Mdciao

A bug regarding example datasets should be fixed
Other release notes:
* Flareplots can have "aura"
* Ions and waters are handled better in the fragmentation heuristics

v2b1
Release candidate

This patches 0.0.5, the release for the [original manuscript](https://www.biorxiv.org/content/10.1101/2022.07.15.500163v1), against deprecations that happened in the meantime, mostly in numpy handling of arrays, but also in pandas and biopython. Also updated _md_compute_contacts.py to its newest version. There's also smaller changes

Release associated with the submission of mdciao's manuscript

This is mdciao's first stable release candidate

This beta release is already a release candidate