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LouisFaure / scFates

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
https://scfates.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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When running scf.tl.curve, module 'networkx' has no attribute 'to_scipy_sparse_matrix' #17

Closed yedeer12 closed 11 months ago

yedeer12 commented 11 months ago

I think the different version of networkx and elpigraph causes this problem. scFates 1.0.2 requires elpigraph-python==0.2.7, but elpigraph-python==0.2.7 uses 'to_scipy_sparse_matrix' of networkx package in 'getProjection' function. There is no 'to_scipy_sparse_matrix' function in the new networkx package, instead there is 'to_scipy_sparse_array' in the new networkx package. elpigraph-python 0.3.1 uses 'to_scipy_sparse_array' in the new networkx package. image image

yedeer12 commented 11 months ago

image

LouisFaure commented 11 months ago

Hi, thank you for notifying that issue! I have bow updated the package to v1.0.3 setting epigraph to 0.3.1