Import and Export Stock and Flow amrs into and from Mira template models. Refactor askenet -> amr

docs/source/modeling.rst

@@ -4,21 +4,27 @@ Modeling
     :members:
     :show-inheritance:
 
-ASKEM AMR Petri net generation (:py:mod:`mira.modeling.askenet.petrinet`)
+ASKEM AMR Petri net generation (:py:mod:`mira.modeling.amr.petrinet`)
 -------------------------------------------------------------------------
-.. automodule:: mira.modeling.askenet.petrinet
+.. automodule:: mira.modeling.amr.petrinet
     :members:
     :show-inheritance:
 
-ASKEM AMR operations (:py:mod:`mira.modeling.askenet.ops`)
+ASKEM AMR Stockflow generation (:py:mod:`mira.modeling.amr.stockflow`)
+-------------------------------------------------------------------------
+.. automodule:: mira.modeling.amr.stockflow
+    :members:
+    :show-inheritance:
+
+ASKEM AMR operations (:py:mod:`mira.modeling.amr.ops`)
 ----------------------------------------------------------
-.. automodule:: mira.modeling.askenet.ops
+.. automodule:: mira.modeling.amr.ops
     :members:
     :show-inheritance:
 
-ASKEM AMR Regulatory net generation (:py:mod:`mira.modeling.askenet.regnet`)
+ASKEM AMR Regulatory net generation (:py:mod:`mira.modeling.amr.regnet`)
 ----------------------------------------------------------------------------
-.. automodule:: mira.modeling.askenet.regnet
+.. automodule:: mira.modeling.amr.regnet
     :members:
     :show-inheritance:
 
@@ -34,12 +40,19 @@ ODE model generation and simulation (:py:mod:`mira.modeling.ode`)
     :members:
     :show-inheritance:
 
-ACSets Petri net model generation (:py:mod:`mira.modeling.petri`)
+ACSets Petri net model generation (:py:mod:`mira.modeling.acsets.petri`)
 -----------------------------------------------------------------
-.. automodule:: mira.modeling.petri
+.. automodule:: mira.modeling.acsets.petri
     :members:
     :show-inheritance:
 
+ACSets Stockflow model generation (:py:mod:`mira.modeling.acsets.stockflow`)
+-----------------------------------------------------------------
+.. automodule:: mira.modeling.acsets.stockflow
+    :members:
+    :show-inheritance:
+
+
 Bilayer model generation (:py:mod:`mira.modeling.bilayer`)
 ----------------------------------------------------------
 .. automodule:: mira.modeling.bilayer

docs/source/sources.rst

@@ -4,27 +4,34 @@ Sources of model content
     :members:
     :show-inheritance:
 
-ASKEM AMR (:py:mod:`mira.sources.askenet`)
+ASKEM AMR (:py:mod:`mira.sources.amr`)
 ------------------------------------------
-.. automodule:: mira.sources.askenet
+.. automodule:: mira.sources.amr
     :members:
     :show-inheritance:
 
-ASKEM AMR Petri nets (:py:mod:`mira.sources.askenet.petrinet`)
+ASKEM AMR Petri nets (:py:mod:`mira.sources.amr.petrinet`)
 --------------------------------------------------------------
-.. automodule:: mira.sources.askenet.petrinet
+.. automodule:: mira.sources.amr.petrinet
     :members:
     :show-inheritance:
 
-ASKEM AMR Regulatory nets (:py:mod:`mira.sources.askenet.regnet`)
+ASKEM AMR Stockflow (:py:mod:`mira.sources.amr.stockflow`)
+--------------------------------------------------------------
+.. automodule:: mira.sources.amr.stockflow
+    :members:
+    :show-inheritance:
+
+
+ASKEM AMR Regulatory nets (:py:mod:`mira.sources.amr.regnet`)
 -----------------------------------------------------------------
-.. automodule:: mira.sources.askenet.regnet
+.. automodule:: mira.sources.amr.regnet
     :members:
     :show-inherita
 
-Reconstruct ODE semantics (:py:mod:`mira.sources.askenet.flux_span`)
+Reconstruct ODE semantics (:py:mod:`mira.sources.amr.flux_span`)
 --------------------------------------------------------------------
-.. automodule:: mira.sources.askenet.flux_span
+.. automodule:: mira.sources.amr.flux_span
     :members:
     :show-inheritance:
 
