Version 1.0

This is a major version update of MELD, and it will break backwards compatibility with previous workflows due to a significant change in nomenclature accompanying our revised manuscript forthcoming in Nature Biotechnology.

You can find an up-to-date version of our article on BioRxiv with the revised language. The main difference is that we have dropped the "RES" and "EES" language for a more rigorous probabilistic interpretation inspired by an update to the algorithm made during the review process.

The output of meld.MELD().fit_transform is now referred to as the sample_densities and is the output of a kernel density estimation of each sample over that cell similarity graph. We then calculate the ratio of these densities using meld.utils.normalize_densities to calculate sample_likelihoods.

This framework reflects the interpretation of the MELD algorithm as a kernel density estimation over a graph. The tutorial and documentation have also been updated.