Irfan Alibay
Irfan Alibay
The encore code has been turned into a separate mdakit. We should deprecate it from core with the aim of removing in 3.0.
In the spirit of reducing the footprint of MDAnalysis, we should make matplotlib an optional dependency. This currently depends on #4312, and the HOLE2 removal - once those are done...
Fixes # Changes made in this Pull Request: - PR Checklist ------------ - [x] Tests? - [x] Docs? - [ ] CHANGELOG updated? - [x] Issue raised/referenced? ## Developers certificate...
This was brought up a while ago by @orbeckst - how do we deal with all these optional dependencies when we need version ranges. This aim of this PR is...
Fixes #3940 (probably some others too) This is a slightly cleaned up version of some mockup code I had knocking about on some branch a few years back. It needs...
This currently relies on #4274 - once complete we can remove joblib.
In multistatesamplersanalyzer, the return of `_get_equilibration_data` can sometimes include a non integer `n_uncorrelated_iterations`. In practice you wouldn't operate on fraction of an iteration, would it make sense for this value...
Context: From today's OpenFE call, @mikemhenry recommended opening this just to review later. Quite simply, should there be explit calls to clearing the context cache in `__del__` for multistatesampler?
Exchanges are quite expensive, how would folks feel about the possibility of adding a control parameter for the number of swap attempts? In the back of my mind I'm thinking...
I'm trying to get some relative free energies done using tip4p/ew and I've noticed that I will get NaN's if `reassign_velocities=False`, but everything runs fine if I set it to...