Consider removing FA2 as a dependency as it is not actively maintained and does not pip install from PyPI on Python 3.9+ - Githubissues

aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

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Consider removing FA2 as a dependency as it is not actively maintained and does not pip install from PyPI on Python 3.9+ #92

Closed dburkhardt closed 1 year ago

dburkhardt commented 1 year ago

Describe the bug To reproduce

Have Python 3.9.15
Build scenicplus from source
Install fails at fa2 dependency due to https://github.com/bhargavchippada/forceatlas2/issues/34

Workaround:

Build fa2 from source
Build scenicplus from source

Error output See https://github.com/bhargavchippada/forceatlas2/issues/34

Additional context

fa2 doesn't seem to be imported in any module of this package
Last commit to fa2 is from December 2020
The lead dev of fa2 acknowledges they are not actively maintaining the package: https://github.com/bhargavchippada/forceatlas2/issues/38

dburkhardt commented 1 year ago

Also, why is scanpy pinned to 1.8.2? It seems like it's only used to log-transform and normalize the data.