[Biopython-dev] next release closer (?)

Brad Chapman chapmanb at arches.uga.edu
Thu Nov 30 15:27:07 EST 2000

[Cayte's Prosite problem]

> I checked in the CVS logs since I wanted to ensure that it was a proper
> code fix and not some side effect of perhaps another bug.  Looks like
> Brad fixed that on 2000/09/27 with the following:
[change because of a different default argument in python 2.0]

Doh! Sorry, that I didn't say anything about this -- I'd actually
forgotten about this fix and it didn't cross my mind that
Cayte's problem could be related to it. This is my fault, I should
have posted to the dev list about this...

[my "fix"]
> Oops.  Just realized this code contains a bug when endpos == 0.

Double Doh! Thanks for the fix on this. I apologize again, I should
have posted to the list on this -- I was just thinking I was making a
"simple" change, but should have been more careful. Since that time
I've become a lot more paranoid, and started posting patches for other
people's code instead of fixing directly in CVS, and this is a good
reason why I should do this.

This brings up a point -- does anyone think it would be worthwhile to
have CVS commits and log messages sent to the dev list? Bioperl has
this and I think it's very worthwhile -- then for cases like this I
would feel more comfortable going ahead with a small "fix" because I
know Andrew would read the log... Then he could think: "hey, what's
this punk doing messing with my code?" and go in and check up on the
fix, if he feels like it. Just an idea, but maybe posting patches is

I would really like to have bugs sent to the dev list when they come
in -- I just noticed a couple from Iddo that I should have dealt with
(I think that is all fixed now, regardless), but didn't realize were
there. Whadda you all think about this?

> Also, BTW, when we make the change to Python 2.0, I suggest changing
> Pattern.py's Prosite.search so that endpos defaults to sys.maxint
> instead of the None it does now.  This keeps it compatible with the
> Python API and prevents the if-branches in the code - I don't like
> branches since they are harder to test fully.

This is true -- your fix would be better, if you are not worried about 
1.5.2 compatibility. As far as I can tell, we are officially requiring 
2.0 and no one seems to mind, so if you personally aren't worried
about people having to have 2.0 to use Prosite, then I give a big +1
to switching to the more stable code. This way I won't have to stay up 
nights worrying about more bugs in my "fixes" :-).


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