[Montana]

Fixes #1415.

What was wrong

ExprTk multiplies a variable, and a bracketed group, against a bracket after it: A(B) and (A)(B) are A·B. After a function call it does not. The bracket opens a second statement, and the expression's value is the last statement's. So the call, and everything before it, was dropped with no word.

A .net with A = 3, B = 5, f() read through the right-hand side, on main:

expression	main	the product
k*exp(-A)(B) (k = 0.5)	5	0.124
sin(A)(B)	5	0.706
2*abs(A)(B) + 1	6	31
time()(B), rint(A)(B), if(A>1,1,0)(B), sin(A)[B], sin(A) (B), sin (A)(B), tfun(...)(B)	5
k*(1 + exp(-A)(B))	refused with ExprTk's bare ERR244 - Expected ')'

BNG2.pl rejects the same text (ABORT: Syntax error at (Bobs)), so a network BioNetGen writes never holds one.

The change

ExprTkEvaluator::compile refuses an expression where a call's closing ) is followed by (, [ or {, and names the call:

Expression 'kexp(-A)(B)': the bracket after the call 'exp(-A)' is not multiplied by it. ExprTk reads it as a second statement, and the expression's value would be that statement's alone, which drops the call and everything before it (issue #1415). BioNetGen rejects it as a syntax error. Write the product with '': 'exp(-A)*(...)'.

• What counts as a call: a name that no variable or constant is registered under, then its argument list. That covers a built-in, a model function, a table, time(), and if/not.
• ExprTk's binary word operators (and, or, xor, nand, nor, xnor, mand, mor, in, like, ilike) are not calls: (A > 1) and (B)(C) is (A > 1) and B·C, as codegen: write C for what ExprTk means, or decline before compiling (#1212) #1348's product table has it.
• Numbers are skipped whole, exponent included: 1e1(B) is a number times a group.
• Every compile path is covered: loader-built expressions and set_function_eval_expression both go through compile.
• Codegen: already declines these since codegen: write C for what ExprTk means, or decline before compiling (#1212) #1348, so the two now agree at load.

The issue offered refusing or reading the product. I chose to refuse because BioNetGen does, and because a text that silently dropped half its value is better fixed by its author than guessed at.

The diff (src/expression.cpp, abridged)

@@ class ExprTkEvaluator::Impl
+    // Issue #1415: the first call in `expr` that a bracket follows, as the
+    // call's text, or "" where there is none. [...]
+    std::string call_before_bracket(const std::string &expr) const {
+        [...]  // numbers are skipped whole, exponent included: `1e1(B)` is a product
+            const std::string name = expr.substr(start, i - start);
+            [...]  // spaces skipped: `sin (A)` is a call
+            static const std::unordered_set<std::string> kBinaryWords = {
+                "and", "or", "xor", "nand", "nor", "xnor", "mand", "mor", "in", "like", "ilike"};
+            if (open >= n || expr[open] != '(' || symbol_table.is_variable(name) ||
+                symbol_table.is_constant_node(name) || kBinaryWords.count(name) != 0) {
+                continue;  // a product, as ExprTk reads it: `A(B)`, `k(B)`, `(x) and (B)(C)`
+            }
+            [...]  // `close` is the call's matching ')'; spaces skipped after it
+            if (next < n && (expr[next] == '(' || expr[next] == '[' || expr[next] == '{')) {
+                return expr.substr(start, close + 1 - start);
+            }
+        }
+        return "";
+    }
@@ int ExprTkEvaluator::compile(const std::string &expr) {
     preprocessed = expr_compat::exact_literals(preprocessed);
 
+    // Issue #1415: refused, where ExprTk would keep only the bracket after it.
+    const std::string call = impl_->call_before_bracket(preprocessed);
+    if (!call.empty()) {
+        throw std::runtime_error(
+            "Expression '" + expr + "': the bracket after the call '" + call +
+            "' is not multiplied by it. ExprTk reads it as a second statement, [...] "
+            "(issue #1415). BioNetGen rejects it as a syntax error. Write "
+            "the product with '*': '" + call + "*(...)'.");
+    }
+
     // Delegate to compile_preprocessed (which also caches the string)
     return compile_preprocessed(preprocessed);

Tests

test_codegen_exprtk_functions.py (#1348's) is updated where it asserted the old reading. test_a_bracket_after_a_call_declines now expects the interpreter to refuse (it asserted B), and still checks codegen's own decline on the text. The table case becomes test_a_bracket_after_a_table_is_refused. exp leaves _NO_C, since that law no longer loads.

python/tests/test_bracket_after_a_call.py (25 tests):

• 11 refusals, each naming the call: every row above, plus sin (A)(B), an inline table (the loader writes it as tfun_f__tfun0(), which is named), and the bracketed k*(1 + exp(-A)(B)). All 11 fail on main.
• A function body given after load: refused the same way.
• 14 controls held to their values (they pass on main too), including (A > 1) and (B)(A) = 1: A(B) = 15, (A)(B), A (B), 2(B) = 10, k(B) = 2.5, k*exp(-A)*(B), exp(-A)+(B), sin(A), 1e-1(B), 1e1(B) = 50, A(B)(A) = 45, k(B)(A) = 7.5, 1e1(B)(A) = 150.

Mutation tests (the core rebuilt for each):

mutant	result
never refuse	killed (the refusal tests)
a variable counted as a call	killed (A(B)(A))
an exponent read as a name	killed (1e1(B)(A))
( only, not [	killed (sin(A)[B])
no space skipped before the bracket	killed (sin(A) (B))
no space skipped before the arguments	killed (sin (A)(B))
a word operator counted as a call	killed ((A > 1) and (B)(A))
a constant counted as a call	survives: equivalent today. Nothing registers a constant (define_constant has no caller); parameters are variables. The check stays for the API.

Corpus

1,323 BioModels plus the repository's 177 .net files: 1,500 loads, identical on main and here (1,468 load, and the same 32 fail on both). No model is written this way.

Checks (macOS arm64)

• python/tests: 17,204 passed, 0 failed.
• parity_checks/tests: 1,015 passed. The 2 failures (test_bngsim_provenance and the reference-archive replay) also fail on main here: their subprocess can't import bngsim without my local import shim.

pre-commit run --all-files, sphinx -W, and ci/changelog.py check/required (changelog.d/1415.fixed.md) are clean.