openworm / openworm/c302

Deprecated dependencies: Use command line interface to create new network

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Dominant language
Python
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Description

This is for the Readme, in Usage Examples: Section 2) Use command line interface to create new network
Specifically, for this command line example code:

c302 MyNetwork parameters_C -cells ["AVBR","VD3"] -cellstostimulate ["AVBR"] -paramoverride {"unphysiological_offset_current":"2.9pA"} -duration 300

There's a lot of things going on here. I had some issue with owmeta that I dont recall what they were.

The wrapt package that was setup on my system, I guess when I installed this, was too new. I had to downgrade to version 1.11.1.

Now I'm getting this:
ImportError: cannot import name inspect.formatargspec. I guess the code, or one of its dependencies, is trying to use the formatargspec function from the inspect module, which has been deprecated and removed in Python 3.11. I'm reading that the inspect.signature function replaced it.

If I try to correct that code on my system, I think I will get sucked into a rabbit hole because I do not know the design of this software.

Reason I want to use this functionality
I was wanting to do a variation on that command in order to generate the LEMS files, and I guess the NeuroML 2 files, for each neuron for a script that:

  1. Iterates over a range of current clamp values.
  2. Runs a simulation for each value.
  3. Records the neuron's response.
  4. Identifies the minimum active response and the maximum sustainable response.
  5. Saves a record of the test results to have the input current value, the output current value, and the ISI if there is one.

These tests would be ran on one neuron each. Not to simulate the interactions between the neurons.

Is there another way I can generate that LEMS file, such as another program, or the possibility of running that command from the openworm docker image?

I don't know how to run the command from the openworm docker image, if doing that is possible. But I can figure it out if the other stuff I am trying does not work. Right now I am setting up older versions of linux in virtual machines trying to find one that is not too old to prevent me from installing this program in it, while not being too new to run that command.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  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 the README Usage Examples, Section 2, and reproduce the c302 command in a supported environment. Then trace the Python 3.11 inspect.formatargspec error and the reported wrapt and owmeta dependency constraints. Done means documenting a working dependency or Docker-based path for generating the requested LEMS/NeuroML files, or clearly identifying the required compatibility changes.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, documentation
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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