[Biophp-dev] CVS - Merging projects

biophp-dev@bioinformatics.org biophp-dev@bioinformatics.org
Tue, 22 Apr 2003 23:56:23 -0600

On Tuesday 22 April 2003 10:32 pm, nicos@itsa.ucsf.edu wrote:
> I think it would be real nice to bring Sean's and Serge's code together
> into a start of something real nice.  It will be very stimulating to
> actually have some code that is doing something usefull.

I agree - it doesn't look like there's any conflicting module 
"functionality" (no two modules that do the same thing) between
our projects so there shouldn't be any conflicts to have to work out...

> I suggest to bring all the files together in a single directory on one of
> the cvs servers (genephp on sourceforge or biophp on the bioinformatics
> one, I don't care which one, sourceforge is a very reliable server,
> biophp is the catchier name).  Having them all in one directory is simply
> a good initial organization and a simple 'cvs update' will give you a
> nice library of (hopefully) working biophp scripts.  Splitting them out
> by author is not a good idea, because it will not be the organization in
> which the files will work together.  Simply put, let's immediately put
> that code to work and let's structure everything such that it is easy to
> use.

So, essentially you would prefer to have all of my modules and all of Serge's
modules put together in a single directory with no specific "structure"
yet?  Actually, you're probably right, I think right now we've got a total
of 10-15 modules or so, so I don't imagine it'll be confusing at all.

> Don't be scared about others doing stuff to your files, cvs is extremely
> nice (once you get used to it), and you will be able to retrieve every
> version of the file that ever existed. cvs will also take care of people
> working on the same file at the same time.

CVS should be good...as soon as I've worked out how to use it properly.

> I am really looking forward to seeing this all move to something nice.
> Once Serge has made the easier constructor for his seqdb class (that does
> not need index files) I am going to use the code in the phplabware
> project and help write more parsers.

I'm looking forward to it as well.  It looks somewhat like Serge's modules
have been mainly focussed towards analysing and storing data, while what
I've been working on has been more towards collecting and converting data, 
so the two module sets should complement each other very well right from the

Speaking of which - if anyone is interested in taking a look at the way
I'm implementing the "generic" extendable XML parser and commenting on
it, I'd be interested in hearing someone's opinion on it besides my 
own egotistical one...