[Bioperl-l] RE: bioperl-db - changes (Chris Mungall)
Jason Stajich
jason@cgt.mc.duke.edu
Wed, 13 Feb 2002 08:26:14 -0500 (EST)
There are only 2 branches on the bioperl-db src -
branch-bioperl-072: which is to allow bioperl-db dev to continue with the
0.7 branch (for singapore mostly) until bioperl 1.0 is
available and bug free.
HEAD: which I suspect you are calling main. Which is where all active
dev is focused.
One issue at times is that the anonymous CVS is synced from the active dev
every two hours so there can be a (up to 2 hr) lag between when the code
is checked in by a dev and it appear on the anonymous srv. That said, I
have not seen Chris's commits on the bioperl-db code yet - either as a msg
on the guts list or when looking at the log for the files.
Chris are you absolutely sure that you did a commit in the db directory?
-jason
On Tue, 12 Feb 2002, Brian Desany wrote:
>
>
> > Oh, I'm just using the default branch rather than HEAD
> >
> > Should I be using HEAD?
>
> I don't know. You're the active developer :)
>
> I thought the default was HEAD anyway, which is consistent with there being
> no difference in the files I get whether I use HEAD or the default.
>
> I'll try to dig some more on the relationship between branches (eg MAIN) and
> tags (eg HEAD) and mail if I figure it out.
>
>
>
> > On Tue, 12 Feb 2002, Brian Desany wrote:
> >
> > > <scratching head> I'm doing a "cvs status" and getting this:
> > >
> > > >cvs status
> > > cvs server: Examining .
> > > ===================================================================
> > > File: BUGS Status: Up-to-date
> > >
> > > Working revision: 1.2
> > > Repository revision: 1.2
> > /home/repository/bioperl/bioperl-db/BUGS,v
> > > Sticky Tag: HEAD (revision: 1.2)
> > > Sticky Date: (none)
> > > Sticky Options: (none)
> > >
> > > ===================================================================
> > > etc.....
> > > So it _seems_ like I've looking in the right spot for the
> > right files
> > > (correct me if I'm wrong).
> > >
> > > Also, since I'm not a cvs expert, I'll tell you that these
> > two commands
> > > bring me the same (old) files (after logging in anonymously):
> > >
> > > cvs -d
> > :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl co -r HEAD
> > > bioperl-db
> > > cvs -d
> > :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl co bioperl-db
> > >
> > > On the other hand, "cvs -d
> > > :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl co -r
> > MAIN bioperl-db"
> > > fails because MAIN isn't a tag (so it tells me). Am I just
> > flat out issuing
> > > the wrong checkout command? I don't do this too often...
> > >
> > > -Brian.
> > >
> > > > -----Original Message-----
> > > > From: Chris Mungall [mailto:cjm@fruitfly.bdgp.berkeley.edu]
> > > > Sent: Tuesday, February 12, 2002 1:17 PM
> > > > To: Brian Desany
> > > > Cc: bioperl-l@bioperl.org
> > > > Subject: Re: [Bioperl-l] RE: bioperl-db - changes (Chris Mungall)
> > > >
> > > >
> > > >
> > > > Hmm, I just committed on the main branch - this is in the
> > bioperl-db
> > > > project remember.
> > > >
> > > > On Tue, 12 Feb 2002, Brian Desany wrote:
> > > >
> > > > > I don't see these changes when I do "cvs -n -q update" or
> > > > "cvs status" or go
> > > > > to WebCVS - is there normally some kind of a delay or is
> > > > there some other
> > > > > cvs command I need to use to find out which files have been
> > > > changed? Do I
> > > > > need to specify a particular branch maybe?
> > > > >
> > > > > Thanks,
> > > > > -Brian.
> > > > >
> > > > > >
> > > > > > I have committed some code to bioperl-db
> > > > > >
> > > > > > * Fuzzy Locations are now handled, using the
> > > > location_qualifier_value
> > > > > > table added to the biosql-schema during the hackathon.
> > > > > >
> > > > > > * Optimisations - all the features and locations for a
> > > > > > sequence entry are
> > > > > > now fetched in a few SQL calls rather than a number of calls
> > > > > > proportional
> > > > > > to the number of features.
> > > > > >
> > > > > > * Tidying - a lot of mysqlisms removed or pushed up to
> > > > the BaseAdaptor
> > > > > > layer, to allow for easier postgres support. Added a few
> > > > > > generic ease of
> > > > > > use methods to BaseAdaptor to more clearly expose the
> > logic in the
> > > > > > individual adaptor layer.
> > > > > >
> > > > > > * DBTestHarness now no longer uses the copy of the
> > schema in the
> > > > > > bioperl-db directory. Instead it checks
> > > > > > ../biosql-schema/sql/biosqldb-mysql.sql - hmmm, this won't
> > > > > > necessarily fit
> > > > > > with the cvs re-organisation. How should we do this? An env
> > > > > > var seems a
> > > > > > bit nasty.
> > > > > >
> > > > > > ---
> > > > > > Chris
> > > > > >
> > > > >
> > > > > _______________________________________________
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> > > > > Bioperl-l@bioperl.org
> > > > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > > >
> > > >
> > > >
> > >
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> > >
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--
Jason Stajich
Duke University
jason@cgt.mc.duke.edu