replicas))]
         elif len(string) == n_replicas:
             rep_str = string
         else:
-            raise ValueError(f"Expected a str or a list of str of length {n_replicas} for {variable_name}")
+            raise ValueError(f"Expected a str or a list of str of length {len(n_replicas)} for {variable_name}")
 
         return rep_str