Hi Gubbins developers,
I'm writing you on behalf of the Debian Med team that has the objective
to package all software that might be relevant in the fields of medicine
and biology. We have received a request to package Gubbins from a user
and thus we have put it on our todo list[1].
I noticed that Andrew Page has dropped some packaging stuff into the
download tarball. Since I intended to keep the history I kept his
changelog entries and added Andrew to the Uploader field in
debian/control. Feel free to checkout the current packaging from
the official Debian development platform[2]. Andrew, you are more
than welcome to join the Debian Med team and take part in the effort
to make Gubbins an official Debian package.
When trying to create the package I stumbled upon some issues I would
like to discuss. At first I'm a bit concerned about the usage of
fastml2. The problem is that this is not Free Software and according
to the license that says:
This repository provides some additional functionality to fastml to allow it to
work with Gubbins. The original code is available from
http://fastml.tau.ac.il/source.html and should be your first port of call. To
modify the original code, or use parts of it for other purposes, permission
should be requested. Please contact Tal Pupko: t...@post.tau.ac.il
the fastml author needs to be contacted. I wonder whether you got a
permission from the author for using it in Gubbins. It would be great
to hear that Gubbins is not fully depending from fastml2 and this code
might provide only some extra functionality that in worst case could be
skipped. In any case it might make sense to discuss the license of
fastml with its author - may be he might consider a really free license
which would relax things. One of the results would be that we could
provide an official Debian package of fastml / fastml2.
I found another issue with DendroPy which is listed in the file
INSTALL.md as
* DendroPy ( >=3.11.1 )
While I noticed that this is not part of the (Build-)Depends in the
Debian packaging I started to package it in python-dendropy[3] and
sended a mail about test failures to its authors[4]. When ignoring the
test failures of the python-dendropy and building the packages anyway to
enable a build of Gubbins I noticed the following issue in the test
suite of Gubbins that is most probably connected to the fact that
official DendroPy has released a new major version (4.0.2). I've just
attached the output of the test suite to this mail and may be you could
comment on this.
BTW, the current Debian policy is to refuse software that is Python 2
only. So it would be great if you could either fully migrate to Python
3 or provide support for both Python versions. I have made good
experiences with the script 2to3 to do the Python2 -> Python3
conversion. Please let us know if you are interested in doing this but
might need any help.
Kind regards for providing Gubbins as Free Software
Andreas.
[1] http://blends.debian.org/med/tasks/bio#gubbins
[2] https://anonscm.debian.org/cgit/debian-med/gubbins.git
[3] http://blends.debian.org/med/tasks/bio-dev#python-dendropy
[4] https://lists.debian.org/debian-med/2015/06/msg00063.html
--
http://fam-tille.de
running build_ext
test_filter_out_alignments_with_too_much_missing_data
(test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_get_sequence_names_from_alignment
(test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_number_of_sequences_in_alignment
(test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_reconvert_fasta_file
(test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_reinsert_gaps_into_fasta_file
(test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_get_recombination_files
(test_converging_recombinations.TestConvergingRecombinations) ... ok
test_multiple_files_have_one_match
(test_converging_recombinations.TestConvergingRecombinations) ... ok
test_reading_embl_file
(test_converging_recombinations.TestConvergingRecombinations) ... ok
test_two_files_are_different
(test_converging_recombinations.TestConvergingRecombinations) ... ok
test_two_files_are_same
(test_converging_recombinations.TestConvergingRecombinations) ... ok
test_fasttree_current_tree_name
(test_string_construction.TestStringConstruction) ... ok
test_fasttree_fastml_command (test_string_construction.TestStringConstruction)
... ok
test_fasttree_gubbins_command (test_string_construction.TestStringConstruction)
... ok
test_fasttree_previous_tree_name
(test_string_construction.TestStringConstruction) ... ok
test_fasttree_regex_for_file_deletions
(test_string_construction.TestStringConstruction) ... ok
test_fasttree_tree_building_command
(test_string_construction.TestStringConstruction) ... ok
test_generate_fastml_command (test_string_construction.TestStringConstruction)
... ok
test_raxml_base_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_current_tree_name (test_string_construction.TestStringConstruction)
... ok
test_raxml_fastml_command (test_string_construction.TestStringConstruction) ...
ok
test_raxml_gubbins_command (test_string_construction.TestStringConstruction)
... ok
test_raxml_previous_tree (test_string_construction.TestStringConstruction) ...
ok
test_raxml_previous_tree_name (test_string_construction.TestStringConstruction)
... ok
test_raxml_regex_for_file_deletions
(test_string_construction.TestStringConstruction) ... ok
test_raxml_regex_for_file_deletions_10
(test_string_construction.TestStringConstruction) ... ok
test_raxml_tree_building_command
(test_string_construction.TestStringConstruction) ... ok
test_rename_files (test_string_construction.TestStringConstruction) ... ok
test_starting_files_regex (test_string_construction.TestStringConstruction) ...
