Re-added asif's test of calculated HH derivatives.

tests/test_model_evaluation.py

@@ -0,0 +1,90 @@
+import os
+
+import networkx
+import pytest
+import sympy
+
+from cellmlmanip import load_model
+
+
+class TestModelEvaluation():
+    """
+    Tests the calculated derivatives of a single model match a known reference.
+    """
+
+    def test_evaluation(self):
+
+        # Load Hodgkin-Huxley model
+        model = load_model(os.path.join(
+            os.path.dirname(__file__),
+            "cellml_files",
+            "hodgkin_huxley_squid_axon_model_1952_modified.cellml"
+        ))
+
+        graph = model.graph_with_sympy_numbers
+
+        # Initial values for the free and state variables
+        initial_values = {
+            'environment$time': 0.0,
+            'membrane$V': -75,
+            'sodium_channel_m_gate$m': 0.05,
+            'sodium_channel_h_gate$h': 0.6,
+            'potassium_channel_n_gate$n': 0.325,
+        }
+
+        # Evaluated derivatives at the initial conditions
+        evaluated_derivatives = {
+            'membrane$V': -6.00768750000000740e-01,
+            'sodium_channel_m_gate$m': 1.23855383553985177e-02,
+            'sodium_channel_h_gate$h': -4.55523906540064583e-04,
+            'potassium_channel_n_gate$n': -1.34157228632045961e-03,
+        }
+
+        # collects all the evaluated lh-sides of the equations
+        evaluated_symbols = dict()
+
+        # saves the evaluated lh-side for the state variables
+        state_derivatives = dict()
+
+        # loop over each of the equations in the model (topologically sorted)
+        sorted_symbols = networkx.lexicographical_topological_sort(graph, key=str)
+        for symbol in sorted_symbols:
+            equation = graph.nodes[symbol]['equation']
+
+            # if this symbol is calculated using an equation
+            if equation is not None:
+
+                # substitute all symbols in the rhs of the equation
+                eq_substituted = equation.rhs.subs(evaluated_symbols)
+
+                # if any symbols remain, we have a problem
+                remaining_symbols = eq_substituted.atoms(sympy.Symbol)
+                if remaining_symbols:
+                    for remaining_symbol in remaining_symbols:
+                        pytest.fail("Unresolved symbol %s in %s" % (remaining_symbol, equation))
+
+                # calculate the result
+                eq_evaluated = eq_substituted.evalf()
+
+                # save the calculation for this symbol (to be used in the next equations)
+                evaluated_symbols[equation.lhs] = eq_evaluated
+
+                # if the symbol on the lhs is a derivative
+                if equation.lhs.is_Derivative:
+                    # save the calculation for testing
+                    state_derivatives[equation.lhs.free_symbols.pop()] = eq_evaluated
+
+            # otherwise the symbol doesn't have an equation
+            # if the symbol has an initial value
+            elif symbol.name in initial_values:
+                # add the symbol's initial value to the substitution dictionary
+                evaluated_symbols[symbol] = sympy.Number(initial_values[symbol.name])
+            else:
+                # something has gone wrong - no equation or initial value
+                pytest.fail("Symbol " + str(symbol) + " does not have equation or initial value.")
+
+        # Check evaluations against expected values
+        for state_symbol, evaluated_deriv in state_derivatives.items():
+            expected = evaluated_derivatives[state_symbol.name]
+            actual = evaluated_deriv
+            assert float(actual) == pytest.approx(expected)