Re: [AMBER-Developers] [ Re: Amber 'configure' now forcing miniconda?]

From: Nhai <>
Date: Thu, 22 Dec 2016 16:52:55 -0500


I just excluded scipy from configure. But I am ok to revert it back since you have more experience than I am. (And always make sense :d).


> On Dec 22, 2016, at 4:39 PM, Jason Swails <jason.swails.gmailcom> wrote:
>> On Thu, Dec 22, 2016 at 12:06 PM, Hai Nguyen <> wrote:
>> Just FYI: I made some changes for configure. Please feel free to reword.
>> - won't install scipy to reduce size (Pengfei is ok with this). The
>> Miniconda size is reduced by half now.
> ​I'm personally -1 on this. scipy is used in some obscure places, like
> minimizing structures within ParmEd using the sander API, for example. If
> we're doing this for typical Amber users, we should assume that anything in
> our Pythoniverse that doesn't work "out-of-the-box" is something that those
> users will not be able to get to work without frustration and irritation.
> So if removing a package results in any kind of feature reduction, that
> should be explicitly requested rather than default behavior (and even then,
> you should think carefully about whether adding the complexity of yet
> another configure-time choice is justified by the benefit of this option --
> my feeling here is 'no').
> - only install cython if we are using unreleased version (by checking
>> mkrelease_at file)
> ​Same as above, although I think our release versions come pre-cythonized
> and therefore this is unnecessary.
> ​All the best,
> Jason
> --
> Jason M. Swails
> _______________________________________________
> AMBER-Developers mailing list

AMBER-Developers mailing list
Received on Thu Dec 22 2016 - 14:00:04 PST
Custom Search