Unable to download the cdlib library in python

Question

I want to use the Algorithms inside of the cdlib library for network analysis. I installed cdlib by:

pip install cdlib

However I am unable to check the version of the same library using

cdlib --version

which gives me an error, saying:

zsh: command not found: cdlib

Moreover, upon using

from cdlib import algorithms

--------------------------------------------------------------------------- ImportError Traceback (most recent call last) /var/folders/gm/d0bzgb6n4k95px0_1x9hqq_h0000gn/T/ipykernel_43989/3546710294.py in ----> 1 from cdlib import algorithms 2 import networkx as nx

~/opt/anaconda3/lib/python3.9/site-packages/cdlib/algorithms/ init .py in 1 from.edge_clustering import * ----> 2 from.crisp_partition import * 3 from.overlapping_partition import * 4 from.attribute_clustering import * 5 from.bipartite_clustering import *

~/opt/anaconda3/lib/python3.9/site-packages/cdlib/algorithms/crisp_partition.py in 52 53 try: ---> 54 import infomap as imp 55 except ModuleNotFoundError: 56 missing_packages.add("infomap")

~/opt/anaconda3/lib/python3.9/site-packages/infomap.py in 36 from. import _infomap 37 else: ---> 38 import _infomap 39 40 try:

ImportError: dlopen(/Users/hrisod/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/opt/llvm/lib/libomp.dylib
Referenced from: /Users/hrisod/opt/anaconda3/lib/python3.9/site-packages/_infomap.cpython-39-darwin.so Reason: tried: '/usr/local/opt/llvm/lib/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file)

This error is found. I tried reinstalling the same library even using the ways in the documentation, all too no avail. I am using jupyter notebook on mac for this project. Can someone please help me find out how to properly download the library.

Answer 1

Reading your error more thoroughly, you'll note that it says 54 import infomap as imp 55 except ModuleNotFoundError: 56 missing_packages.add("infomap") . (Seems to relate to this . this bug report , and here . Since you are on a Mac, is this pertnent ==> here ?)

I note you are using conda but trying to install cldlib with pip. This says maybe trying strictly with cdlib from conda may help. Uninstall via pip maybe first, using python -m pip uninstall cdlib , before trying conda.

If you want to try dealing with the infomap stuff first though...
Since you are using conda, you should try using Anaconda that to install infomap . If you just care about using it in this notebook, you can try that with %conda install -c conda-forge infomap in a cell in the notebook.