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Test failure with FastTree 2.1.9 #102

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tillea opened this issue Sep 14, 2016 · 3 comments
Closed

Test failure with FastTree 2.1.9 #102

tillea opened this issue Sep 14, 2016 · 3 comments

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@tillea
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tillea commented Sep 14, 2016

Hi,

I'm working on the pycogent packaging for Debian. When running the test suite with FastTree version 2.1.9 installed I get:

FAIL: test_build_tree_from_alignment (test_app.test_fasttree.FastTreeTests)

Traceback (most recent call last):
File "/build/python-cogent-1.9/tests/test_app/test_fasttree.py", line 50, in test_build_tree_from_alignment
self.assertEqual(o.Name,e.Name)
File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
(msg or 'Got %s, but expected %s' % (observed, expected))
AssertionError: Got '0.409', but expected '0.466'


Kind regards

     Andreas.
@GavinHuttley
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Hi Andreas,

This is again an issue with being an unsupported version of an application. Unfortunately, @wasade is the maintainer of this and since he has indicated he has no time for updating other app controllers I suspect this applies to this one also.

We would of course welcome any patches you might like to contribute to address this! BUT, please note the python 2 PyCogent series is in maintenance mode.

PyCogent3 (python 3 compatible, available, but not yet released) has dropped all application controllers, amongst numerous other changes. This is because there are now a multitude of alternatives to application controllers than what PyCogent contains.

cheers,

gavin

@tillea
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tillea commented Sep 16, 2016

Hi Gavin,

On Thu, Sep 15, 2016 at 05:23:47PM -0700, GavinHuttley wrote:

This is again an issue with being an unsupported version of an application. Unfortunately, @wasade is the maintainer of this and since he has indicated he has no time for updating other app controllers I suspect this applies to this one also.

We would of course welcome any patches you might like to contribute to address this! BUT, please note the python 2 PyCogent series is in maintenance mode.

Thanks for the explanation - specifically about Pythono 2 series. I was
even wondering whether some Python3 support might be available. For the
moment I deal with this by simply skipping the failed tests and document
what tests have skipped. I think this is slightly better than before
since there was some time when tests were not run at all in the Debian
packaging process.

PyCogent3 (python 3 compatible, available, but not yet released) has dropped all application controllers, amongst numerous other changes. This is because there are now a multitude of alternatives to application controllers than what PyCogent contains.

I would consider uploading a pycogent3 package to Debian experimental.
This might enable early testing for Debian users while clearly stating
that it is not for production.

Kind regards

   Andreas.

http://fam-tille.de

@GavinHuttley
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cogent3 is the port of PyCogent to cogent3. Please see the cogent3 docs for a description of how this is differs from PyCogent.

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