LEMS / LEMS/pylems

Check error when plotting blocking traces in NMDA example

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Dominant language
Python
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12
Forks
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Description

See: https://github.com/NeuroML/NML2_LEMS_Examples/blob/master/Figure5_NMDA.xml#L111

When this commented out code is added back (and population rampPop is readded), model works in jLEMS:

selection_565

but throws error in pylems:

Traceback (most recent call last):
  File "/home/padraig/pylems/pylems", line 13, in <module>
    main()
  File "/home/padraig/pylems/lems/run.py", line 96, in main
    sim = SimulationBuilder(resolved_model).build()
  File "/home/padraig/pylems/lems/sim/build.py", line 63, in build
    runnable = self.build_runnable(component)
  File "/home/padraig/pylems/lems/sim/build.py", line 179, in build_runnable
    self.process_simulation_specs(component, runnable, component.simulation)
  File "/home/padraig/pylems/lems/sim/build.py", line 627, in process_simulation_specs
    target = self.build_runnable(run.component, runnable, cid)
  File "/home/padraig/pylems/lems/sim/build.py", line 182, in build_runnable
    child_runnable = self.build_runnable(child, runnable)
  File "/home/padraig/pylems/lems/sim/build.py", line 199, in build_runnable
    self.build_structure(component, runnable, component.structure)
  File "/home/padraig/pylems/lems/sim/build.py", line 312, in build_structure
    runnable)
  File "/home/padraig/pylems/lems/sim/build.py", line 191, in build_runnable
    runnable.add_child_to_group(children.name, child_runnable)
  File "/home/padraig/pylems/lems/sim/runnable.py", line 186, in add_child_to_group
    self.__dict__[group_name].append(child)
AttributeError: 'Runnable' object has no attribute 'append'

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with Figure5_NMDA.xml at line 111, restore the commented blocking-trace code and rampPop population, then reproduce the failure in pylems. Trace the build path through lems/sim/build.py to lems/sim/runnable.py, especially add_child_to_group. Done means the NMDA example runs in pylems without the Runnable append error.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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