debian/control

@@ -20,22 +20,6 @@ Build-Depends: debhelper-compat (= 12),
                python3-nbsphinx,
                python3-sphinxcontrib.bibtex,
                cython3,
-               ncbi-blast+-legacy,
-               bwa [any-amd64],
-               cd-hit,
-               cdbfasta,
-               clearcut,
-               clustalw,
-               dialign,
-               fasttree,
-               infernal [any-amd64 any-i386],
-               mafft,
-               mothur [!s390x],
-               muscle,
-               parsinsert,
-               raxml [any-amd64 any-i386],
-               rdp-classifier,
-               rtax,
                pandoc
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-cogent
@@ -48,28 +32,14 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${python3:Depends},
          python3-matplotlib,
-         python3-pandas
+         python3-pandas,
          python3-plotly,
          python3-scitrack,
          python3-tqdm,
          python3-tinydb
 Recommends: ncbi-blast+-legacy,
-            bwa [any-amd64],
-            cd-hit,
-            clearcut,
-            dialign,
-            muscle
+            dialign
 Suggests: python-cogent-doc,
-          cdbfasta,
-          clustalw,
-          fasttree,
-          infernal [any-amd64 any-i386],
-          mafft,
-          mothur [!s390x],
-          parsinsert,
-          raxml [any-amd64 any-i386],
-          rdp-classifier,
-          rtax
 Description: framework for genomic biology
  PyCogent is a software library for genomic biology. It is a fully
  integrated and thoroughly tested framework for:

debian/patches/_series_

-accept_newer_cdhit.patch
-fix_python_shebang_line.patch
-parsinsert_not_in_caps.patch
-fasttree_not_in_caps.patch
-raxml_unsupported_version.patch
-cd-hit-test.patch
-rdp_classifier.patch
-skip_weak_tests.patch
-adapt_to_ncbi-data_201609.patch
-ignore_numpy_test_issue.patch
-usr_bin_ls.patch
-numpy_xor.patch
-numpy-doctests.patch
-privacy.patch
-matplotlib-2.2.3.patch
-sphinx.ext.pngmath.patch

debian/patches/accept_newer_cdhit.patch

-Author: Tim Booth <tbooth@ceh.ac.uk>
-Last-Changed: Fri, 25 Apr 2014 17:27:42 +0100
-Description: Get Cogent to work with newer CD-HIT that doesn't leave
- a temporary file sitting around.  This patch has only been quickly tested and
- there may be deeper issues.
-
---- PyCogent-1.5.3.orig/cogent/app/cd_hit.py
-+++ PyCogent-1.5.3/cogent/app/cd_hit.py
-@@ -257,7 +257,10 @@
-     # perform cleanup
-     res.cleanUp()
-     shutil.rmtree(working_dir)
--    remove(params['-o'] + '.bak.clstr')
-+    try:
-+	remove(params['-o'] + '.bak.clstr')
-+    except OSError:
-+	pass #maybe there was no file
- 
-     return remapped_clusters
- 
-@@ -299,7 +302,10 @@
-     # perform cleanup
-     res.cleanUp()
-     shutil.rmtree(working_dir)
--    remove(params['-o'] + '.bak.clstr')
-+    try:
-+	remove(params['-o'] + '.bak.clstr')
-+    except OSError:
-+	pass #maybe there was no file
- 
-     return SequenceCollection(new_seqs, MolType=moltype)
- 

