Add no-ode models

.github/workflows/sbml_test_suite.yml

@@ -20,18 +20,18 @@ jobs:
 
     strategy:
       fail-fast: false
-      # matrix is split by number of passing test cases (~230 per batch)
+      # matrix is split by number of passing test cases (269 per batch)
       matrix:
         include:
           - first_case: "1"
-            last_case: "245"
-          - first_case: "246"
-            last_case: "578"
-          - first_case: "579"
-            last_case: "890"
-          - first_case: "891"
-            last_case: "1267"
-          - first_case: "1268"
+            last_case: "276"
+          - first_case: "277"
+            last_case: "678"
+          - first_case: "679"
+            last_case: "1030"
+          - first_case: "1031"
+            last_case: "1364"
+          - first_case: "1365"
             last_case: "1821"
 
     steps:

chaste_sbml/SbmlRefModels/CMakeLists.txt

@@ -1,2 +1,10 @@
 find_package(Chaste COMPONENTS cell_based)
 chaste_do_project(SbmlRefModels)
+
+# Precompile the heavy header every generated case model includes, to speed up rebuilds. The
+# serialization export wrappers are deliberately excluded (they are order-sensitive and belong in
+# each .cpp, not a shared PCH).
+if (TARGET chaste_project_SbmlRefModels)
+    target_precompile_headers(chaste_project_SbmlRefModels PRIVATE
+        "${CMAKE_CURRENT_SOURCE_DIR}/src/AbstractSbmlOdeSystem.hpp")
+endif()

chaste_sbml/SbmlRefModels/generate_cases.py

@@ -9,7 +9,7 @@
 from typing import TYPE_CHECKING
 
 from chaste_sbml import ChasteSbmlModel
-from chaste_sbml._config import ROOT_DIR, ModelType
+from chaste_sbml._config import ModelType
 from chaste_sbml._names import generate_header_guard
 
 if TYPE_CHECKING:
@@ -20,6 +20,24 @@
 sbml_versions = ["l2v5", "l3v2", "l3v1"]
 
 
+def _cpp_double_literal(value: str) -> str:
+    """Render a reference-CSV cell as a C++ double literal.
+
+    Reference results can be non-finite -- a division by zero gives INF and 0/0 gives NaN -- and
+    the SBML Test Suite writes these as ``INF``/``-INF``/``NaN``, which are not valid C++ tokens.
+    Map them to the ``<cmath>`` macros so the expected-results initialiser list compiles; finite
+    numbers are already valid literals and pass through unchanged.
+    """
+    token = value.strip()
+    magnitude = token.lstrip("+-").lower()
+    sign = "-" if token.startswith("-") else ""
+    if magnitude == "inf":
+        return f"{sign}INFINITY"
+    if magnitude == "nan":
+        return "NAN"
+    return token
+
+
 class TestType(Enum):
     """Enumeration of test types for code generation."""
 
@@ -50,7 +68,9 @@ def __init__(self, sbml_file: str, sbml_version: str, test_params: dict[str, "An
         self._test_hpp_filename = f"Test{self._model_name}.hpp"
 
         test_result_columns = ", ".join(f'"{col}"' for col in test_params["results"][0])
-        test_result_data = ["{ " + ", ".join(row) + " }" for row in test_params["results"][1:]]
+        test_result_data = [
+            "{ " + ", ".join(_cpp_double_literal(cell) for cell in row) + " }" for row in test_params["results"][1:]
+        ]
         test_result_data = ",\n".join(test_result_data)
 
         test_amounts = test_params["settings"]["amount"].split(",")

chaste_sbml/SbmlRefModels/infra/configure.sh

@@ -19,13 +19,13 @@ fi
 
 if [[ ! -d "${chaste_dir}" ]]; then
 	echo "Error: Chaste source directory not found at '${chaste_dir}'." >&2
-	echo "Set CHASTE_SOURCE_DIR to override the default sibling checkout path." >&2
+	echo "Set CHASTE_SOURCE_DIR to override the default checkout path." >&2
 	exit 1
 fi
 
 mkdir -p "${output_dir}" "${build_dir}"
 export CHASTE_TEST_OUTPUT="${output_dir}"
 
 cd "${build_dir}"
-nice -n 9 cmake "${chaste_dir}"
+nice -n 9 cmake -DChaste_UPDATE_PROVENANCE=OFF "${chaste_dir}"
 

chaste_sbml/SbmlRefModels/src/SbmlMath.hpp

@@ -95,6 +95,9 @@ constexpr bool or_(Args... args);
 // not_
 inline bool not_(bool x) { return !x; }
 
+// implies (a implies b == (not a) or b)
+inline bool implies(double antecedent, double consequent) { return !antecedent || consequent; }
+
 // xor_
 template <typename... Args>
 constexpr bool xor_(Args... args);
@@ -149,17 +152,23 @@ inline double asech(double x) { return std::acosh(1.0 / x); }
 // factorial
 inline double factorial(double x) { return std::tgamma(x + 1.0); }
 
-// max
+// max (the max of a single value is that value)
+constexpr double max(double only) { return only; }
 template <typename... Args>
 constexpr double max(double first, double second, Args... rest);
 
-// min
+// min (the min of a single value is that value)
+constexpr double min(double only) { return only; }
 template <typename... Args>
 constexpr double min(double first, double second, Args... rest);
 
 // piecewise
 constexpr double piecewise(double otherwise);
 
+// A piecewise with no otherwise clause: undefined (NaN) when the condition does not hold. Also the
+// recursion base case for an even number of arguments (pieces without a trailing otherwise).
+constexpr double piecewise(double value, bool condition);
+
 constexpr double piecewise(double value, bool condition, double otherwise);
 
 template <typename... Args>
@@ -206,7 +215,9 @@ constexpr bool sbmlmath::or_(Args... args)
 template <typename... Args>
 constexpr bool sbmlmath::xor_(Args... args)
 {
-    return (false ^ ... ^ args);
+    // Cast each operand to bool first: the arguments are numeric booleans (0/non-0), and ^ is
+    // bitwise (undefined for double), so xor them as bools -- true when an odd number are true.
+    return (false ^ ... ^ static_cast<bool>(args));
 }
 
 // Relational (variadic templates) ==============
@@ -296,6 +307,11 @@ constexpr double sbmlmath::piecewise(double otherwise)
     return otherwise;
 }
 
+constexpr double sbmlmath::piecewise(double value, bool condition)
+{
+    return condition ? value : std::numeric_limits<double>::quiet_NaN();
+}
+
 constexpr double sbmlmath::piecewise(double value, bool condition, double otherwise)
 {
     return condition ? value : otherwise;

chaste_sbml/SbmlRefModels/src/cases/README.md

@@ -1,7 +1,10 @@
 # SBML Test Suite Cases
 
 ## Semantic
-
-## Stochastic
+Case support tracked in test/data/sbml_test_suite_status.csv
 
 ## Syntactic
+Covered by libSBML
+
+## Stochastic
+Not supported