added param scan instance

biosimulator_processes/utils.py

@@ -36,24 +36,6 @@ def play_composition(instance: dict, duration: int):
     return results
 
 
-def generate_emitter_schema(
-        emitter_address: str = "local",
-        emitter_type: str = "ram-emitter",
-        **emit_values_schema
-) -> Dict:
-    return {
-        '_type': 'step',
-        'address': 'local:ram-emitter',
-        'config': {
-            'emit': {**emit_values_schema},
-        },
-        'inputs': {  # TODO: make this generalized
-            'floating_species': ['floating_species_store'],
-            'time': ['time_store'],
-        }
-    }
-
-
 def generate_copasi_process_emitter_schema():
     return generate_emitter_schema(
         emitter_address='local',
@@ -95,4 +77,71 @@ def generate_composite_copasi_process_instance(instance_name: str, config: Dict,
     return instance
 
 
+def generate_single_process_instance(
+        instance_name: str,
+        instance_config: dict,
+        inputs_config: dict,
+        outputs_config: dict,
+        instance_type: str = 'step',
+        instance_address: str = 'local:copasi',
+) -> dict:
+    return {
+        instance_name: {
+            '_type': instance_type,
+            'address': instance_address,
+            'config': instance_config,
+            'inputs': inputs_config,
+            'outputs': outputs_config
+        }
+    }
+
+
+def generate_emitter_schema(
+        emitter_address: str = "local",
+        emitter_type: str = "ram-emitter",
+        **emit_values_schema
+) -> Dict:
+    return {
+        '_type': 'step',
+        'address': 'local:ram-emitter',
+        'config': {
+            'emit': {**emit_values_schema},
+        },
+        'inputs': {  # TODO: make this generalized
+            'floating_species': ['floating_species_store'],
+            'time': ['time_store'],
+        }
+    }
+
+
+def generate_parameter_scan_instance(
+        num_iterations: int,
+        entry_config: Dict,
+        modeler: str,
+        add_emitter: bool = True,
+        *parameters,
+        **io_config
+) -> Dict:
+    """Generate a parameter scan instance configuration for a given process."""
+    instance = {}
+    for n in range(num_iterations):
+        iteration_name = f'{modeler}_{n}'
+        iteration_instance = generate_single_process_instance(
+            instance_name=iteration_name,
+            instance_config=entry_config,
+            inputs_config=io_config['inputs'],
+            outputs_config=io_config['outputs'])
+
+        for instance_name, instance_schema in iteration_instance:
+            instance[instance_name] = iteration_instance
+
+    if add_emitter:
+        instance['emitter'] = generate_emitter_schema(
+            floating_species='tree[float]',
+            time='float')
+
+    return instance
+
 
+def perturb_parameter(param: str, degree: float):
+    pass