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

From: Jason Swails <>
Date: Thu, 22 Dec 2016 16:39:50 -0500

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 M. Swails
AMBER-Developers mailing list
Received on Thu Dec 22 2016 - 14:00:03 PST
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