Porting over some issues from https://github.com/MDAnalysis/mdanalysis/issues/2401 - [ ] encore.hes returns unreadable details which are not documented - [ ] encore.ClusteringMethod.KMeans documents precompute_distances without actually having it as a kwarg - [ ] encore.DimensionalityReductionMethod.StochasticProximityEmbeddingNative documents the default number of dimensions as 3, but it's actually 2 - [ ] for encore.hes, ces, dres: document that the method returns averages and standard deviations if estimate_error=True - [ ] for encore.ces_convergence document the output. The shape does not include preference_values.
Porting over some issues from MDAnalysis/mdanalysis#2401