It seems that igraph project changed its name

While I run ‘sc.tl.louvain’, this error raised and told me I should call ‘jgraph’. Is it necessary for me to change the package name of 'igraph’to ‘jgraph’ manually?

---------------------------------------------------------------------------
DeprecationWarning                        Traceback (most recent call last)
<ipython-input-191-71b705e00011> in <module>
----> 1 sc.tl.louvain(ad_2)

/usr/local/lib/python3.6/dist-packages/scanpy/tools/_louvain.py in louvain(adata, resolution, random_state, restrict_to, key_added, adjacency, flavor, directed, use_weights, partition_type, partition_kwargs, copy)
    112             directed = False
    113         if not directed: logg.debug('    using the undirected graph')
--> 114         g = utils.get_igraph_from_adjacency(adjacency, directed=directed)
    115         if use_weights:
    116             weights = np.array(g.es["weight"]).astype(np.float64)

/usr/local/lib/python3.6/dist-packages/scanpy/utils.py in get_igraph_from_adjacency(adjacency, directed)
    379 def get_igraph_from_adjacency(adjacency, directed=None):
    380     """Get igraph graph from adjacency matrix."""
--> 381     import igraph as ig
    382     sources, targets = adjacency.nonzero()
    383     weights = adjacency[sources, targets]

/usr/local/lib/python3.6/dist-packages/igraph/__init__.py in <module>
      6 __license__ = "MIT"
      7 
----> 8 raise DeprecationWarning("To avoid name collision with the igraph project, "
      9                          "this visualization library has been renamed to "
     10                          "'jgraph'. Please upgrade when convenient.")

DeprecationWarning: To avoid name collision with the igraph project, this visualization library has been renamed to 'jgraph'. Please upgrade when convenient.

[LuckyMD]

Hi @YiweiNiu,

Please install python-igraph and not igraph via pip. So run pip install python-igraph and get rid of the igraph package. You may have to update you pip as well.

[flying-sheep]

scanpy could just check on import if one of them is installed instead of the package that should be installed, and raise a nicely phrased ImportError.