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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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louvain deprecation #360

Closed deniskristak closed 1 year ago

deniskristak commented 1 year ago

Hi, I'm trying to install this software as part of the EasyBuild package manager. For that, I need to install it from source. However, my issue is that this package https://pypi.org/project/louvain/ is apparently deprecated and has probably been replaced by https://pypi.org/project/leidenalg/ . I cannot even access documentation of louvain... So my question is - is the louvain package still needed and used or can I simply patch the setup.cfg file and ignore it? Thanks!

mumichae commented 1 year ago

Hi, for reproducibility purposes we still want to include louvain in the package. The repository seems to be available at https://github.com/vtraag/louvain-igraph. I could make it an optional dependency though.

deniskristak commented 1 year ago

Awesome, thanks for the help

deniskristak commented 1 year ago

Hi @mumichae , can we please look into this a bit more? When I run the test pipeline of scib-pipeline, I'm running into trouble with missing louvain (see log). I know it is triggered by scanpy but maybe this is something we could solve / prevent on our end? test_pipeline.log I am having trouble with installing louvain and I find it unecessary, as you stated that it is an optional dependency. It is not clear to me why louvain is still being imported even if scib doesnt use it? Can you shed some light into this? Thank you!