ok
test_translation_of_fasttree_filenames_to_final_filenames
(test_string_construction.TestStringConstruction) ... ok
test_translation_of_raxml_filenames_to_final_filenames
(test_string_construction.TestStringConstruction) ... ok
test_create_pairwise_newick_tree
(test_tree_python_methods.TestTreePythonMethods) ... ok
test_filter_out_removed_taxa_from_tree_and_return_new_file
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_has_tree_been_seen_before (test_tree_python_methods.TestTreePythonMethods)
...
/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py:386:
CriticalDeprecationWarning:
# Deprecated since DendroPy 4: Statistics comparing two trees are now
implemented in the 'dendropy.calculate.treecompare' module, and this method's
functionality is available through the 'weighted_robinson_foulds_distance()'
function. For the *unweighted* RF distance, see
'dendropy.calculate.treecompare.symmetric_difference()'.
# Instead of:
# tree1.robinson_foulds_distance(tree2)
# Use:
# from dendropy.calculate import treecompare
# treecompare.weighted_robinson_foulds_distance(tree1, tree2)
return input_tree.robinson_foulds_distance(output_tree)
ERROR
test_internal_node_taxons_removed_when_used_as_starting_tree
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_remove_internal_node_labels
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_reroot_tree (test_tree_python_methods.TestTreePythonMethods) ...
/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py:454:
CriticalDeprecationWarning: Deprecated since DendroPy 4:
'Tree.encode_splits()' will no longer be supported in future releases; use
'Tree.update_bipartitions()' instead
tree.update_splits()
ERROR
test_reroot_tree_at_midpoint (test_tree_python_methods.TestTreePythonMethods)
... ERROR
test_reroot_tree_with_outgroup (test_tree_python_methods.TestTreePythonMethods)
... ERROR
test_reroot_tree_with_outgroups
(test_tree_python_methods.TestTreePythonMethods) ...
/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py:425:
CriticalDeprecationWarning: Deprecated since DendroPy 4:
'Tree.encode_splits()' will no longer be supported in future releases; use
'Tree.update_bipartitions()' instead
tree.update_splits()
ERROR
test_reroot_tree_with_outgroups_all_in_different_clade
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_reroot_tree_with_outgroups_all_in_one_clade
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_reroot_tree_with_outgroups_all_in_one_clade_large
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_reroot_tree_with_outgroups_with_two_mixed_clades
(test_tree_python_methods.TestTreePythonMethods) ... ERROR
test_robinson_foulds_distance (test_tree_python_methods.TestTreePythonMethods)
... ERROR
test_split_all_non_bi_nodes (test_tree_python_methods.TestTreePythonMethods)
... ERROR
test_are_all_sequence_names_unique
(test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_all_sequences_the_same_length
(test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_there_enough_sequences_to_build_a_tree
(test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_does_each_sequence_have_a_name
(test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_does_the_sequence_have_sensible_characters
(test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_input_file_exists (test_validate_fasta_input.TestValidateInputFastaFile)
... ok
test_there_is_variation_in_the_fasta
(test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_all_names_unique
(test_validate_starting_tree.TestValidationOfStartingTree) ... ok
test_do_the_names_match_the_fasta_file
(test_validate_starting_tree.TestValidationOfStartingTree) ... ok
test_is_it_a_valid_newick_tree
(test_validate_starting_tree.TestValidationOfStartingTree) ... ok
======================================================================
ERROR: test_filter_out_removed_taxa_from_tree_and_return_new_file
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 114, in test_filter_out_removed_taxa_from_tree_and_return_new_file
common.GubbinsCommon.filter_out_removed_taxa_from_tree_and_return_new_file('gubbins/tests/data/robinson_foulds_distance_tree1.tre',
temp_working_dir,
['sequence_1','sequence_2','sequence_3','sequence_4','sequence_5'])
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 868, in filter_out_removed_taxa_from_tree_and_return_new_file
tree.prune_taxa_with_labels(taxa_removed, update_splits=True,
delete_outdegree_one=False)
TypeError: prune_taxa_with_labels() got an unexpected keyword argument
'update_splits'
======================================================================
ERROR: test_has_tree_been_seen_before
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 26, in test_has_tree_been_seen_before
assert
common.GubbinsCommon.has_tree_been_seen_before(['gubbins/tests/data/robinson_foulds_distance_tree1.tre','gubbins/tests/data/robinson_foulds_distance_tree1.tre','gubbins/tests/data/robinson_foulds_distance_tree1_dup.tre'],'weighted_robinson_foulds')
== 1
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 407, in has_tree_been_seen_before
