[Biopython-dev] test_Entrez.py fails on Linux?

Peter biopython at maubp.freeserve.co.uk
Fri Jun 20 12:43:55 UTC 2008

On Fri, Jun 20, 2008 at 1:14 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi Peter,
> Thanks for letting me know.
> It turned out that there were two problems with older Python versions (2.3 and 2.4).
> One issue was not in Bio.Entrez but in the test script itself, using a
> feature that is only available in Python 2.5. This is now fixed in CVS.

Good work.

> The second issue is with Python 2.3: It does not copy data files to the
> build directory. Then, when you run "python run_tests.py test_Entrez.py"
> you will get many error messages about missing DTD files. If you run
> "python test_entrez.py" instead, the tests are done from the installed
> Biopython instead of the one in the build directory, and then no errors occur.

I had suspected there was something like this happening on my Windows
machine (which is on python 2.3) but at the time you were still busy
updating the code so I didn't worry about it.

This issue with non-python files in the build directory reminds me of
something Tiago found with his Population Genetics work.  I'd have to
go over the old emails to double check.

> I guess the only way to solve this is to modify run_tests.py to skip
> test_Entrez if Python is version 2.3. Unless somebody else has a better
> suggestion, I will do that.

We could modify setup.py under python 2.3 to make sure these files are
copied.  Is this related to the (reverted) package_data change you
tried recently?


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