[Bioperl-l] cvs modules?

[Heikki Lehvaslaiho]

Jason,

Thanks a lot for do it!

First I could not see the new cvs modules but I did figure out what was
going on. There is one crucial difference between normal and virtual cvs
modules I had not understood before. I'll outline what I learnt here for
others benefit. Correct me if there is an easier way of doing it.


- When you check out a normal cvs module it creates a directory under 
  your working directory.

  ~/src> cvs -d:yadda:/home/repository/bioperl co bioperl-live

  will create directory ~/src/bioperl-live and to update it you cd into
  it to run 'cvs update'.


- Virtual cvs module will create the sub directory with sub directories 
  for each included cvs module. 

  ~/src> cvs -d:yadda:/home/repository/bioperl co bioperl_all

  adds --> ~/src/bioperl/core, ~/src/bioperl/db, ...

  You can update the files in all of them with one cvs update command 
  in the top directory '~/src/bioperl', but if the module content of 
  the virtual directory changes, you have to explicitly check the new 
  ones out, by rerunning:

  ~/src> cvs -d:yadda:/home/repository/bioperl co bioperl_all
  
  adds --> e.g. ~/src/bioperl/pipeline, ... 



 	-Heikki


On Tue, 2003-04-01 at 14:39, Jason Stajich wrote:
> The alias is called 'bioperl_all', catchier names welcomed =)
> 
> run and pipeline we already included in there as was pedigree.
> 
> I renamed bioperl-run to run in the checkout now.  I've dropped the corba
> client/server modules from the co.  For now gui is removed from that
> default co unless mark/dave protest.
> 
> (Note this is not removing them from CVS just from the cvs shortcut
> 'bioperl_all').  Perhaps we should make 2 aliases, a 'bioperl' and a
> 'bioperl_all' ?
> 
> biodata is in there as well (a cross-project project to generate a set of
> example files of different file and application output formats).  Note it
> can be big.
> 
> In the future you can wield the power if you like:
> 
> % cvs -d:yadda:/home/repository/bioperl co CVSROOT
> % cd CVSROOT
> % EDIT modules
> % cvs commit -m "changed checkout shortcut to remove corba and add run"
> % cd ..
> % cvs -d:yadda:/home/repository/bioperl release -d CVSROOT
> 
> % cvs -d:yadda: co bioperl_all
> 
> The problem is that schema is in a different CVS repository - we can
> symlink it in I guess, which is what I've done for now.  Additionally not
> everyone in the bioperl group can co this so it will cause their cvs co to
> skip (for developers, the anonymous CVS checkout will not have
> problems).
> 
> -j
> 
> On Tue, 1 Apr 2003, Heikki Lehvaslaiho wrote:
> 
> > We have a number of cvs modules in bioperl. Not all of them are active,
> > but some are updated daily. Also, there is a nifty virtual module called
> > simply 'bioperl' which allows you to check out several modules at one
> > go. At the moment there are five modules:
> >
> > corba-client
> > corba-server
> > core         (=bioperl-live)
> > db
> > gui
> >
> > Could we change the module list?
> >
> >
> > I'd like to drop corba-client and corba-server and include bioperl-run.
> >
> > I do not really have any opinion on gui as I do not use it. Drop it as
> > it is not actively developed?
> >
> > Would it make sense to add bioperl-pipeline?
> >
> > If we keep db (bioperl-db = BioPerl component of BIOSQL), we really
> > should include biosql-schema.
> >   The alternative is to have an other virtual module which contains
> > appropriate compatible versions of bioperl-db, biosql-schema and
> > bioperl-live.
> >
> >
> > I suppose the answer to those questions depends on question who this
> > virtual module is meant for. I'd like it give be meant for developers
> > who want to keep up to date in all aspects of bioperl.
> >
> > I'd be happy to do the changes once we have decided, but I do not know
> > where to look in.
> >
> > 	-Heikki
> >
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
-- 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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