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

From: Scott Brozell <>
Date: Wed, 21 Dec 2016 13:28:25 -0500


Let's follow my suggestion of modeling our support for
python package managers and packages like we support
compiler vendors and language standards.

On Wed, Dec 21, 2016 at 12:29:02PM -0500, David Case wrote:
> trying to provide advice to users on how they can install missing items
> is probably impossible--do we have them use pip, conda, apt-get, manual
> download, something else?

>From my state of python ignorance the obvious candidates for
amber supported python package managers are pip and conda.
According wikipedia most pythons come with pip preinstalled;
we are already using conda.

On Wed, Dec 21, 2016 at 12:34:48PM -0500, Hai Nguyen wrote:
> On Wed, Dec 21, 2016 at 12:25 PM, Scott Brozell <>
> >
> > > To avoid spending time on debug different Python distributions, we just
> > > force user to use Miniconda (much lighter than Anaconda) as we ...
> >
> > This seems to be a different standard than we apply to other source
> > languages; for example, we do not force gnu compilers, but rather
> > support several vendors. And we try to advance to the next official
> > language standards only when all or most vendors support that standard.
> >
> My language is quite extreme here. "force" should be "suggest".
> User absolutely does not need to use Miniconda, they just need to specify
> --with-python flag.

Regarding amber supported python packages, what packages do we currently use ?
If you can call that set Miniconda then why isn't it trivial for us to
support Anaconda as well since Anaconda is a superset of Miniconda ?

Treating the package list like a language standard would presumably be
very useful not just for installing Amber but also for programming.

Why should we model our support for python package managers and
packages like we support compiler vendors and language standards?
Because supporting more than one compiler vendor and sticking to
language standards has improved our software, so following that
model for our python software might reap similar benefits.

I am trying to apply the scientific method to our python woes.
Heretofore, it seems like the approach has been we use Miniconda and
for anything else the onus is on you to hack via --with-python because
your python might be screwed up.


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Received on Wed Dec 21 2016 - 10:30:04 PST
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