current_rf_distance =
GubbinsCommon.robinson_foulds_distance(tree_file_name,tree_files_which_exist[-1])
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 386, in robinson_foulds_distance
return input_tree.robinson_foulds_distance(output_tree)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
5361, in robinson_foulds_distance
return treecompare.weighted_robinson_foulds_distance(self, other_tree)
File "/usr/lib/python2.7/dist-packages/dendropy/calculate/treecompare.py",
line 159, in weighted_robinson_foulds_distance
is_bipartitions_updated=is_bipartitions_updated)
File "/usr/lib/python2.7/dist-packages/dendropy/calculate/treecompare.py",
line 500, in _bipartition_difference
is_bipartitions_updated=is_bipartitions_updated)
File "/usr/lib/python2.7/dist-packages/dendropy/calculate/treecompare.py",
line 406, in _get_length_diffs
raise error.TaxonNamespaceIdentityError(tree1, tree2)
TaxonNamespaceIdentityError: Non-identical taxon namespace references:
<TaxonNamespace object at 0x7ff587b13410> is not <TaxonNamespace object at
0x7ff587b29310>
======================================================================
ERROR: test_internal_node_taxons_removed_when_used_as_starting_tree
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 123, in test_internal_node_taxons_removed_when_used_as_starting_tree
common.GubbinsCommon.filter_out_removed_taxa_from_tree_and_return_new_file('gubbins/tests/data/tree_with_internal_nodes.tre',
temp_working_dir, [])
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 868, in filter_out_removed_taxa_from_tree_and_return_new_file
tree.prune_taxa_with_labels(taxa_removed, update_splits=True,
delete_outdegree_one=False)
TypeError: prune_taxa_with_labels() got an unexpected keyword argument
'update_splits'
======================================================================
ERROR: test_remove_internal_node_labels
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 136, in test_remove_internal_node_labels
common.GubbinsCommon.remove_internal_node_labels_from_tree('gubbins/tests/data/final_tree_with_internal_labels.tre',
'final_tree_with_internal_labels.tre')
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 628, in remove_internal_node_labels_from_tree
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
======================================================================
ERROR: test_reroot_tree (test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 32, in test_reroot_tree
common.GubbinsCommon.reroot_tree('gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_at_sequence_4_actual',
'sequence_4')
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 438, in reroot_tree
GubbinsCommon.reroot_tree_with_outgroup(tree_name, outgroups.split(','))
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
======================================================================
ERROR: test_reroot_tree_at_midpoint
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 106, in test_reroot_tree_at_midpoint
common.GubbinsCommon.reroot_tree_at_midpoint('gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_tree_at_midpoint_actual')
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 507, in reroot_tree_at_midpoint
tree.reroot_at_midpoint(update_splits=True, delete_outdegree_one=False)
TypeError: reroot_at_midpoint() got an unexpected keyword argument
'update_splits'
======================================================================
ERROR: test_reroot_tree_with_outgroup
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 47, in test_reroot_tree_with_outgroup
common.GubbinsCommon.reroot_tree_with_outgroup('gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_at_sequence_4_actual',
['sequence_4'])
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
======================================================================
ERROR: test_reroot_tree_with_outgroups
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 55, in test_reroot_tree_with_outgroups
common.GubbinsCommon.reroot_tree_with_outgroup('gubbins/tests/data/robinson_foulds_distance_tree1.tre.reroot_at_sequence_4_actual',
['sequence_4','sequence_2'])
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
======================================================================
ERROR: test_reroot_tree_with_outgroups_all_in_different_clade
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 77, in test_reroot_tree_with_outgroups_all_in_different_clade
self.reroot_tree_check(outgroups,expected_output_file,expected_monophyletic_outgroup)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 89, in reroot_tree_check
common.GubbinsCommon.reroot_tree_with_outgroup('.tmp.outgroups_input.tre',
outgroups)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
-------------------- >> begin captured stdout << ---------------------
Your outgroups do not form a clade.
Using the first taxon A as the outgroup.
Taxon C is in the clade but not in your list of outgroups.
Your outgroups do not form a clade.
Using the first taxon A as the outgroup.
Taxon C is in the clade but not in your list of outgroups.
