[med-svn] r22792 - trunk/packages/python-cogent/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Wed Sep 14 15:17:16 UTC 2016
Author: tille
Date: 2016-09-14 15:17:15 +0000 (Wed, 14 Sep 2016)
New Revision: 22792
Removed:
trunk/packages/python-cogent/trunk/debian/patches/debug_tests.patch
trunk/packages/python-cogent/trunk/debian/patches/skip_random_test_to_enable_testsuite.patch
Modified:
trunk/packages/python-cogent/trunk/debian/patches/series
Log:
Drop unused patches
Deleted: trunk/packages/python-cogent/trunk/debian/patches/debug_tests.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/debug_tests.patch 2016-09-14 15:05:57 UTC (rev 22791)
+++ trunk/packages/python-cogent/trunk/debian/patches/debug_tests.patch 2016-09-14 15:17:15 UTC (rev 22792)
@@ -1,163 +0,0 @@
---- a/tests/alltests.py
-+++ b/tests/alltests.py
-@@ -117,83 +117,83 @@ def suite():
- 'test_maths.test_unifrac.test_fast_tree',
- 'test_maths.test_unifrac.test_fast_unifrac',
- 'test_motif.test_util',
-- 'test_parse.test_aaindex',
-- 'test_parse.test_agilent_microarray',
-- 'test_parse.test_binary_sff',
-- 'test_parse.test_blast',
-- 'test_parse.test_bowtie',
-- 'test_parse.test_bpseq',
-- 'test_parse.test_cigar',
-- 'test_parse.test_clustal',
-- 'test_parse.test_column',
-- 'test_parse.test_comrna',
-- 'test_parse.test_consan',
-- 'test_parse.test_cove',
-- 'test_parse.test_ct',
-- 'test_parse.test_cut',
-- 'test_parse.test_cutg',
-- 'test_parse.test_dialign',
-- 'test_parse.test_ebi',
-- 'test_parse.test_fasta',
-- 'test_parse.test_fastq',
-- 'test_parse.test_gbseq',
-- 'test_parse.test_gibbs',
-- 'test_parse.test_genbank',
-- 'test_parse.test_gff',
-- 'test_parse.test_greengenes',
-- 'test_parse.test_ilm',
-- 'test_parse.test_illumina_sequence',
-- 'test_parse.test_locuslink',
-- 'test_parse.test_mage',
-- 'test_parse.test_meme',
-- 'test_parse.test_msms',
-- 'test_parse.test_ncbi_taxonomy',
-- 'test_parse.test_nexus',
-- 'test_parse.test_nupack',
-- 'test_parse.test_pdb',
-- 'test_parse.test_psl',
-- 'test_parse.test_structure',
-- 'test_parse.test_pamlmatrix',
-- 'test_parse.test_phylip',
-- 'test_parse.test_pknotsrg',
-- 'test_parse.test_rdb',
-- 'test_parse.test_record',
-- 'test_parse.test_record_finder',
-- 'test_parse.test_rfam',
-- 'test_parse.test_rnaalifold',
-- 'test_parse.test_rna_fold',
-- 'test_parse.test_rnaview',
-- 'test_parse.test_rnaforester',
-- 'test_parse.test_sprinzl',
-- 'test_parse.test_tinyseq',
-- 'test_parse.test_tree',
-- 'test_parse.test_unigene',
-- 'test_seqsim.test_analysis',
-- 'test_seqsim.test_birth_death',
-- 'test_seqsim.test_markov',
-- 'test_seqsim.test_microarray',
-- 'test_seqsim.test_microarray_normalize',
-- 'test_seqsim.test_randomization',
-- 'test_seqsim.test_searchpath',
-- 'test_seqsim.test_sequence_generators',
-- 'test_seqsim.test_tree',
-- 'test_seqsim.test_usage',
-- 'test_struct.test_knots',
-- 'test_struct.test_pairs_util',
-- 'test_struct.test_rna2d',
-- 'test_struct.test_asa',
-- 'test_struct.test_contact',
-- 'test_struct.test_annotation',
-- 'test_struct.test_selection',
-- 'test_struct.test_manipulation',
-- 'test_util.test_unit_test',
-- 'test_util.test_array',
-- 'test_util.test_dict2d',
-- 'test_util.test_misc',
-- 'test_util.test_organizer',
-- 'test_util.test_recode_alignment',
-- 'test_util.test_table.rst',
-- 'test_util.test_transform',
-+# 'test_parse.test_aaindex',
-+# 'test_parse.test_agilent_microarray',
-+# 'test_parse.test_binary_sff',
-+# 'test_parse.test_blast',
-+# 'test_parse.test_bowtie',
-+# 'test_parse.test_bpseq',
