Oliver Beckstein

move waterdynamics to MDAKit

3

Following the 3.0 roadmap (decided at UGM2023): - [x] create a MDAKit with the [waterdynamics](https://docs.mdanalysis.org/stable/documentation_pages/analysis/waterdynamics.html) functionality - [x] deprecate analysis.waterdynamics in MDAnalysis - [ ] #4541

move Path Similarity Analysis to MDAKit

1

Following the 3.0 roadmap (decided at UGM2023): - [x] create a MDAKit with the [Path Similarity Analysis](https://docs.mdanalysis.org/stable/documentation_pages/analysis/psa.html#module-MDAnalysis.analysis.psa) (PSA) functionality - [x] deprecate analysis.psa in MDAnalysis - [ ] #4542

potential performance improvements for H-bond analysis 'between'

11

## Is your feature request related to a problem? ## In the review of PR #4092 , @richardjgowers observed that there's an opportunity for improving the performance for the "between"...

remove analysis.psa in 3.0

5

Remove analysis.psa - [ ] code - [ ] tests - [ ] CI - [ ] add note to #4539

remove MDAnalysis.visualization in 3.0

1

Remove visualization package - [ ] code - [ ] tests - [ ] CI - [ ] add note to #4539

remove LeafletFinder in 3.0

1

Remove analysis.leaflet - [ ] code - [ ] tests - [ ] CI - [ ] add note to #4539

remove analysis.helanal in 3.0

2

Remove analysis.helanal - [ ] code - [ ] tests - [ ] CI - [ ] add note to #4539

Remove analysis.waterdynamics - [ ] code - [ ] tests - [ ] CI - [ ] add note to #4539

deprecate LeafletFinder and schedule for removal in 3.0

2

The original LeafletFinder algorithm lacks a bit in robustness (#2843) and is also fairly specialized. It also adds networkx as a MDAnalysis dependency. Similar algorithms are available in the [MDAKit...

move helanal to MDAKit

1

Following the 3.0 roadmap (decided at UGM2023): - [ ] create a MDAKit with the helanal functionality - [ ] deprecate analysis.helanal in MDAnalysis - [ ] #4543