I asked copilot for a suggestion and it wrote the following code. I couldn't pinpoint the exact place in my VCML file that is causing this error, but the traceback is below:
File "/Users/smgroves/Documents/GitHub/VCell_Analysis/run_pyvcell/1_run_CPC_model.py", line 28, in <module>
result = vc.simulate(biomodel=bio_model, simulation=sim.name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smgroves/Documents/anaconda3/envs/pyvcell_env/lib/python3.11/site-packages/pyvcell/vcml/vcml_simulation.py", line 48, in simulate
return Result(solver_output_dir=out_dir, sim_id=sim_id, job_id=job_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/smgroves/Documents/anaconda3/envs/pyvcell_env/lib/python3.11/site-packages/pyvcell/sim_results/result.py", line 61, in __init__
write_zarr(
File "/Users/smgroves/Documents/anaconda3/envs/pyvcell_env/lib/python3.11/site-packages/pyvcell/_internal/simdata/zarr_writer.py", line 137, in write_zarr
function_name = f.name.split("::")[1]
~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
This seems to be another problem with converting VCML language to python expressions.
pyvcell__internal_simdata_zarr_writer.py