Hi Jason,
Again I reiterate my point. Why are we requiring lots of non-default
packages to be installed?
Note - a LOT of people have to build AMBER on machines they do not have
root for. They also have to build it on non-Linux systems - such as AIX.
Thus I would suggest getting a machine and doing a default install - with
most Linux systems the packages needed for Xleap etc are there. If they
are not then right now they get a message asking them to specify -noX11.
With this setup they will then get another message telling them to specify
-nopysander - at this point the poor user is like - WTF?? what are all
these things I am turning off, do I need pysander? What will it break etc
etc etc... Bad news... Probably we should just have it automatically skip
non-core packages if it does not find the relevant libraries.
As you had it the configure script would fail with a FATAL error if one
did not have python-dev installed. This requires root access to install.
I would suggest changing this to be non-fatal - if it does not detect
python-dev it just skips the building of pysander. This removes the fatal
dependency on the external package rather than requiring the user to
explicitly specify -nopysander.
Some things to remember when developing code in AMBER:
1) Users will NOT necessarily have root access so you cannot just say
things like - do yum install blah blah blah.
2) Users will NOT necessarily be running Linux or OSX
3) Users should NOT be expected to consult webpages outside of the
ambermd.org domain.
4) Users cannot be considered to be Linux admins.
We need to make things as simple as possible.
All the best
Ross
On 10/1/14, 11:12 AM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Wed, 2014-10-01 at 10:57 -0700, git repository hosting wrote:
>> The project "git repository for AMBER":
>>
>> The branch, master has been updated
>> via 9d5737077690e468e33971168de3b031e4529958 (commit)
>> from 9ff7b996a9ae5818396d4e9d56e783e655955bde (commit)
>>
>>
>> - Log -----------------------------------------------------------------
>> commit 9d5737077690e468e33971168de3b031e4529958
>> Author: Ross C. Walker <ross.rosswalker.co.uk>
>> Date: Wed Oct 1 10:57:14 2014 -0700
>>
>> RCW: Change -nopysander to -pysander - make skipping of pysander build
>> default since it requires external libraries that are not installed by
>> default on most systems. - Should fix CruiseControl builds.
>
>I don't want to do this. And if the only purpose is to get CC to work
>again, I don't think that's a good enough reason (nobody has noticed it
>hasn't worked in ~2 weeks). Besides, you can just add -nopython to the
>buildbot script. It doesn't cost users anything to configure, see that
>they are missing Python.h, and either "yum install python-dev" or
>configure -nopysander.
>
>Python development headers are common for people that use Python in
>their work (which is a dramatically growing portion of people). I think
>the functionality is useful enough that it should be enabled by default
>(requiring a flag to enable it is a good way to make sure it never gets
>used). There is no getting around the dependency (and I worked hard to
>make sure we didn't introduce something additional like Cython or
>Boost-Python).
>
>We do the same thing with X11 and xleap, so it's not like this is
>unprecedented.
>
>I copied Dave here so he can tell me to deal with it if he disagrees.
>
>All the best,
>Jason
>
>--
>Jason M. Swails
>BioMaPS,
>Rutgers University
>Postdoctoral Researcher
>
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Received on Wed Oct 01 2014 - 11:30:02 PDT
