PhenoGraph multi-processing error

[team-tomato-salad]

Hi,

I was trying to use Palantir.presults.cluster_gene_trends funtion and run into a Type Error showing- "expected list, got np.ndarray". The function worked perfectly before the scanpy update, and I also updated Palantir package. I also followed the latest Palantir tutorial notebook.

/usr/lib/python3.8/site-packages/scipy/sparse/lil.py in tocsr(self, copy)
475 indices = np.empty(nnz, dtype=idx_dtype)
476 data = np.empty(nnz, dtype=self.dtype)
--> 477 _csparsetools.lil_flatten_to_array(self.rows, indices)
478 _csparsetools.lil_flatten_to_array(self.data, data)

_csparsetools.pyx in scipy.sparse._csparsetools.lil_flatten_to_array()

_csparsetools.pyx in scipy.sparse._csparsetools._lil_flatten_to_array_int32()

TypeError: Expected list, got numpy.ndarray

The issue was fixed by setting n_job parameter to 1. I am not sure why n_job -1 would cause the issue and would like to know if this issue happens on other systems.

Thank you for your time!

[ManuSetty]

Thanks for bringing this to our attention. This looks like an issues with scipy and more details are here: dpeerlab/PhenoGraph#4.

[hisplan]

@team-tomato-salad we have just released PhenoGraph v1.5.7. Please try again with this version.

[hisplan]

Please reopen if you have any issue.