--------------------- >> end captured stdout << ----------------------
======================================================================
ERROR: test_reroot_tree_with_outgroups_all_in_one_clade
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 65, in test_reroot_tree_with_outgroups_all_in_one_clade
self.reroot_tree_check(outgroups,expected_output_file,expected_monophyletic_outgroup)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 89, in reroot_tree_check
common.GubbinsCommon.reroot_tree_with_outgroup('.tmp.outgroups_input.tre',
outgroups)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
======================================================================
ERROR: test_reroot_tree_with_outgroups_all_in_one_clade_large
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 71, in test_reroot_tree_with_outgroups_all_in_one_clade_large
self.reroot_tree_check(outgroups,expected_output_file,expected_monophyletic_outgroup)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 89, in reroot_tree_check
common.GubbinsCommon.reroot_tree_with_outgroup('.tmp.outgroups_input.tre',
outgroups)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
======================================================================
ERROR: test_reroot_tree_with_outgroups_with_two_mixed_clades
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 83, in test_reroot_tree_with_outgroups_with_two_mixed_clades
self.reroot_tree_check(outgroups,expected_output_file,expected_monophyletic_outgroup)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 89, in reroot_tree_check
common.GubbinsCommon.reroot_tree_with_outgroup('.tmp.outgroups_input.tre',
outgroups)
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 471, in reroot_tree_with_outgroup
node_label_compose_func=None
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
624, in as_string
self._format_and_write_to_stream(stream=s, schema=schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
3245, in _format_and_write_to_stream
tree_list.write_to_stream(stream, schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/basemodel.py", line
597, in write_to_stream
return self._format_and_write_to_stream(stream=dest, schema=schema,
**kwargs)
File
"/usr/lib/python2.7/dist-packages/dendropy/datamodel/treecollectionmodel.py",
line 706, in _format_and_write_to_stream
writer = dataio.get_writer(schema, **kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/__init__.py", line 68,
in get_writer
writer = writer_type(**kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/newickwriter.py", line
200, in __init__
self.check_for_unused_keyword_arguments(kwargs)
File "/usr/lib/python2.7/dist-packages/dendropy/dataio/ioservice.py", line
57, in check_for_unused_keyword_arguments
attach_taxon_namespace, taxon_namespace =
taxonmodel.process_attached_taxon_namespace_directives(kwargs_dict)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/taxonmodel.py",
line 138, in process_attached_taxon_namespace_directives
raise TypeError("'{}' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace".format(kw))
TypeError: 'taxon_set' is no longer supported as a keyword argument. Use the
instance method 'attach_taxon_namespace()' of the data object instead to bind
the object to a single TaxonNamespace
-------------------- >> begin captured stdout << ---------------------
Your outgroups do not form a clade.
Using the first taxon A as the outgroup.
Taxon E is in the clade but not in your list of outgroups.
Your outgroups do not form a clade.
Using the first taxon A as the outgroup.
Taxon E is in the clade but not in your list of outgroups.
--------------------- >> end captured stdout << ----------------------
======================================================================
ERROR: test_robinson_foulds_distance
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 20, in test_robinson_foulds_distance
assert
common.GubbinsCommon.robinson_foulds_distance('gubbins/tests/data/robinson_foulds_distance_tree1.tre','gubbins/tests/data/robinson_foulds_distance_tree2.tre')
== 17.263494
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 386, in robinson_foulds_distance
return input_tree.robinson_foulds_distance(output_tree)
File "/usr/lib/python2.7/dist-packages/dendropy/datamodel/treemodel.py", line
5361, in robinson_foulds_distance
return treecompare.weighted_robinson_foulds_distance(self, other_tree)
File "/usr/lib/python2.7/dist-packages/dendropy/calculate/treecompare.py",
line 159, in weighted_robinson_foulds_distance
is_bipartitions_updated=is_bipartitions_updated)
File "/usr/lib/python2.7/dist-packages/dendropy/calculate/treecompare.py",
line 500, in _bipartition_difference
is_bipartitions_updated=is_bipartitions_updated)
File "/usr/lib/python2.7/dist-packages/dendropy/calculate/treecompare.py",
line 406, in _get_length_diffs
raise error.TaxonNamespaceIdentityError(tree1, tree2)
TaxonNamespaceIdentityError: Non-identical taxon namespace references:
<TaxonNamespace object at 0x7ff587b136d0> is not <TaxonNamespace object at
0x7ff5879db490>
======================================================================
ERROR: test_split_all_non_bi_nodes
(test_tree_python_methods.TestTreePythonMethods)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/tests/test_tree_python_methods.py",
line 98, in test_split_all_non_bi_nodes
common.GubbinsCommon.reroot_tree_at_midpoint('gubbins/tests/data/non_bi_tree.tre.actual')
File
"/home/tillea/debian-maintain/alioth/debian-med_git/build-area/gubbins-1.3.4/python/gubbins/common.py",
line 507, in reroot_tree_at_midpoint
tree.reroot_at_midpoint(update_splits=True, delete_outdegree_one=False)
TypeError: reroot_at_midpoint() got an unexpected keyword argument
'update_splits'
----------------------------------------------------------------------
Ran 55 tests in 1.764s
FAILED (errors=14)
