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Leiden now included in python-igraph

See original GitHub issue

The Leiden algorithm is now included in the latest release of python-igraph, version 0.8.0. I believe this alleviates the need to depend on the leidenalg packages. The Leiden algorithm provided in python-igraph is substantially faster than the leidenalg package. It is simpler though, providing fewer options, but I believe the more extensive options of the leidenalg package are not necessarily needed for the purposes of scanpy. We provide binary wheels on PyPI and binaries for conda are available from the conda-forge channel, also for Windows.

Issue Analytics

State:
Created 4 years ago
Reactions:4
Comments:27 (9 by maintainers)

Top GitHub Comments

2reactions

mezwickcommented, Feb 15, 2022

The Leiden algorithm is now included in the latest release of python-igraph, version 0.8.0. I believe this alleviates the need to depend on the leidenalg packages. The Leiden algorithm provided in python-igraph is substantially faster than the leidenalg package. It is simpler though, providing fewer options, but I believe the more extensive options of the leidenalg package are not necessarily needed for the purposes of scanpy. We provide binary wheels on PyPI and binaries for conda are available from the conda-forge channel, also for Windows.

I have now done a speed comparison with adata object of 1.85 million cells.

igraph on adata as implemented above ran in 33 minutes vs sc.tl.leiden() which took ~14 hours

1reaction

mezwickcommented, Apr 19, 2022

This issue appears due to a memory overflow on the number of edges in my graph. Fixing will probably need to wait till igraph 0.10, which should handle 64-bit integers, and so be able to handle far larger graphs https://github.com/igraph/python-igraph/issues/531#issuecomment-1102792526

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