[BioPython] biopython installation

[Jeffrey Chang]

On Thursday, June 5, 2003, at 12:03  AM, Cath Lawrence wrote:
>
> I'd like to request a couple of things -
>
> 1. Minor navigation quibble - give the website a default index in each 
> directory, if you try to navigate by trimming URLs you get "directory 
> listing denied" (eg this obvious trim doesn't work - 
> http://www.biopython.org/docs/ )

I don't know if this is possible anymore, since most of the website is 
now dynamically generated.


> 2. Make the install documents be more explicit on the associated 
> modules.

Yep, I agree.  We've been wanting to do this for a while.  There's no 
question we desperately need more people working on documentation!


> Background:
> I have been updating my CVS version (after a couple of months of doing 
> other tasks) and thought I should probably re-run the setup and tests 
> since the move to python 2.2.
>
> I have followed the 
> http://www.biopython.org/docs/install/Installation.html instructions 
> and tests along, but since I was CVS updating much didn't apply. 
> Anyway the step 5 'happy place" tests are fine.
>
> But when I run the test suite I get many tests skipped due to import 
> errors - and the documentation appears to be silent on these modules 
> and their purposes.
>
> Here's the total test output:
> Skipping test because of import error: No module named Crystal
> Skipping test because of import error: No module named MySQLdb
> Skipping test because of import error: No module named MySQLdb
> Skipping test because of import error: No module named Polypeptide
> Skipping test because of import error: No module named Ais
> Skipping test because of import error: No module named CDD
> Skipping test because of import error: cannot import name ECell
> Skipping test because of import error: No module named Geo
> Skipping test because of import error: No module named 
> LocusLink.web_parse
> Skipping test because of import error: No module named LocusLink
> Skipping test because of import error: cannot import name Ndb
> Skipping test because of import error: No module named Saf
> Skipping test because of import error: cannot import name trie
> Skipping test because of import error: cannot import name trie

This does not look right.  There should not be import errors on 
packages like Crystal, Polypeptide, Saf, etc.  You mentioned that you 
were using the CVS version.  Some of these modules look relatively 
recent.  Is it possible that when you are running python, it is trying 
to import from an old version of biopython?  The regression tests might 
get confused if there were multiple installations of biopython on the 
machine.

Jeff