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Re: Packaging DendroPy for Debian - test suite failures

Hi Andreas,
The reason for these failures is because these particular tests rely on PAUP* being installed on the system.
We will add some logic that skips the tests if PAUP* is not available and push. Will let you know when this is ready! 

-- jeet

On 6/23/15 3:56 AM, Andreas Tille wrote:

Hi Jeet and Mark,

I'm writing you on behalf of the Debian Med team who tries to integrate
any software that is relevant in medicine and biology for official
Debian.  Your Python module DendroPy would fit nicely into our Biology
Development task and thus we have put it on our todo list and started
to work on it[1].  BTW, I was stumbling upon this module since it is
used in Gubbins[2] which is listed on our todo list for biological
applications[3].

When building packages for Debian it is best practice to run the full
test suite if available.  To do so I fetched the test data from Git and
included it into the packaging.  When running the test suite with these
data unfortunatel 4 out of 790 tests are failing:

...

======================================================================
ERROR: test_group1 (dendropy.test.test_paup.PaupWrapperSplitsParse)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_paup.py", line 212, in test_group1
     expected_num_trees=num_trees-paup_burnin)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_paup.py", line 93, in check_splits_counting
     burnin=paup_burnin,
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 245, in count_splits_from_files
     returncode, stdout, stderr = self._execute_command_sequence()
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 530, in _execute_command_sequence
     returncode, stdout, stderr = PaupService.call(self.commands)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 121, in call
     env=env,
   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
     errread, errwrite)
   File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
     raise child_exception
OSError: [Errno 2] No such file or directory

======================================================================
ERROR: test_basic_split_count_with_incorrect_rootings_raises_error (dendropy.test.test_datamodel_split_bitmasks.SplitCountTest)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_datamodel_split_bitmasks.py", line 214, in test_basic_split_count_with_incorrect_rootings_raises_error
     parser_rooting_interpretation=parser_rooting_interpretation)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_datamodel_split_bitmasks.py", line 165, in check_split_counting
     taxa_definition_filepath=tree_filepath
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 308, in get_split_distribution_from_files
     taxon_namespace=taxon_namespace)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 245, in count_splits_from_files
     returncode, stdout, stderr = self._execute_command_sequence()
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 530, in _execute_command_sequence
     returncode, stdout, stderr = PaupService.call(self.commands)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 121, in call
     env=env,
   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
     errread, errwrite)
   File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
     raise child_exception
OSError: [Errno 2] No such file or directory

======================================================================
ERROR: test_basic_split_count_with_incorrect_weight_treatment_raises_error (dendropy.test.test_datamodel_split_bitmasks.SplitCountTest)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_datamodel_split_bitmasks.py", line 229, in test_basic_split_count_with_incorrect_weight_treatment_raises_error
     dp_ignore_tree_weights=False,
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_datamodel_split_bitmasks.py", line 165, in check_split_counting
     taxa_definition_filepath=tree_filepath
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 308, in get_split_distribution_from_files
     taxon_namespace=taxon_namespace)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 245, in count_splits_from_files
     returncode, stdout, stderr = self._execute_command_sequence()
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 530, in _execute_command_sequence
     returncode, stdout, stderr = PaupService.call(self.commands)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 121, in call
     env=env,
   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
     errread, errwrite)
   File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
     raise child_exception
OSError: [Errno 2] No such file or directory

======================================================================
ERROR: test_basic_split_counting_under_different_rootings (dendropy.test.test_datamodel_split_bitmasks.SplitCountTest)
----------------------------------------------------------------------
Traceback (most recent call last):
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_datamodel_split_bitmasks.py", line 248, in test_basic_split_counting_under_different_rootings
     parser_rooting_interpretation=rooting)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/test/test_datamodel_split_bitmasks.py", line 165, in check_split_counting
     taxa_definition_filepath=tree_filepath
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 308, in get_split_distribution_from_files
     taxon_namespace=taxon_namespace)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 245, in count_splits_from_files
     returncode, stdout, stderr = self._execute_command_sequence()
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 530, in _execute_command_sequence
     returncode, stdout, stderr = PaupService.call(self.commands)
   File "/tmp/buildd/python-dendropy-4.0.2/dendropy/interop/paup.py", line 121, in call
     env=env,
   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
     errread, errwrite)
   File "/usr/lib/python2.7/subprocess.py", line 1335, in _execute_child
     raise child_exception
OSError: [Errno 2] No such file or directory

----------------------------------------------------------------------
Ran 790 tests in 322.660s

FAILED (errors=4)


Could you provide any hints how these tests could pass successfully?

Kind regards and thanks for providing DendroPy as Free Software

       Andreas.


[1] http://blends.debian.org/med/tasks/bio-dev#python-dendropy
[2] https://sanger-pathogens.github.io/gubbins/
[3] http://blends.debian.org/med/tasks/bio#gubbins



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