thanks. The plan here is that user should never need to explicitly type
"export AMBERHOME=`pwd`"
For example: We are experimenting distributing binary AT. Users can get
everything done within 5-10 minutes.
https://github.com/Amber-MD/setup-scripts
The final step is just simply as "source /path/to/amber.sh"
(similar to phenix package).
(We certainly still keep AMBERHOME for sure but it should be less important)
Hai
On Mon, Feb 6, 2017 at 7:32 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> Hi,
>
> The plan is not clear to me, so i'll cover some possible plans:
>
> if AMBERHOME will be completely eliminated from every Amber file then
> we don't need to validate it;
> presumably users do not need to source amber.sh ?
> else if AMBERHOME is only to be defined in amber.sh which users must
> source then
> we need validation:
> A. validation in configure to find a conflicting AMBERHOME.
> B. validation in Makefiles to ensure AMBERHOME is defined.
> end if
>
> Note that we already have done A. and B. For A. see check_amberhome
> in configure2. For B. see target is_amberhome_defined in some Makefiles:
>
> is_amberhome_defined:
> .(if [ -z "$(AMBERHOME)" ] ; then \
> echo "Error: AMBERHOME should be defined or else some tests
> will fail !" ;\
> exit 2 ;\
> fi ;\
> )
>
> scott
>
> On Mon, Feb 06, 2017 at 04:48:12PM -0500, Hai Nguyen wrote:
>
> > thanks Scott. I will keep two points in mind.
> >
> > Just have a question regarding #2:
> > What's your recommendation here?
> >
> > If user set the wrong AMBERHOME, raise error saying
> > either unset AMBERHOME or correct it?
> >
> > My point of gradually eliminating AMBERHOME is to force the installation
> to
> > use variables in config.h. For example. I added AMBER_SOURCE and
> > AMBER_PREFIX to point to source code and install dir respectively. Those
> > envs are set by configure script, not
> > by users and they are only needed at compile time (and testing time).
> >
> > Ideally, user just need
> >
> > cd amber17
> > ./configure gnu
> > source amber.sh
> > make install
> >
> > In my opinion, AMBERHOME is only helpful (now) for backward compatibility
> > (e.g: for the tutorials in amber website).
> >
> > Hai
> >
> > On Mon, Feb 6, 2017 at 4:08 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
> > wrote:
> >
> > > Hi,
> > >
> > > As a way to encourage best practices, here are some comments:
> > >
> > > 1. Clarity - communicate effectively.
> > >
> > > commit ad2afeaf39e9a8ddc9b2f59a8583cbe2e633a78a
> > > configure: users do not need to set AMBERHOME to install it
> > >
> > > This log leaves no doubt about intent.
> > > Please write accurate logs because some actually do read the logs.
> > >
> > >
> > > 2. Generality - validate user inputs.
> > >
> > > What the commit above did in practice was to disable the existing
> > > user validation of AMBERHOME. We should try to support a broad range
> > > of users which includes the dumb ones and the forgetful ones...
> > >
> > >
> > > For more principles of programming, including some on testing, see
> > >
> > > .book{kernighan99,
> > > author = "{Brian W. Kernighan and Rob Pike}",
> > > title = "The Practice of Programming",
> > > publisher = "Addison--Wesley",
> > > address = "Reading, Mass.",
> > > year = 1999 }
> > >
> > >
> > > scott
> > >
> > > On Mon, Feb 06, 2017 at 02:19:27PM -0500, Hai Nguyen wrote:
> > > > On Mon, Feb 6, 2017 at 2:12 PM, Scott Brozell <
> sbrozell.rci.rutgers.edu>
> > > > > Just to set the record straight, I was not referring to
> --skip-python.
> > > > > As i wrote in my post, an example is the commit regarding
> AMBERHOME;
> > > > > that commit added this to configure:
> > > > > export AMBERHOME=`pwd`
> > > > >
> > > > > Not testing this in an environment where AMBERHOME is undefined
> > > > > is like adding feature x to program y and then not testing the
> > > > > x y combination.
> > > > >
> > > > >
> > > > Just make thing clear: My comment in $AMBERHOME/configure about no
> need
> > > to
> > > > set AMBERHOME is actually mis-leading. I only meant that user do not
> need
> > > > to explicitly doing
> > > >
> > > > export AMBERHOME=`pwd` before running ./configure. (Of course
> he/shell
> > > can
> > > > still do that).
> > > >
> > > > but he/she still need to source amber.sh before "make install" (which
> > > also
> > > > setting AMBERHOME env).
> > > >
> > > > So basically AMBERHOME is never been undefined at install time.
> (that's
> > > why
> > > > I have never tested this).
>
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Received on Mon Feb 06 2017 - 17:30:03 PST
