Irfan Alibay
Irfan Alibay
Checklist * [ ] Added a ``news`` entry ## Developers certificate of origin - [ ] I certify that this contribution is covered by the MIT License [here](https://github.com/OpenFreeEnergy/openfe/blob/main/LICENSE) and the...
Folks will sometimes get error messages in the form of Potential energy is NaN after x attempts of integration with move LangevinDynamicsMove Atempting a restart...". These may recover and folks...
Users have reported that it wasn't clear exactly what was happening when they got this warning: https://github.com/OpenFreeEnergy/kartograf/blob/0c5d3bc166d76027f0454dd2477ab20a334f84f4/src/kartograf/atom_mapper.py#L770-L771 We should update the warning to make it clearer that it is a...
Several mdakits' CI broke overnight with the following error: ValueError: there is no reference attributes in this universeto guess types froma This means that the new guessers interface did a...
We want to do a new release of MDAnalysis. The target date is the 20th of October 2024. TODOs: - [ ] Complete remaining issues on the v2.8.0 milestone -...
Related to #4748 ## Expected behavior ## In a non-API breaking release, I would expect to find the things I used to use in the same place, unless it was...
Related to #4748 The Guessers PR removed `MDAnalysis.topology.guessers`, however it is being actively used downstream, see pytim for an example of this. Since this is a major API break, we...
Related to #4748 The following worked before we introduced the new guesser API: ```python import MDAnalysis as mda import numpy as np a = np.array([ [0., 0., 150.], [0., 0.,...
Related to #4748 In the new guesser API, we often do a check for an attribute and then except on an AttributeError. This makes for an ugly capture for users...
Fixes #4751 #4753 TODO: - [ ] Add tests back - [ ] Add DeprecationWarning for old guessers and tables - [ ] Make sure tables is still exposed in...