[Biopython-dev] maintenance release

[Michiel Jan Laurens de Hoon]

I tried this on Windows. I don't get any error messages when compiling 
and building the installer.

The *.dtd files get installed in C:\Python23\Bio\EUtils\DTDs, while 
C:\Python23\Lib\site-packages\Bio\EUtils\DTDs contains the .py, .pyc, 
and .pyo files.

However, on Cygwin the *.dtd and *.py, *.pyc files both get installed 
into /usr/local/lib/python2.3/site-packages/Bio/EUtils/DTDs.

Are these the correct locations? Is there a way to check if EUtils is 
working correctly?

--Michiel

Jeffrey Chang wrote:
> 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 
> installed.
> 
> 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.
> 
> Thanks,
> Jeff
> 
> 
> 
> 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
> 
> 
> 
> 

-- 
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