Re: [AMBER-Developers] Python request

From: Eric Pettersen <>
Date: Fri, 15 Oct 2010 11:59:06 -0700

Yeah, we bundle Python with Chimera for much the same reasons; to
ensure we have a compatible version that includes the modules we
expect. We leave the system Python alone.


On Oct 15, 2010, at 8:52 AM, Jason Swails wrote:

> Hello,
> This is something I wanted to bring up as well. I am all for
> bundling the necessary python in with AmberTools, and we can even
> create wrappers for the python programs to force it to invoke the
> bundled Python. I'm pretty sure that Python will allow that, since
> pymol does just that. I've started with it kind of, by adding a
> configure_python script, but I don't know how people feel about
> adding Python to the git repo, since it's 12MB zipped.
> That being said, though, we could automate the building of package
> dependencies like mpi4py, numpy, etc. At the latest, we can address
> this during the developers meeting.
> Thoughts are welcome.
> Jason
> On Oct 15, 2010, at 11:23 AM, "B. Lachele Foley" <>
> wrote:
>> The new Amber depends on Python. My experience with Python as a
>> sysadmin has not been enjoyable -- to the point where I feel
>> contempt every time I think of learning or using it.
>> The problem is that Python versions are not necessarily backward or
>> forward compatible. So, one must keep multiple versions
>> installed, and it is inadvisable to permanently set any in ones
>> path. Because of this, my request is to either (or both):
>> 1. Bundle the required Python with Amber and build it as a matter
>> of course. Have internals always point to the Python down in
>> AMBERHOME. Will Python's license allow this? I think it should,
>> given the way it operates.
>> 2. Allow, somehow, for Amber to know an "AMBERPYTHONHOME" setting
>> so that I can point it to whatever Python build it wants without
>> having to permanently set a specific Python in my path (or having
>> to remember reset it every time I use Amber and heaven forbid I
>> want to use another program that wants a different Python in the
>> same session...).
>> :-) Lachele
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Received on Fri Oct 15 2010 - 12:30:03 PDT
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