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Feature request: support for tfun (inline tabulated functions) #65

Closed
#102
Closed
Feature request: support for tfun (inline tabulated functions)#65
#102

Description

@wshlavacek
wshlavacek
opened on Mar 19, 2026

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

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Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
      Skip to content
      Feature request: support for tfun (inline tabulated functions) #65
      Closed
      #102
      Closed
      Feature request: support for tfun (inline tabulated functions)#65
      #102
      Description
      @wshlavacek
      wshlavacek
      opened on Mar 19, 2026
      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
      Metadata
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Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
          Skip to content
          Feature request: support for tfun (inline tabulated functions) #65
          Closed
          #102
          Closed
          Feature request: support for tfun (inline tabulated functions)#65
          #102
          Description
          @wshlavacek
          wshlavacek
          opened on Mar 19, 2026
          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
          Metadata
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
              Skip to content
              Feature request: support for tfun (inline tabulated functions) #65
              Closed
              #102
              Closed
              Feature request: support for tfun (inline tabulated functions)#65
              #102
              Description
              @wshlavacek
              wshlavacek
              opened on Mar 19, 2026
              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
              Metadata
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try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
                  Skip to content
                  Feature request: support for tfun (inline tabulated functions) #65
                  Closed
                  #102
                  Closed
                  Feature request: support for tfun (inline tabulated functions)#65
                  #102
                  Description
                  @wshlavacek
                  wshlavacek
                  opened on Mar 19, 2026
                  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
                  Metadata
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
                      Skip to content
                      Feature request: support for tfun (inline tabulated functions) #65
                      Closed
                      #102
                      Closed
                      Feature request: support for tfun (inline tabulated functions)#65
                      #102
                      Description
                      @wshlavacek
                      wshlavacek
                      opened on Mar 19, 2026
                      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
                      Metadata
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                          No branches or pull requests
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(function(){
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
                          Skip to content
                          Feature request: support for tfun (inline tabulated functions) #65
                          Closed
                          #102
                          Closed
                          Feature request: support for tfun (inline tabulated functions)#65
                          #102
                          Description
                          @wshlavacek
                          wshlavacek
                          opened on Mar 19, 2026
                          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
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Feature request: support for `tfun` (inline tabulated functions) · Issue #65 · RuleWorld/PyBioNetGen · GitHub
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                              Feature request: support for tfun (inline tabulated functions) #65
                              Closed
                              #102
                              Closed
                              Feature request: support for tfun (inline tabulated functions)#65
                              #102
                              Description
                              @wshlavacek
                              wshlavacek
                              opened on Mar 19, 2026
                              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
                              Metadata
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