[Biopython-dev] [Bug 2361] Test Suite Failures from Martel/Sax with egenix mxTextTools 3.0

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http://bugzilla.open-bio.org/show_bug.cgi?id=2361





------- Comment #36 from mdehoon at ims.u-tokyo.ac.jp  2007-10-18 01:21 EST -------
Looking at the test_GenBankFormat failure again. This is the only test that
fails with the Biopython currently in CVS, using mxTextTools 3.0.

This test is the only test for Bio.expressions. If we remove
test_GenBankFormat, we should deprecate Bio.expressions. Of all the Biopython
tests, only test_format_registry depends on Bio.expressions. This test relies
on the function _load_registries() in Bio/__init__.py. Skipping this function
call in Bio/__init__.py affects no other Biopython test.

So I'd like to suggest the following for the upcoming release:
-) Remove test_GenBankFormat.py and test_format_registry.py
-) Add DeprecationWarnings to Bio.expressions.
-) Skip the call to _load_registries() in Bio/__init__.py

We then have a working Biopython again with the recent mxTextTools, with
minimal disruptive changes to the code.

Any objections?


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