NotImplementedError: We have not yet implemented 1D sparse slices; please index using explicit indices, e.g. `x[:, [0]]`

[Feyrbrand]

Hello,

I'm trying to use the create toy data.ipynb to generate a new set of dendritic trees for testing and model fitting, but I get the following error, trying to generate random walks.

# sample RANDOM walks

np.random.seed(17)

n_walks=256
N = len(neurons)
NUM_CORES = 15

for walk_length in [32]:
    rw_list = []
    with multiprocessing.Pool(NUM_CORES) as pool:
        rw_list += pool.map(get_rw_representation, neurons)
    RW_representation = np.array([e[0] for e in rw_list])

    with open('./data/toy_data/5_populations/walk_representation.npy', 'wb') as f:
        np.save(f, walk_representation)

Following Error:

Truncated Traceback (Use C-c C-$ to view full TB):
File /usr/lib/python3.12/multiprocessing/pool.py:774, in ApplyResult.get(self, timeout)
    772     return self._value
    773 else:
--> 774     raise self._value

NotImplementedError: We have not yet implemented 1D sparse slices; please index using explicit indices, e.g. `x[:, [0]]`

I had several issues loading the notebook, regarding libraries, one is the morphopy library, which uses an old version of scipy (through testing ~ 0.14.0) because scipy.signal.gaussian is not used for the newer scipy versions anymore.

Is there an environment or requirements.txt for building a running Python environment to test this notebook?

Thanks for the help!

[Feyrbrand]

I fixed the problem through building an environment with the following requirements and python==3.7:

requirements.txt