debian/patches/adapt_to_ncbi-data_201609.patch

-Description: Since ncbi-tools6 6.1.20160908-1 some blast relatet tests
- are failing at package Build time.  These tests are deleted here.
- .
- Without the patches in tests/test_app/test_blast.py the build hangs totally
- and needs to be interrupted by ^C.
- .
- The patches in tests/test_app/test_formatdb.py lead to regular test suite
- failures with proper output of the problem.
-Bug-Debian: https://bugs.debian.org/847082
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 05 Dec 2016 13:23:40 +0100
-
---- a/tests/test_app/test_blast.py
-+++ b/tests/test_app/test_blast.py
-@@ -174,71 +174,6 @@ MSGNIKKIVEPNSGIDYSLEKDFKIFTLSKELPITTYPSY
-         self.assertEqualItems(k, \
-             ['ece:Z4181','ecs:ECs3717','spt:SPA2730','cvi:CV2421','ece:Z4182'])
- 
--    def test_ids_from_seq_lower_threshold(self):
--        "ids_from_seq_lower_threshold returns psiblast hits, decreasing sens"
--        bdb_seqs = self.fasta_recs
--        f = open('test_bdb', 'w')
--        f.write(bdb_seqs)
--        f.close()
--        temp = popen('formatdb -i test_bdb -o T -p T')
--        params = {'-j':2,
--                '-d':'test_bdb'}
--        query = self.query_1.split('\n')
--        app = PsiBlast(params=params, 
--                InputHandler='_input_as_lines')
--        #the command below should result in finding itself and 2554
--        #it should run for max_iterations
--        result = ids_from_seq_lower_threshold(query, n=12, \
--                max_iterations=4, app=app, core_threshold=1e-50, \
--                lower_threshold=1e-20, step=10000)
--        self.assertEqual(result[0],\
--                [('gi|100002553', '0.0'), ('gi|100002554', '0.0')])
--        self.assertEqual(result[1], 4)
--        #if n=2, it should find the same sequences but only run for 1 iteration
--        #since it would hit n after the first blast search
--        result = ids_from_seq_lower_threshold(query, n=2, \
--                max_iterations=4, app=app, core_threshold=1e-50, \
--                lower_threshold=1e-20, step=10000)
--        self.assertEqual(result[0],\
--                [('gi|100002553', '0.0'), ('gi|100002554', '0.0')])
--        self.assertEqual(result[1], 1)
--        query = self.query_2.split('\n')
--        #query_2_s e-value for itself is 9e-47, it should not be found
--        #with the lower_threshold set to 1e-48
--        result = ids_from_seq_lower_threshold(query, n=12, \
--                max_iterations=4, app=app, core_threshold=1e-50, \
--                lower_threshold=1e-48, step=10000)
--        self.assertEqual(result[0], [])
--        #it also should not be found if the max_iterations is set to 1
--        result = ids_from_seq_lower_threshold(query, n=12, \
--                max_iterations=1, app=app, core_threshold=1e-50, \
--                lower_threshold=1e-20, step=10000)
--        self.assertEqual(result[0], [])
--        for fname in ['formatdb.log'] + glob('test_bdb*'):
--            remove(fname)
--
--    def test_psiblast_n_neighbors(self):
--        "psiblast_n_neighbors psiblasts and stops when n neighbors are reached"
--        bdb_seqs = self.fasta_recs
--        f = open('test_bdb', 'w')
--        f.write(bdb_seqs)
--        f.close()
--        temp = popen('formatdb -i test_bdb -o T -p T')
--        params = {'-j':11}
--        lines = bdb_seqs.split('\n')
--        results = psiblast_n_neighbors(lines, n=12, blast_db='test_bdb', \
--                method='lower_threshold', params=params,\
--                core_threshold=1e-50, step=10000)
--        #there should be 10 result entries since there were 10 queries
--        self.assertEqual(len(results), 10)
--        for i in results:
--            #each query should at least find itself
--            self.failUnless(len(results[i][0]) >= 1)
--            #each query should iterate 8 times since it can never reach max
--            self.assertEqual(results[i][1], 11)
--        for fname in ['formatdb.log'] + glob('test_bdb*'):
--            remove(fname)
--        
- 
- def wrap_qmes(qmes):
-     """Converts qmes into a dict of {q:{m:e}}"""
---- a/tests/test_app/test_formatdb.py
-+++ b/tests/test_app/test_formatdb.py
-@@ -76,120 +76,6 @@ class FormatDbTests(TestCase):
-             self.assertFalse(exists(outpath),\
-              "%s was not cleaned up." % outpath)
-     
--    def test_blast_against_new_db(self):
--        """Formatdb: blastall against a newly created DB functions as expected
--        """
--        fdb = FormatDb(WorkingDir='/tmp')
--        result = fdb(self.in_seqs1_fp)
--        blast_res = blastn(self.test_seq,blast_db=self.in_seqs1_fp)
--        result.cleanUp()
--        
--        # Test that a blast result was returned
--        self.assertTrue('s1' in blast_res,\
--         "Not getting any blast results.")
--        # Test that the sequence we expect was a good blast hit
--        subject_ids = [r['SUBJECT ID'] for r in blast_res['s1'][0]]
--        self.assertTrue('11472384' in subject_ids,\
--         "Not getting expected blast results.")
--         
--    def test_build_blast_db_from_seqs(self):
--        """build_blast_db_from_seqs convenience function works as expected
--        """
--        blast_db, db_files = build_blast_db_from_seqs(self.in_seqs1,output_dir='/tmp')
--        self.assertTrue(blast_db.startswith('/tmp/Blast_tmp_db'))
--        self.assertTrue(blast_db.endswith('.fasta'))
--        expected_db_files = set([blast_db + ext\
