Warn if IPM contains unused compartments or requirements.

epymorph/compartment_model.py

@@ -23,6 +23,7 @@
     TypeVar,
     final,
 )
+from warnings import warn
 
 import numpy as np
 from numpy.typing import NDArray
@@ -477,6 +478,17 @@ def validate_compartment_model(model: BaseCompartmentModel) -> None:
         )
         raise IpmValidationException(err)
 
+    # declared compartments minus used compartments is ideally empty,
+    # otherwise raise a warning
+    extra_comps = set(model.symbols.all_compartments).difference(trx_comps)
+    if len(extra_comps) > 0:
+        msg = (
+            f"Possible issue in {name}: "
+            "not all declared compartments are being used in transitions.\n"
+            f"Extra compartments: {', '.join(map(str, extra_comps))}"
+        )
+        warn(msg)
+
     # transition requirements minus declared requirements should be empty
     missing_reqs = trx_reqs.difference(model.symbols.all_requirements)
     if len(missing_reqs) > 0:
@@ -487,6 +499,17 @@ def validate_compartment_model(model: BaseCompartmentModel) -> None:
         )
         raise IpmValidationException(err)
 
+    # declared requirements minus used requirements is ideally empty,
+    # otherwise raise a warning
+    extra_reqs = set(model.symbols.all_requirements).difference(trx_reqs)
+    if len(extra_reqs) > 0:
+        msg = (
+            f"Possible issue in {name}: "
+            "not all declared requirements are being used in transitions.\n"
+            f"Extra requirements: {', '.join(map(str, extra_reqs))}"
+        )
+        warn(msg)
+
 
 ####################################
 # Single-strata Compartment Models #

epymorph/test/compartment_model_test.py

@@ -1,4 +1,3 @@
-# pylint: disable=missing-docstring,unused-variable
 import unittest
 from typing import Sequence
 
@@ -214,6 +213,58 @@ def edges(self, symbols):
 
         self.assertIn("invalid compartments", str(e.exception).lower())
 
+    def test_create_07(self):
+        # Test for warning: unused requirements.
+        with self.assertWarns(Warning) as w:
+
+            class MyIpm(CompartmentModel):
+                compartments = [
+                    compartment("S", tags=["test_tag"]),
+                    compartment("I"),
+                    compartment("R"),
+                ]
+                requirements = [
+                    AttributeDef("beta", float, Shapes.N),
+                    AttributeDef("gamma", float, Shapes.N),
+                    AttributeDef("extraneous", float, Shapes.N),
+                ]
+
+                def edges(self, symbols):
+                    S, I, R = symbols.all_compartments
+                    beta, gamma, extraneous = symbols.all_requirements
+                    return [
+                        edge(S, I, rate=beta * S * I),
+                        edge(I, R, rate=gamma * I),
+                    ]
+
+        self.assertIn("extra requirements: extraneous", str(w.warning).lower())
+
+    def test_create_08(self):
+        # Test for warning: unused compartments.
+        with self.assertWarns(Warning) as w:
+
+            class MyIpm(CompartmentModel):
+                compartments = [
+                    compartment("S", tags=["test_tag"]),
+                    compartment("I"),
+                    compartment("R"),
+                    compartment("Q"),
+                ]
+                requirements = [
+                    AttributeDef("beta", float, Shapes.N),
+                    AttributeDef("gamma", float, Shapes.N),
+                ]
+
+                def edges(self, symbols):
+                    S, I, R, Q = symbols.all_compartments
+                    beta, gamma = symbols.all_requirements
+                    return [
+                        edge(S, I, rate=beta * S * I),
+                        edge(I, R, rate=gamma * I),
+                    ]
+
+        self.assertIn("extra compartments: q", str(w.warning).lower())
+
     def test_compartment_name(self):
         # Test for compartment names that include spaces.
         with self.assertRaises(ValueError):