Report on PyNEST examples test run

[jessica-mitchell]

This issue reports on recent check of the PyNEST examples for v3.7_rc1

@heplesser @terhorstd FYI

In this case, NEST was built locally without libneurosim/mpi/music/hdf5.
Running the run_examples.sh script lead to 11 failing examples (5 of which can be excluded due to the missing compiler options).
Also tested some on EBRAINS experimental and just running the examples locally.

1. MUSIC gives this error:

NESTErrors.UnknownModelName: UnknownModelName in SLI function Create_l_i: /music_cont_out_proxy is not a known model name.

2. Sonata errors out on EBRAINS:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[1], line 1
----> 1 base_path = Path(__file__).resolve().parent
      2 sonata_path = base_path / "300_pointneurons"
      3 net_config = sonata_path / "circuit_config.json"

NameError: name 'Path' is not defined

3. Sudoku examples fail because of missing dependency imageio
   When the dependency is added, the examples work when running python3 sudoku/plot_progress.py but in the shell script the examples give another error:

File "/home/mitchell/Work/envs/lib/python3.12/site-packages/numpy/core/shape_base.py", line 449, in stack
    raise ValueError('all input arrays must have the same shape')
ValueError: all input arrays must have the same shape

Works on EBRAINS

5.. Pong example takes too long (had to be interrupted) suggest reducing the number of runs so it can show some output in a reasonable time frame

6. Microcircuit example fails in run_examples.sh with

 Traceback (most recent call last):
 File "/home/mitchell/Work/repo/release_candidates/nest-simulator/pynest/examples/Potjans_2014/run_microcircuit.py", line 60, in  <module>
  net.connect()
 File "/home/mitchell/Work/repo/release_candidates/nest-simulator/pynest/examples/Potjans_2014/network.py", line 126, in connect
  nest.Prepare()
  File "/home/mitchell/Work/envs/lib/python3.12/site-packages/nest/ll_api.py", line 216, in stack_checker_func
  return f(*args, **kwargs)
          ^^^^^^^^^^^^^^^^^^
 File "/home/mitchell/Work/envs/lib/python3.12/site-packages/nest/lib/hl_api_simulation.py", line 122, in Prepare
   sr("Prepare")
  File "/home/mitchell/Work/envs/lib/python3.12/site-packages/nest/ll_api.py", line 103, in catching_sli_run
 raise exceptionCls(commandname, message)
 nest.lib.hl_api_exceptions.NESTErrors.IOError: IOError in SLI function Prepare:  

BUT it works when running python3 run_microcircuit.py. Tried it also on EBRAINS but it got stuck during the simulation - unclear to what the issue is (memory does not seem to be full).

7. hpc_benchmark (py and sli) gets killed (also on EBRAINS) seemingly during the connect calls

Apr 03 15:04:20 build_network [Info]: 
    Connecting inhibitory -> excitatory population.
Killed

8. CSA fails but I think it's due to missing libraries, also fails on EBRAINS
   Unknown Python type: <class 'csa.connset.ConnectionSet'