[Biopython-dev] maintenance release
Michiel Jan Laurens de Hoon
mdehoon at ims.u-tokyo.ac.jp
Mon Sep 15 21:41:38 EDT 2003
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
Are these the correct locations? Is there a way to check if EUtils is
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
> 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.
>> $ /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
>>> 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?
>>> Biopython-dev mailing list
>>> Biopython-dev at biopython.org
>> 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
>> Biopython-dev mailing list
>> Biopython-dev at biopython.org
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
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