TypeError: Expected list, got numpy.ndarray

[vincent6liu]

Numpy version is 1.18.5. Running phenograph.cluster(pca_df), where pca_df is either a np.ndarray or pd.DataFrame, gives the following error

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-127-8f4599a5b0ca> in <module>
      2 
      3 # Cluster and cluster centrolds
----> 4 communities, graph, Q = phenograph.cluster(pca_df.values)
      5 communities = pd.Series(communities, index=pca_df.index)

~/software/miniconda3/lib/python3.8/site-packages/phenograph/cluster.py in cluster(data, clustering_algo, k, directed, prune, min_cluster_size, jaccard, primary_metric, n_jobs, q_tol, louvain_time_limit, nn_method, partition_type, resolution_parameter, n_iterations, use_weights, seed, **kargs)
    243     else:
    244         del d
--> 245         graph = neighbor_graph(kernel, kernelargs)
    246         print(
    247             "Jaccard graph constructed in {} seconds".format(time.time() - subtic),

~/software/miniconda3/lib/python3.8/site-packages/phenograph/core.py in neighbor_graph(kernel, kernelargs)
     82     :return graph: n-by-n COO sparse matrix
     83     """
---> 84     i, j, s = kernel(**kernelargs)
     85     n, k = kernelargs["idx"].shape
     86     graph = sp.coo_matrix((s, (i, j)), shape=(n, n))

~/software/miniconda3/lib/python3.8/site-packages/phenograph/core.py in parallel_jaccard_kernel(idx)
    152         graph.data[i] = tup[1]
    153 
--> 154     i, j = graph.nonzero()
    155     s = graph.tocoo().data
    156     return i, j, s[s > 0]

~/software/miniconda3/lib/python3.8/site-packages/scipy/sparse/base.py in nonzero(self)
    774 
    775         # convert to COOrdinate format
--> 776         A = self.tocoo()
    777         nz_mask = A.data != 0
    778         return (A.row[nz_mask], A.col[nz_mask])

~/software/miniconda3/lib/python3.8/site-packages/scipy/sparse/base.py in tocoo(self, copy)
    904         the resultant coo_matrix.
    905         """
--> 906         return self.tocsr(copy=False).tocoo(copy=copy)
    907 
    908     def tolil(self, copy=False):

~/software/miniconda3/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)
    479 

_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

[hisplan]

Hi Vincent!

I think your input to phenograph.cluster() is actually fine, but the call to the function graph.nonzero() inside the function neighbor_graph() is causing this issue...

This could be a scipy backward compatibility issue. We will try to fix this issue, but in the meantime please let us know if one of the following works for you.

1. Set n_jobs=1 to suppress parallel processing. Undesirable, but I suspect the error might have something to do with scatter-gather. Trying to see if this is indeed the case.
2. Downgrade scipy to version 1.4.1.

Thanks.

[YubinXie]

Actually downgrading to scipy 1.4.1 works.

[hisplan]

Cool. We will have this fixed as soon as we can. But in the meantime, please use scipy 1.4.1.

[hisplan]

@vincent6liu @YubinXie we have released v1.5.7. It should now work with the latest scipy version. Please give it a try and let me know. Thanks.

[hisplan]

I'm closing this. Please reopen if you still have an issue.