Merge pull request #350 from gyorilab/scenarios_202408

Add updated notebooks and exports for 2024.08 scenarios

mira/metamodel/ops.py

@@ -229,6 +229,8 @@ def stratify(
                     # We now apply the stratum assigned to each controller in this particular
                     # tuple to the controller
                     for controller, c_stratum in zip(stratified_controllers, c_strata_tuple):
+                        if controller.name in exclude_concepts:
+                            continue
                         stratified_template.name += f"_{c_stratum}"
                         controller.with_context(do_rename=modify_names, inplace=True,
                                                 **{key: c_stratum})

mira/metamodel/utils.py

@@ -76,4 +76,4 @@ def sanity_check_tm(tm):
             assert symbol.name in all_symbols, f"missing symbol: {symbol.name}"
     all_initial_names = {init.concept.name for init in tm.initials.values()}
     for concept in all_concept_names:
-        assert concept in all_initial_names
+        assert concept in all_initial_names, f"missing initial condition for {concept}"

mira/modeling/amr/petrinet.py

@@ -12,8 +12,8 @@
 
 from pydantic import BaseModel, Field
 
-from mira.metamodel import expression_to_mathml, safe_parse_expr, \
-    TemplateModel
+from mira.metamodel import expression_to_mathml, TemplateModel
+from mira.sources.amr import sanity_check_amr
 
 from .. import Model
 from .utils import add_metadata_annotations
@@ -228,7 +228,7 @@ def to_json(
         : JSON
             A JSON dict representing the Petri net model.
         """
-        return {
+        json_data = {
             'header': {
                 'name': name or self.model_name,
                 'schema': SCHEMA_URL,
@@ -250,6 +250,11 @@ def to_json(
             }},
             'metadata': self.metadata,
         }
+        try:
+            sanity_check_amr(json_data)
+        except Exception as e:
+            logger.warning("Error in AMR sanity check: %s", str(e))
+        return json_data
 
     def to_pydantic(self, name=None, description=None, model_version=None) -> "ModelSpecification":
         """Return a Pydantic model representation of the Petri net model.
@@ -349,6 +354,19 @@ def template_model_to_petrinet_json(tm: TemplateModel):
     return AMRPetriNetModel(Model(tm)).to_json()
 
 
+def template_model_to_petrinet_json_file(tm: TemplateModel, fname):
+    """Convert a template model to a PetriNet JSON file.
+
+    Parameters
+    ----------
+    tm :
+        The template model to convert.
+    fname : str
+        The file name to write to.
+    """
+    AMRPetriNetModel(Model(tm)).to_json_file(fname)
+
+
 class Initial(BaseModel):
     target: str
     expression: str