net_to_sbml refuses a derived parameter that uses _pi() or _e(): BNG2.pl writes "k2 _pi()*k1" in the .net, and converting it raises "function call(s) '__bngsim_const_pi__' that net2sbml cannot translate to MathML"

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Since Nov 15, 2026.

  • #1765 by @Montana — open

Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
68/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Active
Tech stack
python, xml
Domain
data

Research direction

Start in python/bngsim/convert/_sbml_writer.py, at _exprtk_to_ast and _normalize_exprtk, and check how the zero-argument _pi() becomes __bngsim_const_pi__ and why _e() is not rewritten. Reproduce with the script in the issue, which needs BNGPATH set. Done when net_to_sbml and net_to_omex convert a derived parameter using _pi() or _e() into <pi/> and <exponentiale/> in MathML, and the constant no longer appears in sedml_lossy.

Written by the indexing model from the issue text.

Description

bug

net_to_sbml, and so net_to_omex, refuse a network whose derived parameter uses BNGL's _pi() or _e(). With k2 _pi()*k1 declared, BNG2.pl 2.9.3 runs the model and writes k2 _pi()*k1 # ConstantExpression in the .net. Converting that network raises:

ConversionError: derived parameter 'k2': expression uses function call(s) '__bngsim_const_pi__' that net2sbml cannot translate to MathML.

_e() fails the same way, naming '_e'. BNG2.pl 2.9.3 rejects bare _pi and _e in a parameter, so the call form is the only way to write them. MathML has the constants <pi/> and <exponentiale/>.

The same constant in an action (setParameter("kr","_pi()*k1")) is left out of the SED-ML's standard elements, with a warning, and is recorded in sedml_lossy.

Found in the review of the branch for #1733. Reproduced on main at f9d245ff.

Repro (needs BNGPATH)

import os, subprocess, tempfile, warnings, zipfile, re
from pathlib import Path
import numpy as np, bngsim
from bngsim.convert import net_to_omex, read_sedml_protocol, read_omex
print("bngsim", bngsim.__file__)

def bng(model_text):
    d = Path(tempfile.mkdtemp()); (d / "m.bngl").write_text(model_text)
    subprocess.run(["perl", os.path.join(os.environ["BNGPATH"], "BNG2.pl"), "m.bngl"], cwd=d, check=True, capture_output=True)
    return d

def network(d):
    """The network as generate_network writes it."""
    bngsim.Model.from_bngl(d / "m.bngl", net_out=d / "gen.net", cache=False)
    return d / "gen.net"

for fn in ("_pi()", "_e()"):
    MODEL = f"""begin model
begin parameters
  k1 1
  k2 {fn}*k1
end parameters
begin seed species
  A() 100
  B() 0
end seed species
begin observables
  Molecules Atot A()
end observables
begin reaction rules
  A() <-> B() k1, k2
end reaction rules
end model
generate_network({{overwrite=>1}})
simulate({{method=>"ode",t_end=>1,n_steps=>1}})
"""
    d = Path(tempfile.mkdtemp()); (d / "m.bngl").write_text(MODEL)
    net = network(d)
    print(fn, "in the .net:", [l.strip() for l in net.read_text().splitlines() if " k2 " in l])
    try:
        net_to_omex(net, d / "m.omex", bngl=d / "m.bngl", gate="none")
        print("  net_to_omex: ok")
    except Exception as e:
        print("  net_to_omex:", type(e).__name__, str(e)[:200])
    try:
        bngsim.convert.net_to_sbml(net, validate=None); print("  net_to_sbml: ok")
    except Exception as e:
        print("  net_to_sbml:", type(e).__name__, str(e)[:120])

Output (main, f9d245ff)

_pi() in the .net: ['2 k2    _pi()*k1  # ConstantExpression', '2 2 1 k2 #_reverse__R1']
  net_to_omex: ConversionError derived parameter 'k2': expression uses function call(s) '__bngsim_const_pi__' that net2sbml cannot translate to MathML.
  net_to_sbml: ConversionError derived parameter 'k2': expression uses function call(s) '__bngsim_const_pi__' that net2sbml cannot translate to MathML.
_e() in the .net: ['2 k2    _e()*k1  # ConstantExpression', '2 2 1 k2 #_reverse__R1']
  net_to_omex: ConversionError derived parameter 'k2': expression uses function call(s) '_e' that net2sbml cannot translate to MathML.
  net_to_sbml: ConversionError derived parameter 'k2': expression uses function call(s) '_e' that net2sbml cannot translate to MathML.

Where to look

_exprtk_to_ast and _normalize_exprtk in python/bngsim/convert/_sbml_writer.py. The zero-argument call _pi() is apparently rewritten to an internal name, __bngsim_const_pi__, that is never turned into <pi/>; _e() is not rewritten at all. _walk_fix_pi handles a bare pi name only.

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