[Biopython] Fasta.index_file: functionality removed?

[Peter]

On Thu, Jun 18, 2009 at 7:45 PM, Cedar McKay <cmckay at u.washington.edu> wrote:
>
> 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

You had such an old version that it even predates our practice of keeping
the Martel version in sync. If ViewCVS was working I would probably
check if it really was Biopython 1.43 but it sounds quite possible.

We can't do anything about the past, but Bio.__version__ is now in use.

> 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.

I see - that was always a possibility even if the deprecation warnings
were in place for several releases. Hopefully on balance we've not
been removing things too quickly.

>> 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

Yes, that is unfortunate timing for you. The OBF are looking into the
issue, which was an unexpected side effect from a server move.

> 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.

I too prefer the ViewCVS history for individual files to github, and
generally speaking find our ViewCVS server more robust than github.

> 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!

At least you tried. I have the advantage of having several years
of Biopython emails in GoogleMail, which seems to be better at
searching than http://search.open-bio.org/ even though that too
is done by Google. It doesn't work as well as it could...

> 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.

That is a good policy - but as you point out, the odds were a bit
against you.

Peter