error after reinstall

[robban80]

Hi,
I have recently reinstalled my operating system and all python packages needed for the element-centric similarity score. When I rerun code that worked in my old setup I get an error.

I'm following the example here to compare two hierarchical clusterings:
https://github.com/Hoosier-Clusters/clusim/blob/master/examples/CluSim%20Examples%20-%20application%20with%20hierarchical%20clustering.ipynb

from clusim.clustering import Clustering, remap2match
import clusim.sim as sim

cinp = Clustering().from_scipy_linkage(l1, dist_rescaled = True)
cout = Clustering().from_scipy_linkage(l2, dist_rescaled = True)

elsim = sim.element_sim(cinp, cout, r=1.0, alpha=0.9)

and get the following error:

line 977, in print_elementcentric_similarity
elsim = sim.element_sim(cinp, cout, r=r, alpha=alpha)
File "/home/robert/.local/lib/python3.10/site-packages/clusim/clusimelement.py", line 60, in element_sim
result_tuple = element_sim_elscore(clustering1, clustering2, alpha=alpha,
File "/home/robert/.local/lib/python3.10/site-packages/clusim/clusimelement.py", line 130, in element_sim_elscore
clu_affinity_matrix1 = make_affinity_matrix(clustering1, alpha=alpha, r=r,
File "/home/robert/.local/lib/python3.10/site-packages/clusim/clusimelement.py", line 221, in make_affinity_matrix
cielg = make_cielg(clustering=clustering, r=r,
File "/home/robert/.local/lib/python3.10/site-packages/clusim/clusimelement.py", line 338, in make_cielg
cielg = igraph.Graph.Weighted_Adjacency(projected_adj.tolist(),
AttributeError: 'csr_matrix' object has no attribute 'tolist'. Did you mean: 'tolil'?

[ajgates42]

Hi @robban80, can you check the version of clusim you are using? that code looks old.

One fix could be to install the latest version using this:
pip install pip@git+https://github.com/Hoosier-Clusters/clusim

[JacobH140]

I can reproduce this error by running pip install clusim in a fresh conda environment and then executing the code here: https://github.com/Hoosier-Clusters/clusim/blob/master/examples/CluSim%20Examples%20-%20basic%20element-centric%20similarity.ipynb.

As suggested, installing instead via pip install git+https://github.com/Hoosier-Clusters/clusim.git resolved the issue!