--         for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])
--        self.assertEqual(set(db_files),expected_db_files)
--        
--        # result returned when blasting against new db
--        self.assertEqual(\
--            len(blastn(self.test_seq,blast_db=blast_db)),1)
--            
--        # Make sure all db_files exist
--        for fp in db_files:
--            self.assertTrue(exists(fp))
--        
--        # Remove all db_files exist   
--        remove_files(db_files)
--        
--        # Make sure nothing weird happened in the remove
--        for fp in db_files:
--            self.assertFalse(exists(fp))
--        
--    def test_build_blast_db_from_fasta_path(self):
--        """build_blast_db_from_fasta_path convenience function works as expected
--        """
--        blast_db, db_files = \
--         build_blast_db_from_fasta_path(self.in_seqs1_fp)
--        self.assertEqual(blast_db,self.in_seqs1_fp)
--        expected_db_files = set([self.in_seqs1_fp + ext\
--         for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])
--        self.assertEqual(set(db_files),expected_db_files)
--
--        # result returned when blasting against new db
--        self.assertEqual(\
--            len(blastn(self.test_seq,blast_db=blast_db)),1)
--
--        # Make sure all db_files exist
--        for fp in db_files:
--            self.assertTrue(exists(fp))
--        
--        # Remove all db_files exist   
--        remove_files(db_files)
--        
--        # Make sure nothing weird happened in the remove
--        for fp in db_files:
--            self.assertFalse(exists(fp))
--            
--    def test_build_blast_db_from_fasta_path_aln(self):
--        """build_blast_db_from_fasta_path works with alignment as input
--        """
--        blast_db, db_files = build_blast_db_from_fasta_path(self.in_aln1_fp)
--        self.assertEqual(blast_db,self.in_aln1_fp)
--        expected_db_files = set([blast_db + ext\
--         for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])
--        self.assertEqual(set(db_files),expected_db_files)
--        # result returned when blasting against new db
--        self.assertEqual(\
--            len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)
--        
--        # Make sure all db_files exist
--        for fp in db_files:
--            self.assertTrue(exists(fp))
--        
--        # Remove all db_files exist   
--        remove_files(db_files)
--        
--        # Make sure nothing weird happened in the remove
--        for fp in db_files:
--            self.assertFalse(exists(fp))
--            
--    def test_build_blast_db_from_fasta_file(self):
--        """build_blast_db_from_fasta_file works with open files as input
--        """
--        blast_db, db_files = \
--         build_blast_db_from_fasta_file(open(self.in_aln1_fp),output_dir='/tmp/')
--        self.assertTrue(blast_db.startswith('/tmp/BLAST_temp_db'))
--        self.assertTrue(blast_db.endswith('.fasta'))
--        expected_db_files = set([blast_db] + [blast_db + ext\
--         for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']])
--        self.assertEqual(set(db_files),expected_db_files)
--        # result returned when blasting against new db
--        self.assertEqual(\
--            len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1)
--        
--        # Make sure all db_files exist
--        for fp in db_files:
--            self.assertTrue(exists(fp))
--        
--        # Remove all db_files exist   
--        remove_files(db_files)
--        
--        # Make sure nothing weird happened in the remove
--        for fp in db_files:
--            self.assertFalse(exists(fp))
--        
- 
- in_seqs1 = """>11472286
- GATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGAACACTTTGTGTTTTGAGTTAATAGTTCGATAGTAGATAGTAAATAGTGAACACTATGAACTAGTAAACTATTTAACTAGAAACTCTTAAACGCAGAGCGTTTAGTGGCGAACGGGTGAGTAATACATTGGTATCTACCTCGGAGAAGGACATAGCCTGCCGAAAGGTGGGGTAATTTCCTATAGTCCCCGCACATATTTGTTCTTAAATCTGTTAAAATGATTATATGTTTTATGTTTATTTGATAAAAAGCAGCAAGACAAATGAGTTTTATATTGGTTATACAGCAGATTTAAAAAATAGAATTAGGTCTCATAATCAGGGAGAAAACAAATCAACTAAATCTAAAATACCTTGGGAATTGGTTTACTATGAAGCCTACAAAAACCAAACATCAGCAAGGGTTAGAGAATCAAAGTTGAAACATTATGGGCAATCATTAACTAGACTTAAGAGAAGAATTGGTTTTTGAGAACAAATATGTGCGGGGTAAAGCAGCAATGCGCTCCGAGAGGAACCTCTGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGACGGGTAGCTGGTGTGAGAGCACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCACAATGGGCGCAAGCCTGATGGAGCAATGCCGCGTGAAGGATGAAGATTTTCGGATTGTAAACTTCTTTTAAGTAGGAAGATTATGACGGTACTACTTGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATTACTGGGCGTAAAGCGTGTGTAGGTGGTTTATTAAGTTAAATGTTAAATTTTCAGGCTTAACTTGGAAACCGCATTTAATACTGGTAGACTTTGAGGACAAGAGAGGCAGGCGGAATTAGCGGAGTAGCGGTGAAATGCGTAGATATCGCTAAGAACACCAATGGCGAAGGCAGCCTGCTGGTTTGCACCTGACACTGAGATACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGTCACTAGCTGTTAGGGGCTCGACCCCTTTAGTAGCGAAGCTAACGCGTTAAGTGACCCGCCTGGGGAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAACGTGAGGTTTAATTCGTCTCTAAGCGAAAAACCTTACCGAGGCTTGACATCTCCGGAAGACCTTAGAAATAAGGTTGTGCCCGAAAGGGAGCCGGATGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTCGGTTAAGTCCGTTAACGAGCGCAACCCTTGCTGTGTGTTGTATTTTTCACACAGGACTATCCTGGTCAACAGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCTCTTACGCCTCGGGCTACACTCGCGTTACAATGGCCGGTACAATGGGCTGCCAACTCGTAAGGGGGAGCTAATCCCATCAAAACCGGTCCCAGTTCGGATTGAGGGCTGCAATTCGCCCTCATGAAGTCGGAATCGCTAGTAACCGCGAATCAGCACGTCGCGGTGAATGCGTTCTCGGGTCTTGTACACACTGCCCGTCACACCACGAAAGTTAGTAACGCCCGAAGTGCCCTGTATGGGGTCCTAAGGTGGGGCTAGCGATTGGGGTG

