Scanpy: module 'louvain._c_louvain' has no attribute '_set_rng_seed'

[YubinXie]

trying to run louvain clustering but got the error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-22-fe1390cdc24a> in <module>
----> 1 sc.tl.louvain(adata, resolution=1.0)

~/miniconda3/envs/scrna/lib/python3.7/site-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)
    136                 partition_kwargs["weights"] = weights
    137             logg.info('    using the "louvain" package of Traag (2017)')
--> 138             louvain.set_rng_seed(random_state)
    139             part = louvain.find_partition(
    140                 g, partition_type,

~/miniconda3/envs/scrna/lib/python3.7/site-packages/louvain/functions.py in set_rng_seed(seed)
     23 def set_rng_seed(seed):
     24   """ Set seed for internal random number generator. """
---> 25   _c_louvain._set_rng_seed(seed)
     26 
     27 def find_partition(graph, partition_type, initial_membership=None, weights=None, **kwargs):

AttributeError: module 'louvain._c_louvain' has no attribute '_set_rng_seed'

sc.tl.louvain(adata, resolution=1.0)

Python 3.7

Versions:

scanpy==1.4.6 anndata==0.7.1 umap==0.4.2 numpy==1.18.3 scipy==1.4.1 pandas==1.0.3 scikit-learn==0.22.2.post1 statsmodels==0.11.1 python-igraph==0.8.2 louvain==0.6.2

[ivirshup]

This looks like an bug in the most recent release of louvain. Try downgrading?

I would also recommend using leiden clustering instead.

[ivirshup]

Fixed in 7c65221c5a9a4c1ccf924cc0ff4dbd505116c8ec

[dburkhardt]

FYI, it appears that this bug remains in louvain version 0.7

In [1]: import numpy as np
   ...: import scanpy as sc
   ...:
   ...: adata = sc.AnnData(np.random.normal(size=(100,3)))
   ...:
   ...: sc.pp.neighbors(adata)
   ...: sc.tl.louvain(adata)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-1-3505d1878068> in <module>
      5
      6 sc.pp.neighbors(adata)
----> 7 sc.tl.louvain(adata)

~/.local/lib/python3.7/site-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)
    136                 partition_kwargs["weights"] = weights
    137             logg.info('    using the "louvain" package of Traag (2017)')
--> 138             louvain.set_rng_seed(random_state)
    139             part = louvain.find_partition(
    140                 g, partition_type,

AttributeError: module 'louvain' has no attribute 'set_rng_seed'

In [2]: import louvain

In [3]: louvain.__version__
Out[3]: '0.7.0'

[morganee261]

Hello,

I am having the same issue, here is my code and error :

sc.tl.louvain(adata,resolution=0.4)
running Louvain clustering
using the "louvain" package of Traag (2017)
Traceback (most recent call last):
File "", line 1, in
File "/home/Morgane/anaconda3/lib/python3.7/site-packages/scanpy/tools/_louvain.py", line 138, in louvain
louvain.set_rng_seed(random_state)
AttributeError: module 'louvain' has no attribute 'set_rng_seed'

I am using Louvain version 0.7.0

Did you fix this issue in that version?

thanks for your help,
Morgane

[ivirshup]

The API for setting the random seed changed in the recent release (v0.7) of louvain, this is fixed on master, which should see a release soon.

[davemcg]

If anyone is stuck waiting for the new release, you can edit your .../lib/python3.7/site-packages/scanpy/tools/_louvain.py with these changes:

Add: partition_kwargs["seed"] = random_state
Remove: louvain.set_rng_seed(random_state)

From:
https://github.com/theislab/scanpy/pull/1197/commits/b54d67b9d6b41269c1612df0242210d1279ede85

[mhanedCBNU]

If anyone is stuck waiting for the new release, you can edit your .../lib/python3.7/site-packages/scanpy/tools/_louvain.py with these changes:

Add: partition_kwargs["seed"] = random_state
Remove: louvain.set_rng_seed(random_state)

From:
b54d67b

Thankx this worked

[vanhoan310]

Install old louvain package will solve the problem: pip install louvain==0.6.1