Generalize parsing and add tests

BlueBrain · Dec 3, 2024 · 34824f6 · 34824f6
1 parent 8a2cd24
commit 34824f6
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/src/visitors/cvode_visitor.cpp b/src/visitors/cvode_visitor.cpp
@@ -36,9 +36,12 @@ static void remove_conserve_statements(ast::StatementBlock& node) {
     }
 }
 
-// remove units using state-of-the-art technology
+// remove units from CVODE block so sympy can parse it properly
 static void remove_units(ast::BinaryExpression& node) {
-    std::regex unit_pattern(R"((\d*\.?\d+)\([a-zA-Z]+\))");
+    // matches either an int or a float, followed by any (including zero)
+    // number of spaces, followed by an expression in parentheses, that only
+    // has letters of the alphabet
+    std::regex unit_pattern(R"((\d+\.?\d*|\.\d+)\s*\([a-zA-Z]+\))");
     auto rhs_string = to_nmodl(node.get_rhs());
     auto rhs_string_no_units = fmt::format("{} = {}",
                                            to_nmodl(node.get_lhs()),

diff --git a/test/usecases/cvode/derivative.mod b/test/usecases/cvode/derivative.mod
@@ -2,6 +2,10 @@ NEURON {
     SUFFIX scalar
 }
 
+UNITS {
+    (um) = (micron)
+}
+
 PARAMETER {
     freq = 10
     a = 5
@@ -14,7 +18,7 @@ PARAMETER {
     k = 0.2
 }
 
-STATE {var1 var2 var3}
+STATE {var1 var2 var3 var4}
 
 INITIAL {
     var1 = v1
@@ -34,4 +38,6 @@ DERIVATIVE equation {
     var2' = -var2 * a
     : logistic ODE
     var3' = r * var3 * (1 - var3 / k)
+    : ODE with some units
+    var4' = 1(um) * var4 + a * .1(um) + r * 1.(um) + 1.0    (um)
 }