debian/patches/cd-hit-test.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 14 Sep 2016 16:43:40 +0200
-Description: Upstream confirmed that the app controller only supports
- cd-hit 3.1.1.
- .
- See https://github.com/pycogent/pycogent/issues/101
- .
- Exclude some tests for the moment since otherwise there is no chance
- to get the new cogent version uploaded which in turn fixes lots of
- other bugs
-
---- a/tests/test_app/test_cd_hit.py
-+++ b/tests/test_app/test_cd_hit.py
-@@ -46,11 +46,6 @@ class CD_HIT_Tests(TestCase):
-         rmdir('/tmp/cdhit_test')
-         rmdir('/tmp/cdhit_test2')
- 
--    def test_cdhit_from_seqs(self):
--        """CD_HIT should return expected seqs"""
--        res = cdhit_from_seqs(protein_seqs, PROTEIN, {'-c':0.8})
--        self.assertEqual(res.toFasta(), protein_expected)
--
- class CD_HIT_EST_Tests(TestCase):
-     """Tests for the CD-HIT application controller"""
- 
-@@ -82,17 +77,6 @@ class CD_HIT_EST_Tests(TestCase):
-         rmdir('/tmp/cdhitest_test')
-         rmdir('/tmp/cdhitest_test2')
- 
--    def test_cdhit_from_seqs(self):
--        """CD_HIT should return expected seqs"""
--        res = cdhit_from_seqs(dna_seqs, DNA, {'-c':0.8})
--        self.assertEqual(res.toFasta(), dna_expected)
--        
--    def test_cdhit_from_seqs_synonym(self):
--        """CD_HIT should return expected seqs with -c synonym"""
--        res = cdhit_from_seqs(dna_seqs, DNA, {'Similarity':0.8})
--        self.assertEqual(res.toFasta(), dna_expected)
--        
--
- class CD_HIT_SupportMethodTests(TestCase):
-     """Tests for supporting methods"""
-     def test_clean_cluster_seq_id(self):
-@@ -110,16 +94,6 @@ class CD_HIT_SupportMethodTests(TestCase
-         obs = parse_cdhit_clstr_file(data)
-         self.assertEqual(obs, exp)
- 
--    def test_cdhit_clusters_from_seqs(self):
--        """cdhit_clusters_from_seqs returns expected clusters"""
--        exp = [['cdhit_test_seqs_0'],['cdhit_test_seqs_1'],\
--               ['cdhit_test_seqs_2'],['cdhit_test_seqs_3'],\
--               ['cdhit_test_seqs_4'],['cdhit_test_seqs_5'],\
--               ['cdhit_test_seqs_6','cdhit_test_seqs_8'],\
--               ['cdhit_test_seqs_7'],['cdhit_test_seqs_9']]
--        obs = cdhit_clusters_from_seqs(dna_seqs, DNA)
--        self.assertEqual(obs, exp)
--
- dna_seqs = """>cdhit_test_seqs_0
- AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
- >cdhit_test_seqs_1

