[Biopython-dev] maintenance release

Jeffrey Chang jchang at jeffchang.com
Mon Sep 15 18:33:03 EDT 2003

Yuck, this was broken.

Previously, the dtd installation was hacked in by modifying the 
Distutils "install" command.  This only gets called from unix, so 
nothing was happening for bdist_wininst.  The dtds were not getting 

I've gone back and reworked the dtd installation so that the dtd 
filenames are passed into the Distutils.setup function as a data file.  
However, the directory layout for python packages in windows and unix 
are different.  I took a best guess at how to do this for windows based 
on what I've seen documented on the web.

Michiel, do you mind checking this again and seeing whether it works on 
windows?  Specifically, I need to know 1) whether the ".dtd" files are 
getting installed, 2) whether they are installed in the right place, 
and 3) where they are installed if they are in the wrong place.


On Saturday, September 13, 2003, at 11:54  PM, Michiel Jan Laurens de 
Hoon wrote:

> I tried to install the CVS version of Biopython with Cygwin and with 
> Windows. On Cygwin, I don't get any errors. On Windows, I am still 
> getting the error with EUtils\DTDs. It wasn't clear to me from CVS if 
> the fix for this error has been committed yet, so maybe I should just 
> try again later.
> --Michiel.
> $ /cygdrive/c/Python23/python setup.py bdist_wininst
> ...
> error: build\bdist.win32\wininst\PURELIB\Bio\EUtils\DTDs: No such file 
> or directory
> Jeffrey Chang wrote:
>> Hello everybody,
>> It's about time to make a release that fixes the Martel install bug.  
>> I've fixed this in the version in the CVS.  Could everyone please try 
>> it out?  If things go smoothly, I'll make a release later this week.  
>> The main changes in this version will be:
>> Martel - The setup script was not detecting that Martel would be 
>> installed, and complained that it was missing.  This is now fixed.
>> EUtils DTDs - Brad fixed this in setup.py.  This will go into the 
>> release.
>> Numeric Python - If numeric is missing, Bio.Cluster does not compile. 
>>  Thus, the setup script now only install Bio.Cluster if Numeric is 
>> installed.  I have documented this dependency in README.
>> There are also some other miscellaneous changes I've documented in 
>> the NEWS file.
>> Also, test_Time.py in the Martel regression tests is failing.  Can 
>> someone fix this?
>> Jeff
>> _______________________________________________
>> Biopython-dev mailing list
>> Biopython-dev at biopython.org
>> http://biopython.org/mailman/listinfo/biopython-dev
> -- 
> Michiel de Hoon, Assistant Professor
> University of Tokyo, Institute of Medical Science
> Human Genome Center
> 4-6-1 Shirokane-dai, Minato-ku
> Tokyo 108-8639
> Japan
> http://bonsai.ims.u-tokyo.ac.jp/~mdehoon
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at biopython.org
> http://biopython.org/mailman/listinfo/biopython-dev

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