Re: Shoule Wise2 be installed by default by biopython ?
On Saturday 24 November 2007 01:03:48 Philipp Benner wrote:
> > I just realised that biopython recommends wise. With the default
> > behaviour of apt-get and aptitude in Lenny, wise will be installed by
> > default with biopython. I just wanted to make sure that the relationship
> > between the two packages is that strong.
> >
> > In the case of bioperl, although it was not discussed before, I think
> > that we will only suggest the packages that provide binaries for which
> > bioperl has a parser or a wrapper.
>
> I have to admit that I'm always unsure about this. However, I would
> prefer to have all modules just working after a standard installation of
> biopython so that users don't have to cope with strange error
> messages. If a user then decides that he will never use Bio.Wise he can
> just purge wise. Just correct me if this is not reasonable...
Have a look at bioperl-run, a set of wrapper modules which I am kind of
working at for its inclusion with Debian. We have most of what it wraps with
Debian but I think you would agree that just because you want to work with
something and install bioperl-run for that purpose, you still do not want to
remove that zoo of other progs. It unnecessarily takes resources of you
twice - for the installation and for the removal.
> On the other hand I would like to have either all dependencies for all
> modules recommended or none. That is, if I move wise to the suggests
> field I would also move python-numeric-ext back. I don't see a reason
> why one should distinguish between libraries and binaries since from the
> user's perspective a module is just working or not. Whether this is
> because a library or a binary is missing doesn't actually matter.
This depends. If it is "grep" or so that is expected for some bits of a
program then the coder may not have prepared the program for its absence and
the program might experience an ugly failure. With higher-level applications,
the coder is more likely to have foreseen its absence and just raises a kind
exception of some usable sort.
So I think the difference is in the degree of embeddedness of the binary with
the harbouring app and libraries just tend to be deeper integrated than bins.
Though there is no explicit rule for that. It is your maintainer's gut
feeling to decide and the amount of complaints of your user base and to "feel
uncertain about it all" sounds like a very reasonable stance towards it. The
world is gray here.
retfluijhtg
Our cat just jumped on my keyboard
Steffen
Reply to: