Epic: Introduce breaking changes and improvements required for 1.0

[CSchoel]

Sub-issues

• Go through TODOs in the code.
• Reduce the size of unit tests so that they run in less than three minutes.
• Make unit tests fully deterministic.
• Adjust default values such that the version of the algorithm run with default settings is as close to the corresponding paper as possible.
• Add general tips for finding correct settings for emb_dim and other parameters (always look at the plots!).
• (optional) Allow to input multidimensional data and skip the embedding step for algorithms where this makes sense.