-+# 'test_parse.test_cigar',
-+# 'test_parse.test_clustal',
-+# 'test_parse.test_column',
-+# 'test_parse.test_comrna',
-+# 'test_parse.test_consan',
-+# 'test_parse.test_cove',
-+# 'test_parse.test_ct',
-+# 'test_parse.test_cut',
-+# 'test_parse.test_cutg',
-+# 'test_parse.test_dialign',
-+# 'test_parse.test_ebi',
-+# 'test_parse.test_fasta',
-+# 'test_parse.test_fastq',
-+# 'test_parse.test_gbseq',
-+# 'test_parse.test_gibbs',
-+# 'test_parse.test_genbank',
-+# 'test_parse.test_gff',
-+# 'test_parse.test_greengenes',
-+# 'test_parse.test_ilm',
-+# 'test_parse.test_illumina_sequence',
-+# 'test_parse.test_locuslink',
-+# 'test_parse.test_mage',
-+# 'test_parse.test_meme',
-+# 'test_parse.test_msms',
-+# 'test_parse.test_ncbi_taxonomy',
-+# 'test_parse.test_nexus',
-+# 'test_parse.test_nupack',
-+# 'test_parse.test_pdb',
-+# 'test_parse.test_psl',
-+# 'test_parse.test_structure',
-+# 'test_parse.test_pamlmatrix',
-+# 'test_parse.test_phylip',
-+# 'test_parse.test_pknotsrg',
-+# 'test_parse.test_rdb',
-+# 'test_parse.test_record',
-+# 'test_parse.test_record_finder',
-+# 'test_parse.test_rfam',
-+# 'test_parse.test_rnaalifold',
-+# 'test_parse.test_rna_fold',
-+# 'test_parse.test_rnaview',
-+# 'test_parse.test_rnaforester',
-+# 'test_parse.test_sprinzl',
-+# 'test_parse.test_tinyseq',
-+# 'test_parse.test_tree',
-+# 'test_parse.test_unigene',
-+# 'test_seqsim.test_analysis',
-+# 'test_seqsim.test_birth_death',
-+# 'test_seqsim.test_markov',
-+# 'test_seqsim.test_microarray',
-+# 'test_seqsim.test_microarray_normalize',
-+# 'test_seqsim.test_randomization',
-+# 'test_seqsim.test_searchpath',
-+# 'test_seqsim.test_sequence_generators',
-+# 'test_seqsim.test_tree',
-+# 'test_seqsim.test_usage',
-+# 'test_struct.test_knots',
-+# 'test_struct.test_pairs_util',
-+# 'test_struct.test_rna2d',
-+# 'test_struct.test_asa',
-+# 'test_struct.test_contact',
-+# 'test_struct.test_annotation',
-+# 'test_struct.test_selection',
-+# 'test_struct.test_manipulation',
-+# 'test_util.test_unit_test',
-+# 'test_util.test_array',
-+# 'test_util.test_dict2d',
-+# 'test_util.test_misc',
-+# 'test_util.test_organizer',
-+# 'test_util.test_recode_alignment',
-+# 'test_util.test_table.rst',
-+# 'test_util.test_transform',
- ]
-
- try:
Modified: trunk/packages/python-cogent/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/series 2016-09-14 15:05:57 UTC (rev 22791)
+++ trunk/packages/python-cogent/trunk/debian/patches/series 2016-09-14 15:17:15 UTC (rev 22792)
@@ -1,9 +1,6 @@
-## Test suite does not run properly the patches are just for debugging and not activated in the release package
-# skip_random_test_to_enable_testsuite.patch
accept_newer_cdhit.patch
fix_python_shebang_line.patch
parsinsert_not_in_caps.patch
fasttree_not_in_caps.patch
raxml_unsupported_version.patch
-# debug_tests.patch
cd-hit-test.patch
Deleted: trunk/packages/python-cogent/trunk/debian/patches/skip_random_test_to_enable_testsuite.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/skip_random_test_to_enable_testsuite.patch 2016-09-14 15:05:57 UTC (rev 22791)
+++ trunk/packages/python-cogent/trunk/debian/patches/skip_random_test_to_enable_testsuite.patch 2016-09-14 15:17:15 UTC (rev 22792)
@@ -1,67 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 25 Apr 2014 20:40:39 +0200
-Description: It was realised that the test suite is crashing
- uncontroled. Some investigation has shown that a remaining set
- of about five tests is capable to trigger this crash. If you
- remove a random one of these five tests the crash silently
- disappears.
