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michellab / Sire

Sire Molecular Simulations Framework
http://siremol.org
GNU General Public License v3.0
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pymbar 4.0 #395

Open lohedges opened 2 years ago

lohedges commented 2 years ago

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.)

annamherz commented 2 years ago

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.

lohedges commented 2 years ago

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.