@@ -46,8 +53,14 @@ Bilayer extraction (:py:mod:`mira.sources.bilayer`)
     :members:
     :show-inheritance:
 
-ACSets Petri Net extraction (:py:mod:`mira.sources.petri`)
+ACSets Petri Net extraction (:py:mod:`mira.sources.acsets.petri`)
+----------------------------------------------------------
+.. automodule:: mira.sources.acsets.petri
+    :members:
+    :show-inheritance:
+
+ACSets Stockflow extraction (:py:mod:`mira.sources.acsets.stockflow`)
 ----------------------------------------------------------
-.. automodule:: mira.sources.petri
+.. automodule:: mira.sources.acsets.stockflow
     :members:
     :show-inheritance:

mira/dkg/model.py

@@ -29,13 +29,13 @@
     counts_to_dimensionless
 )
 from mira.modeling import Model
-from mira.modeling.askenet.petrinet import AskeNetPetriNetModel, ModelSpecification
+from mira.modeling.amr.petrinet import AMRPetriNetModel, ModelSpecification
 from mira.modeling.bilayer import BilayerModel
 from mira.modeling.acsets.petri import PetriNetModel, PetriNetResponse
 from mira.modeling.viz import GraphicalModel
-from mira.sources.askenet.flux_span import reproduce_ode_semantics, \
+from mira.sources.amr.flux_span import reproduce_ode_semantics, \
     test_file_path, docker_test_file_path
-from mira.sources.askenet.petrinet import template_model_from_askenet_json
+from mira.sources.amr.petrinet import template_model_from_amr_json
 from mira.sources.bilayer import template_model_from_bilayer
 from mira.sources.biomodels import get_sbml_model
 from mira.sources.acsets.petri import template_model_from_petri_json
@@ -89,8 +89,8 @@
 
 #: PetriNetModel json example
 petrinet_json = PetriNetModel(Model(sir)).to_pydantic()
-askenet_petrinet_json = AskeNetPetriNetModel(Model(sir)).to_pydantic()
-askenet_petrinet_json_units_values = AskeNetPetriNetModel(
+amr_petrinet_json = AMRPetriNetModel(Model(sir)).to_pydantic()
+amr_petrinet_json_units_values = AMRPetriNetModel(
     Model(sir_parameterized_init)
 ).to_pydantic()
 
@@ -148,12 +148,12 @@ def petri_to_model(petri_json: Dict[str, Any] = Body(..., example=petrinet_json)
         consumed by other project members that implement this standard.
     """.rstrip()),
 )
-def model_to_askenet(template_model: Dict[str, Any] = Body(..., example=template_model_example)):
-    """Create an AskeNet Petri model from a TemplateModel."""
+def model_to_amr(template_model: Dict[str, Any] = Body(..., example=template_model_example)):
+    """Create an AMR Petri model from a TemplateModel."""
     tm = TemplateModel.from_json(template_model)
     model = Model(tm)
-    askenet_petrinet_model = AskeNetPetriNetModel(model)
-    return askenet_petrinet_model.to_pydantic()
+    amr_petrinet_model = AMRPetriNetModel(model)
+    return amr_petrinet_model.to_pydantic()
 
 
 @model_blueprint.post(
@@ -167,9 +167,9 @@ def model_to_askenet(template_model: Dict[str, Any] = Body(..., example=template
         with the MIRA ecosystem to do model extension, stratification, and comparison. 
     """.rstrip()),
 )
-def askenet_to_model(askenet_json: Dict[str, Any] = Body(..., example=askenet_petrinet_json)):
-    """Create a TemplateModel from an AskeNet model."""
-    return template_model_from_askenet_json(askenet_json)
+def amr_to_model(amr_json: Dict[str, Any] = Body(..., example=amr_petrinet_json)):
+    """Create a TemplateModel from an AMR model."""
+    return template_model_from_amr_json(amr_json)
 
 
 # Model stratification
@@ -330,7 +330,7 @@ def dimension_transform(
         query: Dict[str, Any] = Body(
             ...,
             example={
-                "model": askenet_petrinet_json_units_values,
+                "model": amr_petrinet_json_units_values,
                 "counts_units": "persons",
                 "norm_factor": 1e5,
             },
@@ -339,13 +339,13 @@ def dimension_transform(
     """Convert all entity concentrations to dimensionless units"""
     # convert to template model
     amr_json = query.pop("model")
-    tm = template_model_from_askenet_json(amr_json)
+    tm = template_model_from_amr_json(amr_json)
 