-
---- a/tests/test_struct/test_rna2d.py
-+++ b/tests/test_struct/test_rna2d.py
-@@ -1033,31 +1033,31 @@ class ViennaNodeTests(TestCase):
- op[4].extendHelix(Rna('AAACCCAAAAGGGAA'))
- self.assertEqual(str(op), '...(((....)))..')
-
-- def test_extendHelices(self):
-- """StructureNode extendHelices should extend all helices"""
-- e = ViennaStructure('........')
-- t = e.toTree()
-- t.extendHelices(Rna('CCCCCCCCCC'))
-- self.assertEqual(str(t), e)
-- #no pairs if sequence can't form them
-- s = ViennaStructure('(.....(...)..)...((.....))...')
-- r = Rna('AAAAAAAAAAAAAAAAAAAAAAAAAAAAA')
-- t = s.toTree()
-- t.extendHelices(r)
-- self.assertEqual(str(t), s)
-- #should be able to extend a single helix
-- s = ViennaStructure('(.....(...)..)...((.....))...')
-- r = Rna('CAAAAACAAAGAAGCCCCCCCAGGGGGGG')
-- t = s.toTree()
-- t.extendHelices(r)
-- self.assertEqual(str(t), '(.....(...)..)((((((...))))))')
-- #should be able to extend multiple helices
-- s = ViennaStructure('(.....(...)..)...((.....))...')
-- r = Rna('AAAAACCCAGGGUUCCCCCAUAAAGGGAA')
-- t = s.toTree()
-- t.extendHelices(r)
-- self.assertEqual(str(t), '((...((...))))..(((.....)))..')
--
-+# def test_extendHelices(self):
-+# """StructureNode extendHelices should extend all helices"""
-+# e = ViennaStructure('........')
-+# t = e.toTree()
-+# t.extendHelices(Rna('CCCCCCCCCC'))
-+# self.assertEqual(str(t), e)
-+# #no pairs if sequence can't form them
-+# s = ViennaStructure('(.....(...)..)...((.....))...')
-+# r = Rna('AAAAAAAAAAAAAAAAAAAAAAAAAAAAA')
-+# t = s.toTree()
-+# t.extendHelices(r)
-+# self.assertEqual(str(t), s)
-+# #should be able to extend a single helix
-+# s = ViennaStructure('(.....(...)..)...((.....))...')
-+# r = Rna('CAAAAACAAAGAAGCCCCCCCAGGGGGGG')
-+# t = s.toTree()
-+# t.extendHelices(r)
-+# self.assertEqual(str(t), '(.....(...)..)((((((...))))))')
-+# #should be able to extend multiple helices
-+# s = ViennaStructure('(.....(...)..)...((.....))...')
-+# r = Rna('AAAAACCCAGGGUUCCCCCAUAAAGGGAA')
-+# t = s.toTree()
-+# t.extendHelices(r)
-+# self.assertEqual(str(t), '((...((...))))..(((.....)))..')
-+
- def test_fitSeq(self):
- """StructureNode fitSeq should adjust structure to match sequence"""
- #this is just a minimal test, since we know that both breakBadPairs()
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