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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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A compatibility with Networkx v2.0 #6

Closed mstubb closed 1 year ago

mstubb commented 7 years ago

Quite a lot has changed in Networkx v2.0 (https://networkx.github.io/documentation/stable/release/migration_guide_from_1.x_to_2.0.html) and it breaks summarise.

For now, the requirements file specifies v1.11 exactly but we need to add v2.0 compatibility.

Japrin commented 7 years ago

Good idea! For example, the code in 1226 line of bracer_func.py: to_remove = [n for n in deg if deg[n] == 0] works for Networkx v1.111, but for Networkx v2.0, it should be changed to to_remove = [n for n in deg if n[1] == 0]

NickEngland commented 1 year ago

This is now fixed in v0.2