     # Create a dimensionless model
     dimless_model = counts_to_dimensionless(tm=tm, **query)
 
-    # Transform back to askenet model
-    return AskeNetPetriNetModel(Model(dimless_model)).to_pydantic()
+    # Transform back to amr model
+    return AMRPetriNetModel(Model(dimless_model)).to_pydantic()
 
 
 @model_blueprint.get(
@@ -668,15 +668,15 @@ def model_comparison(
 class AMRComparisonQuery(BaseModel):
     petrinet_models: List[Dict[str, Any]] = Field(
         ..., example=[  # fixme: create more examples
-            askenet_petrinet_json,
+            amr_petrinet_json,
         ]
     )
 
 
 @model_blueprint.post("/askenet_model_comparison",
                       response_model=ModelComparisonResponse,
                       tags=["modeling"],
-                      description="This endpoint consumes a list of askenet "
+                      description="This endpoint consumes a list of amr "
                                   "petrinet JSON objects and returns "
                                   "similarity scores and the data comparing "
                                   "the models")
@@ -686,7 +686,7 @@ def askepetrinet_model_comparison(
 ):
     """Compare a list of models to each other"""
     template_models = [
-        template_model_from_askenet_json(m) for m in query.petrinet_models
+        template_model_from_amr_json(m) for m in query.petrinet_models
     ]
     graph_comparison_data = ModelComparisonGraphdata.from_template_models(
         template_models,
@@ -724,5 +724,5 @@ def reproduce_ode_semantics_endpoint(
 ):
     """Reproduce ODE semantics from a stratified model (flux span)."""
     tm = reproduce_ode_semantics(query.model)
-    am = AskeNetPetriNetModel(Model(tm))
+    am = AMRPetriNetModel(Model(tm))
     return am.to_pydantic()

mira/metamodel/units.py

@@ -47,8 +47,8 @@ class Config:
 
     @classmethod
     def from_json(cls, data: Dict[str, Any]) -> "Unit":
-        # Use get_sympy from askenet.petrinet, but avoid circular import
-        from mira.sources.askenet.petrinet import get_sympy
+        # Use get_sympy from amr.petrinet, but avoid circular import
+        from mira.sources.amr.petrinet import get_sympy
         data["expression"] = get_sympy(data, local_dict=UNIT_SYMBOLS)
         assert data.get('expression') is None or not isinstance(
             data['expression'], str

mira/modeling/acsets/stockflow.py

@@ -2,7 +2,7 @@
 from mira.metamodel import *
 
 
-class AskeNetStockFlowModel:
+class ACSetsStockFlowModel:
 
     def __init__(self, model: Model):
         self.properties = {}
@@ -81,4 +81,4 @@ def to_json(self):
 
 
 def template_model_to_stockflow_ascet_json(tm: TemplateModel):
-    return AskeNetStockFlowModel(Model(tm)).to_json()
+    return ACSetsStockFlowModel(Model(tm)).to_json()

mira/modeling/askenet/ops.py → mira/modeling/amr/ops.py

@@ -2,7 +2,7 @@
 import sympy
 from mira.metamodel import SympyExprStr, Unit
 import mira.metamodel.ops as tmops
-from mira.sources.askenet.petrinet import template_model_from_askenet_json
+from mira.sources.amr.petrinet import template_model_from_amr_json
 from .petrinet import template_model_to_petrinet_json
 from mira.metamodel.io import mathml_to_expression
 from mira.metamodel.template_model import Parameter, Distribution, Observable, \
@@ -14,7 +14,7 @@
 
 def amr_to_mira(func):
     def wrapper(amr, *args, **kwargs):
-        tm = template_model_from_askenet_json(amr)
+        tm = template_model_from_amr_json(amr)
         result = func(tm, *args, **kwargs)
         amr = template_model_to_petrinet_json(result)
         return amr
@@ -60,7 +60,7 @@ def replace_transition_id(tm, old_id, new_id):
 
