[Biopython] Fasta.index_file: functionality removed?

[Cedar McKay]

On Jun 18, 2009, at 2:23 AM, Peter wrote:
> What version of Biopython were you using, and did you suddenly try
> installing a very recent version and discover this? I'm trying to  
> understand
> if there is anything our deprecation process we could have done  
> differently.
>
I think I was using 1.43, but as I explained, it is kind of hard to  
tell for sure until Bio.__version__ started working. For what it is  
worth:

 >>> print Martel.__version__
0.84

I don't think you could have done something better. I kept using 1.43  
for a long time because I have a pretty intricate pipeline that I  
didn't want to disturb. When I moved to a more modern version, I had  
skipped right over versions with the deprication warning.


> Apparently there is glitch with one of the virtual machines hosting  
> that,
> the OBF are looking into it - I was hoping it would fixed by now. CVS
> itself is fine (if you want to use it directly), or you can also  
> browse the
> the history on github (although this doesn't show the release tags  
> nicely).
> http://github.com/biopython/biopython/tree/master

I find it a bit hard to try to answer questions like this on my own.
1)CVS browser is down
2)github seems to serve a "page not found" page very often, and I  
don't find it easy to browse the history of any particular file.
3)I find it very difficult to search the mailing lists. For instance  
when I go to the mailing list search page at http://search.open- 
bio.org/ (outsourced to google?) and search for something that should  
be there, like "index_file", I get a single spurious result from the  
bioperl project!

All in all, I find it hard to do self-service support. On the other  
hand, everyone on the mailing list seems very responsive, and generous  
with their time answering questions. I just like to try to figure out  
things for myself before I bother everyone.


Thanks!
Cedar