Urgent! Error using clustering.fit

[cz239]

I got the following error when using the clustering function

I installed it using the following command and set up the environment:
#conda install clustcr -c svalkiers -c bioconda -c pytorch -c conda-forge
#conda env create -f env.yml

Could you please take a look at it?
Many thanks!

[svalkiers]

Hi, I believe this error results from a version inconsistency with the networkx package. The new syntax for this command is to_scipy_sparse_matrix. I will try to resolve this issue in the next ClusTCR release by updating the networkx version.

For now, you can work around this issue by setting up a fresh conda environment and installing the clustcr package using the conda install clustcr -c svalkiers -c bioconda -c pytorch -c conda-forge command as mentioned. No need to set up the environment manually, all the package dependencies are downloaded with the installation of clustcr.

Alternatively, in your current environment, you can try to remove both clustcr and networkx, and reinstall clustcr subsequently.

Hope this helps.