[BioPython] biopython installation

[Omid Khalouei]

I also agree to some modifications made to the software documents. I didn't 
find it very clear although I went through it several times and I still 
wasn't able to instal the software, so I gave up! :)
It's alright I'll keep myself busy with other stuff till there will be more 
people to work on that part.
Saying this, I do appreciate all your dedications to bring this software 
freely available to the public. It sure requires lots of reading, updating, 
maintenance, ...

Keep up with the good work guys!

Sam K.




________________________________________________
Sam(Omid) Khalouei
Departments of Computer Science & Human Biology
University of Toronto
Alt. e-mail: sam.khalouei at utoronto.ca
________________________________________________





>From: Jeffrey Chang <jchang at smi.stanford.edu>
>To: Cath Lawrence <Cath.Lawrence at anu.edu.au>
>CC: biopython at biopython.org
>Subject: Re: [BioPython] biopython installation
>Date: Fri, 6 Jun 2003 12:50:39 -0700
>
>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
>
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