'tuple' object has no attribute 'tocsr'

‘tuple’ object has no attribute ‘tocsr’

...
# neighborhood graph of cells (determine optimal number of PCs here)
sc.pp.neighbors(adata, n_neighbors=15, n_pcs=30)
# compute UMAP
sc.tl.umap(adata)
# tSNE
tsne = TSNE( n_jobs=20 )
adata.obsm['X_tsne'] = tsne.fit_transform( adata.X )
adata.write( f_anndata_path )

computing neighbors
    using 'X_pca' with n_pcs = 30
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-38-e2dd1fe70ab9> in <module>
      6 sc.settings.n_jobs = 15
      7 with parallel_backend('threading', n_jobs=20):
----> 8     sc.pp.neighbors(adata, n_neighbors=15, n_pcs=30)
      9 
     10 #sc.settings.n_jobs = 15

~/miniconda3/envs/scanpy/lib/python3.6/site-packages/scanpy/neighbors/__init__.py in neighbors(adata, n_neighbors, n_pcs, use_rep, knn, random_state, method, metric, metric_kwds, copy)
     93         n_neighbors=n_neighbors, knn=knn, n_pcs=n_pcs, use_rep=use_rep,
     94         method=method, metric=metric, metric_kwds=metric_kwds,
---> 95         random_state=random_state,
     96     )
     97     adata.uns['neighbors'] = {}

~/miniconda3/envs/scanpy/lib/python3.6/site-packages/scanpy/neighbors/__init__.py in compute_neighbors(self, n_neighbors, knn, n_pcs, use_rep, method, random_state, write_knn_indices, metric, metric_kwds)
    681                 knn_distances,
    682                 self._adata.shape[0],
--> 683                 self.n_neighbors,
    684             )
    685         # overwrite the umap connectivities if method is 'gauss'

~/miniconda3/envs/scanpy/lib/python3.6/site-packages/scanpy/neighbors/__init__.py in compute_connectivities_umap(knn_indices, knn_dists, n_obs, n_neighbors, set_op_mix_ratio, local_connectivity)
    322     distances = get_sparse_matrix_from_indices_distances_umap(knn_indices, knn_dists, n_obs, n_neighbors)
    323 
--> 324     return distances, connectivities.tocsr()
    325 
    326 

AttributeError: 'tuple' object has no attribute 'tocsr'

Versions:

scanpy==1.4.4.post1 anndata==0.6.22.post1 umap==0.4.0 numpy==1.18.1 scipy==1.4.1 pandas==1.0.3 scikit-learn==0.22.2.post1 statsmodels==0.11.1 python-igraph==0.8.0 louvain==0.6.1

… Could you please help me resolve it? I looked up older issues but could not find solution to this. Thank you very much

[Flope]

I am getting this error when I run scanpy.pp.neighbors(adata) As far as I know, I have the latest packages mentioned here. anndata 0.7.6 pypi_0 pypi louvain 0.7.0 py38h9dedd22_1 conda-forge pandas 1.1.3 py38hb1e8313_0 python-igraph 0.9.1 py38h3dab7cd_0 conda-forge scanpy 1.7.2 pypi_0 pypi scikit-learn 0.23.2 py38h959d312_0 scipy 1.6.3 py38h431c0a8_0 conda-forge statsmodels 0.12.0 py38haf1e3a3_0 umap-learn 0.5.1 py38h50d1736_0 conda-forge

Is there probably another package that is outdated?

EDIT: Not sure what module I updated but now it works. I use ‘conda update --all’ and others to do that.

thanks

[Ahmed-fub]

I face the same problem. However I used latest version </scanpy==1.4.6 anndata==0.7.4 umap==0.5.1 numpy==1.20.3 scipy==1.6.3 pandas==1.2.4 scikit-learn==0.22.2.post1 statsmodels==0.11.1 python-igraph==0.8.2 , bbknn : 1.5.0