 @amr_to_mira
 def replace_observable_id(tm, old_id, new_id, name=None):
-    """Replace the ID of an observable"""
+    """Replace the ID and display name (optional) of an observable"""
     for obs, observable in copy.deepcopy(tm.observables).items():
         if obs == old_id:
             observable.name = new_id
@@ -82,9 +82,8 @@ def remove_observable(tm, removed_id):
 @amr_to_mira
 def remove_parameter(tm, removed_id, replacement_value=None):
     """
-    If a replacement_value is supplied, substitute every instance of the parameter
-    in all expressions with the given replacement_value. If replacement_value is none,
-    substitute the parameter with 0.
+    Substitute every instance of the parameter with the given replacement_value.
+    If replacement_value is none, substitute the parameter with 0.
     """
     if replacement_value:
         tm.substitute_parameter(removed_id, replacement_value)
@@ -230,7 +229,7 @@ def add_transition(tm, new_transition_id, src_id=None, tgt_id=None,
        Returns
        -------
        :
-            The updated template model
+            The updated template model object
         """
     if src_id is None and tgt_id is None:
         ValueError("You must pass in at least one of source and target id")
@@ -264,7 +263,7 @@ def replace_rate_law_sympy(tm, transition_id, new_rate_law: sympy.Expr):
 # This function isn't wrapped because it calls a wrapped function and just
 # passes the AMR through
 def replace_rate_law_mathml(amr, transition_id, new_rate_law):
-    """Replace the rate law of a transition. THe new rate law passed in will be a MathML str object"""
+    """Replace the rate law of a transition. The new rate law passed in will be a MathML str object"""
     new_rate_law_sympy = mathml_to_expression(new_rate_law)
     return replace_rate_law_sympy(amr, transition_id, new_rate_law_sympy)
 
@@ -282,7 +281,7 @@ def replace_observable_expression_sympy(tm, obs_id,
 @amr_to_mira
 def replace_initial_expression_sympy(tm, initial_id,
                                      new_expression_sympy: sympy.Expr):
-    """Replace the expression of an initial. THe new rate law passed in will be a sympy.Expr object"""
+    """Replace the expression of an initial. The new rate law passed in will be a sympy.Expr object"""
     for init, initial in tm.initials.items():
         if init == initial_id:
             initial.expression = SympyExprStr(new_expression_sympy)
@@ -301,7 +300,7 @@ def replace_observable_expression_mathml(amr, obs_id, new_expression_mathml):
 # This function isn't wrapped because it calls a wrapped function and just
 # passes the AMR through
 def replace_initial_expression_mathml(amr, initial_id, new_expression_mathml):
-    """Replace the expression of an initial. THe new rate law passed in will be a MathML str object"""
+    """Replace the expression of an initial. The new rate law passed in will be a MathML str object"""
     new_expression_sympy = mathml_to_expression(new_expression_mathml)
     return replace_initial_expression_sympy(amr, initial_id,
                                             new_expression_sympy)

mira/modeling/askenet/petrinet.py → mira/modeling/amr/petrinet.py

@@ -2,7 +2,7 @@
 at https://github.com/DARPA-ASKEM/Model-Representations/tree/main/petrinet.
 """
 
-__all__ = ["AskeNetPetriNetModel", "ModelSpecification",
+__all__ = ["AMRPetriNetModel", "ModelSpecification",
            "template_model_to_petrinet_json"]
 
 import json
@@ -26,7 +26,7 @@
               'petrinet_schema.json') % SCHEMA_VERSION
 
 
-class AskeNetPetriNetModel:
+class AMRPetriNetModel:
     """A class representing a PetriNet model."""
 
     def __init__(self, model: Model):
@@ -291,7 +291,7 @@ def template_model_to_petrinet_json(tm: TemplateModel):
     -------
     A JSON dict representing the PetriNet model.
     """
-    return AskeNetPetriNetModel(Model(tm)).to_json()
+    return AMRPetriNetModel(Model(tm)).to_json()
 
 
 class Initial(BaseModel):

mira/modeling/askenet/regnet.py → mira/modeling/amr/regnet.py

@@ -2,7 +2,7 @@
 at https://github.com/DARPA-ASKEM/Model-Representations/tree/main/petrinet.
 """
 
-__all__ = ["AskeNetRegNetModel", "ModelSpecification"]
+__all__ = ["AMRRegNetModel", "ModelSpecification"]
 
 
 import json
@@ -26,7 +26,7 @@
               'regnet_schema.json') % SCHEMA_VERSION
 
 
-class AskeNetRegNetModel:
+class AMRRegNetModel:
     """A class representing a PetriNet model."""
 
     def __init__(self, model: Model):