[BioPython] biopython installation

[Cath Lawrence]

On Tuesday, May 27, 2003, at 12:57  PM, Jeffrey Chang wrote:
> Hi Sam,
> Have you taken a look through Brad's installation instructions on the 
> website?
> http://www.biopython.org/docs/install/Installation.html
> Please let us know if the documentation there is insufficient, 
> particularly if there are any areas that need better coverage.

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/ )

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

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


regards
Cath
-- 
Cath dot Lawrence at anu dot edu dot au
Senior Scientific Programmer, Centre for BioInformation Science, 
Australian National University