Miscellany
I'm busily preparing for a 7-9 wk absence; I'll be attending the
Embryology course at Woods Hole for 6 weeks, starting June 11th. I'll
still have e-mail access, but it sounds like the course is nasty & brutish
in its abuse of one's time, so I expect time for coding to be minimal.
One thing I'll need to do while at the course is admin my
bioinformatics servers: the sysadmin they hired (after they fired the
competent guy) has just quit. Whee. That'll be fun.
In other news:
I'm trying to get the Quixote persistent sessions package "out the door",
which basically means (a) checking it into the cafepy.com qxtras SVN repository, (b) writing some minimal
docs, and (c) shoving the rest onto Mike Orr, who has been busy getting
the stuff to actually work. He suggested naming it
session2, so that's its new name...
sessions2 will provide persistent session stores for shelve, a
file/directory setup, Durus, PostgreSQL, and MySQL. It's easy to add
new stores; I hope to add ZODB, sqlite, and SQLObject stores when I
get back. I'm planning to write it up in my Quixote
tutorial before I leave.
I'm also hoping to get out the next version of twill. It's
going to take a few hours of programming to fix the bugs and get the
requested new features in, but it seems like it's fairly solid at the
moment. I've also created a twill mailing list so
that people can help each other out, if they're having problems.
Doubt it'll see much action, but ya gotta try, you know?
Meanwhile, Ian
Bicking is trash-talking twill. I have this to say: he's
absolutely right. If you have your Web application implemented within
a WSGI-compatible app framework and can use Paste to do your testing,
that's the way I'd do it. You're also going to want to be able to
stress-test the deployment, and sometimes you have to worry about
legacy applications, and you might want to test browser <--> code
interactions like cookies. Or (heaven forfend!) you might be testing
a package not written in Python, or you might be working with
people who don't really program but are writing "black box" tests. I
think twill could be useful in all of these situations, and that's
what I'm aiming it at. People also seem to find it a neat concept,
and the comments I've gotten indicate general enjoyment.
Personally, I'd like to see WSGI record/playback middleware. Should
be pretty easy to get something simple working...
Bio + Python
Met with Chris Lee @ UCLA the other day, and talked about Pygr,
blastgres,
and bioinformatics in general. Chris was interested in putting more
effort into open source Python software for bioinformatics, and wanted
to know if I had suggestions, info, etc. He also showed me some of
the pygr stuff, which looks like a fantastic way to take at least some
of the repetitive scripting out of bioinformatics.
It sounds like he's hoping to make a more general toolkit that will
fill the niche that (IMO) BioPython should be filling but
isn't. (I may sign on for that effort once I defend, which will
hopefully be by October or November.) Chris is completely into
Python and open source, and he's already "let go" of the code;
it's good to see.
Books!
I'm eagerly awaiting the release of Bonehunters, the 6th
Malazan Book of the Fallen. At this point I'm about 2 yrs ahead of
the US publishers; I've been getting the paperbacks from bagabooks, an
Amazon reseller that must import them from England directly. (Let me
tell you: it's worth it... a great series, and it's just getting
better!) I've got a whole list of UK books that I hope to grab
sometime soon, but I doubt I'll have the time or $$ to get them while
I'm gone over the summer.
I've been reading the Dresden Files recently, by Jim Butcher. They're
about a practicing wizard in Chicago named Harry Dresden. The series
is starting to get repetitious; hopefully the next book will introduce
something fresh. Still, they're good enough for my regular pulp
fiction fix.
I also read Hallowed Hunt by Lois McMaster Bujold: fun, but not
as good as the Curse of Chalion, which I really enjoyed. I just
finished The Fly in the Cathedral, about the splitting of the
atom; and Tracy Kidder's Soul of a New Machine. Some good stuff.
--titus