module 'networkx' has no attribute 'biconnected_component_subgraphs

[Shunsuke-1994]

description

conda install -c rdkit -c mordred-descriptor mordred installed the newest version of networkx(2.4.0, as for today). But biconnected_component_subgraphs is already depricated in networkx (>2.1.0).

minimal reproduction code

I installed mordred via conda as following,

conda create -n mordred python=3.8
conda activate mordred
conda install -c rdkit -c mordred-descriptor mordred

and then I ran the following code.

from mordred import Calculator, descriptors
from rdkit import Chem

smiles = "c1ccccc1"
calc = Calculator(descriptors, ignore_3D=True)
df = calc.pandas([Chem.MolFromSmiles(smiles)])
df["DetourIndex"] # this returns "module 'networkx' has no attribute 'biconnected_component_subgraphs"

environment

macOS High Sierra 10.13.6
conda version : 4.8.2

Best regards,
Shunsuke

[ademidun]

@Shunsuke-1994 I have proposed a simple fix in #87. Though I'm not sure when it will get resolved as this repo does not seem to be actively monitored.

@philopon do you think you will have a chance to look into this?

If you are busy, we completely undestand, maybe you could give some other people ability to contribute to this repo?

[Shunsuke-1994]

@ademidun Thank you! I didn't notice! Or, if you know somebody forked this repository, I would use it.

[mkrompiec]

Instead of forcing an old version of networkx, change line 121 in DetourMatrix.py from:
for bcc in networkx.biconnected_component_subgraphs(self.G, False):
to:
for bcc in (self.G.subgraph(c) for c in networkx.biconnected_components(self.G)):