Irfan Alibay
Irfan Alibay
Follow up from #1043 - specifically a comment by @hannahbaumann on the usage of host/guest when it comes to defining a flatbottom distance restraint between two molecules (which doesn't make...
This warning gets thrown a lot when using alchemiscale: "UserWarning: RDKit does not preserve Mol properties when pickled by default, which may drop e.g. atom charges; consider setting `Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AllProps)`" It's...
Kartograf deploys over PyPi, but there are no suitable releases of gufe on PyPi, so unless you conda install gufe first you should resolve to a bad install. Should we...
Follow up from #54 `atom_mapping_scorer` is effectively just a stub file that imports other things. We should review if we want to keep it around or deprecate & remove it...
_Originally reported and debugged by @yuxuanzhuang_ We're getting Pytest worker crashes with Cython 3.1, see: https://github.com/MDAnalysis/mdanalysis/actions/runs/15360620736/job/43227245666?pr=5055 Pinning to
I know that folks would like to keep x86-64 support for macos, but the only remaining gh runners with that architecture are super slow and buggy. I would like to...
## Expected behavior ## All post-deployment tests for TestPypi pass. ## Actual behavior ## Full dependency tests (named FULL in the matrix) are failing for macos-latest and python 3.13 This...
The macos-12 runners are going away in December, and the macos-13 runners can be somewhat problematic. Now might be a good time to review if we want to keep x86_64...
## Expected behavior ## NoJump should fail when applied outside of the first frame (at least it makes sense to me), but it should do so in a way that...
## Overview Looking at the definition for `sources`, my understanding is that the docstring always seems to indicate that a file or file-like object is required. This can be seen...