Feature request: support for tfun (inline tabulated functions) #65
Description
Feature request: support for tfun (inline tabulated functions)
Summary
PyBioNetGen 0.8.6 bundles a version of BNG2.pl that does not recognize tfun syntax in begin functions blocks. The BioNetGen Perl engine in the development repo already supports tfun (inline tabulated data functions), but this support has not yet made it into the BNG distribution bundled with PyBioNetGen.
Reproducer
begin model
begin parameters
end parameters
begin molecule types
X()
end molecule types
begin seed species
X() 0
end seed species
begin observables
Molecules Xtot X()
end observables
begin functions
f() = tfun([0, 1, 2, 3], [0, 10, 20, 30], time)
end functions
begin reaction rules
0 -> X() f()
end reaction rules
end model
generate_network({overwrite=>1})
simulate({method=>"ode", t_end=>3, n_steps=>30})
Running with bionetgen run:
ABORT: Expecting operator argument in tfun([0, 1, 2, 3], [0, 10, 20, 30], time)
at [0, 1, 2, 3], [0, 10, 20, 30], time)
Running the same file with perl /path/to/bionetgen/bng2/BNG2.pl from the development repo succeeds (reads 1 function, simulates correctly).
Environment
- PyBioNetGen: 0.8.6 (pip)
- Bundled BNG: 2.9.3 (
site-packages/bionetgen/bng-mac/) - Platform: macOS (Darwin 24.6.0)
Context
tfun enables inline tabulated data functions with linear or step interpolation, indexed by time, a parameter, or an observable:
f() = tfun([x0, x1, ...], [y0, y1, ...], index_var)
f() = tfun([x0, x1, ...], [y0, y1, ...], index_var, method=>"step")
This is useful for embedding experimental data directly in BNGL model files for comparison with simulation output (e.g., in parameter_scan actions).
The development BNG repo includes tfun parsing and evaluation in both BNG2.pl and run_network. The Validate directory contains several test_tfun_*.bngl files exercising the feature. Updating the BNG distribution bundled with PyBioNetGen to include these changes would resolve the issue.
Workaround
Setting BNGPATH to a local clone of the development repo before invoking bionetgen run:
export BNGPATH=/path/to/bionetgen/bng2
bionetgen run -i model.bngl -o outdir