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Louvain package is deprecated in favor of leidenalg #1379

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@scottgigante

Description

@scottgigante
  • I have checked that this issue has not already been reported.
  • I have confirmed this bug exists on the latest version of scanpy.
  • (optional) I have confirmed this bug exists on the master branch of scanpy.

import warnings
warnings.simplefilter('always')
import scanpy
/home/scottgigante/.local/lib/python3.6/site-packages/scanpy/tools/_louvain.py:17: DeprecationWarning: This package has been superseded by the `leidenalg` package and will no longer be maintained. Please upgrade to the `leidenalg` package.
  from louvain.VertexPartition import MutableVertexPartition

Versions

-----
anndata     0.7.3
scanpy      1.6.0
sinfo       0.3.1
-----
PIL                 7.2.0
anndata             0.7.3
apport_python_hook  NA
cffi                1.14.1
colorama            0.3.7
cycler              0.10.0
cython_runtime      NA
dateutil            2.8.1
get_version         2.1
h5py                2.10.0
igraph              0.8.2
importlib_metadata  1.6.1
joblib              0.16.0
kiwisolver          1.2.0
legacy_api_wrap     1.2
llvmlite            0.33.0
louvain             0.7.0
matplotlib          3.3.0
mpl_toolkits        NA
natsort             7.0.1
numba               0.50.1
numexpr             2.7.1
numpy               1.19.1
packaging           20.4
pandas              1.0.5
pkg_resources       NA
psutil              5.7.2
pyparsing           2.4.7
pytz                2020.1
scanpy              1.6.0
scipy               1.5.2
setuptools_scm      NA
sinfo               0.3.1
sitecustomize       NA
six                 1.15.0
sklearn             0.23.1
tables              3.6.1
texttable           1.6.2
wcwidth             0.2.5
yaml                3.12
zipp                NA
zope                NA
-----
Python 3.6.9 (default, Nov  7 2019, 10:44:02) [GCC 8.3.0]
Linux-4.4.0-18362-Microsoft-x86_64-with-Ubuntu-18.04-bionic
8 logical CPU cores, x86_64
-----
Session information updated at 2020-08-18 15:10

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