[Biophp-dev] where are the exporters

S Clark biophp-dev@bioinformatics.org
Tue, 27 Apr 2004 19:11:40 -0600

Hash: SHA1

P.S. ("Pre-Script") - Welcome aboard, Can Tran.  You should now
have developer access (let me know if it doesn't work for some reason,=20
but it should - you're listed, anyway.).

On Tuesday 27 April 2004 06:21 pm, Nico Stuurman wrote:
> Good to hear from you Sean.
> How do you like the phpdocumentor documentation
> (http://valelab.ucsf.edu/~nico/biophpdoc)?

Looks pretty spiffy.  Presumably proper placement and formatting of=20
comments will have them show up as descriptions in the same output?  (It's
been way too long since I looked at phpdocumentor...)

I know I've still got some ways to go to get my coding style properly
"PEAR-compliant", but I'm working on it...

> Right, that is why I would like to get a single repository for biophp...

I agree completely - right now I have about 4(!) slightly different copies =
the "biophp" trees.  The latest was checked out fresh from bioinformatics.o=
with the files I just added copied in and added/committed like new files, so
I SHOULD be in sync now.  Theoretically.  I'll keep the others around long
enough to make sure I don't have uncommitted updates in any of them but I=20
should be able to remember to use the new copy officially from now.

> I did not see the fasta exporter (or any other exporter) yet..

Grrrr.  Okay, fixed it.  (I thought my CVS client would automatically
select the contents of the new directory at the same time as I added
the directory itself).  The "exporters" directory is intended to be analogo=
to the "parsers" directory that seqIOimport uses.  The fasta output module =
now there.

> It is only getting worse from here on.  (B.t.w., what are you
> studying?).

Well, really I'm studying "whatever will get me to a so-called four-year=20
degree in the shortest period of time" (15 years seems a bit excessive for
getting a "4-year" degree.  In 'raw credits' I should be well past the
4-year-degree point by now, but I keep ending up moving, running out of mon=
to pay tuition and fees, running out of time to take classes...and I WOULD
like to end up with a degree that is at least SOMEHOW relevant to the sort =
work I want to be doing.)

On paper, my major is NOW "Environmental Science", as it was the only local=
available program that seemed to even come close to the sort of thing I'm=20
interested in (biotech in non-medical applications, and as a bonus, GIS and
similar fun technologies [population genetics studies?...]).  Southeastern
Idaho isn't particularly great for college programs.  Disappointingly,=20
"Environmental Science" thus far seems to be a "science" only in the same
way that "Political Science" is...

(My job-that-nearly-disappeared-out-from-under-me-but-came-back has been=20
heating up and getting distracting at the same time.  Good news for
future career prospects, but not so great for outside projects...)

> Could we run SubVersion at bioinformatics.org?  I don't really think it
> will make a whole lot of a difference at the moment, considering the
> immense number of people contributing =20

(sniff...sniff...say, do you smell sarcasm?.... :-) )

I don't think bioinformatics.org has a SubVersion repository running,
so it'd be something that I'd set up here (on my blazing fast 640k/640k=20
DSL line - hey it beats telephone) for experimentation.  You're probably
right, though - right this moment I don't think it'd make much difference.
If there's interest and I manage to get some of that mysterious "free time"=
stuff I keep hearing so much about, I could try to set up one that sync's
itself with the official CVS at bioinformatics.org as a trial.

On the other hand, just sticking with CVS for now will give the=20
CVS-to-SubVersion migration tools time to mature further...

> (B.t.w, could you add Can Tran=20
> as a developer?)

Done!  I'll try to keep up a bit better with ongoing development myself, to=


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