Sire pymbar 4.0

Just a note regarding the release of pymbar 4.0, which has breaking API changes, as documented here. We'll likely need to update the analyse_freenrg script if we want to use the new API, or take advantage of the new features. (I know that BioSImSpace will be moving to alchemlyb, with pymbar as a backup in future.) For now I'll pin pymbar to version 3 in our conda recipe. (pymbar is actually missing at present following the 2023.0.0 merge, so I'll re-add.)

Jul 21 '22 12:07 lohedges

Just to add on to this, pymbar is a dependency for alchemlyb, as alchemlyb does end up feeding the extracted data into pymbar during the MBAR analysis. This is also currently not able to use pymbar 4.0.

Sep 30 '22 14:09 annamherz

Thanks for this. I had also noticed this the other day when I checked their recipe having discovered that version 4 pulls in cudnn and jaxlib, which come to over a GB in size. If/when we do support version 4, I really hope that we can avoid the overhead of these packages if we don't need their functionality.

Sep 30 '22 19:09 lohedges