Since SciPy v1.15.0 https://github.com/scipy/scipy/releases/tag/v1.15.0 there is a new interface for the scipy.sparse module. From the release notes: “Sparse arrays are now fully functional for 1-D and 2-D arrays. We recommend that all new code use sparse arrays instead of sparse matrices and that developers start to migrate their existing code from sparse matrix to sparse array”.

A migration guide is provided here: https://docs.scipy.org/doc/scipy/reference/sparse.migration_to_sparray.html#migration-to-sparray

The following files should be considered:
stwfsapy/thesaurus_features.py
stwfsapy/predictor.py
stwfsapy/util/passthrough_transformer.py

Furthermore, the unit tests associated with these scripts should be considered and modified if needed.