debian/patches/fasttree_not_in_caps.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 25 Apr 2014 21:27:42 +0100
-Description: make script compatible with spelling of Debian's
- fasttree package
- .
- One test had to be excluded.  This is reported upstream as issue #102
-
---- a/cogent/app/fasttree.py
-+++ b/cogent/app/fasttree.py
-@@ -25,7 +25,7 @@ __status__ = "Development"
- class FastTree(CommandLineApplication):
-     """FastTree application Controller"""
- 
--    _command = 'FastTree'
-+    _command = 'fasttree'
-     _input_handler = '_input_as_multiline_string'
-     _parameters = {
-             '-quiet':FlagParameter('-',Name='quiet'),
---- a/cogent/app/fasttree_v1.py
-+++ b/cogent/app/fasttree_v1.py
-@@ -20,7 +20,7 @@ __status__ = "Development"
- class FastTree(CommandLineApplication):
-     """FastTree application Controller"""
- 
--    _command = 'FastTree'
-+    _command = 'fasttree'
-     _input_handler = '_input_as_multiline_string'
-     _parameters = {
-             '-quiet':FlagParameter('-',Name='quiet'),
---- a/tests/test_app/test_fasttree.py
-+++ b/tests/test_app/test_fasttree.py
-@@ -27,15 +27,15 @@ class FastTreeTests(TestCase):
-     def test_base_command(self):
-         app = FastTree()
-         self.assertEqual(app.BaseCommand, \
--                         ''.join(['cd "',getcwd(),'/"; ','FastTree']))
-+                         ''.join(['cd "',getcwd(),'/"; ','fasttree']))
-         app.Parameters['-nt'].on()
-         self.assertEqual(app.BaseCommand, \
--                         ''.join(['cd "',getcwd(),'/"; ','FastTree -nt']))
-+                         ''.join(['cd "',getcwd(),'/"; ','fasttree -nt']))
- 
-     def test_change_working_dir(self):
-         app = FastTree(WorkingDir='/tmp/FastTreeTest')
-         self.assertEqual(app.BaseCommand, \
--                       ''.join(['cd "','/tmp/FastTreeTest','/"; ','FastTree']))
-+                       ''.join(['cd "','/tmp/FastTreeTest','/"; ','fasttree']))
-         rmtree('/tmp/FastTreeTest')
- 
-     def test_build_tree_from_alignment(self):
-@@ -47,8 +47,9 @@ class FastTreeTests(TestCase):
-                 self.assertFloatEqual(o.Length,e.Length)
-         except AssertionError:
-             for o,e in zip(tree.traverse(), DndParser(exp_tree_201).traverse()):
--                self.assertEqual(o.Name,e.Name)
--                self.assertFloatEqual(o.Length,e.Length)
-+                # self.assertEqual(o.Name,e.Name) # --> AssertionError: Got '0.409', but expected '0.466' see issue #102
-+                # self.assertFloatEqual(o.Length,e.Length) # --> AssertionError: Got 6e-09, but expected 0.00015 (diff was -0.00014999399999999997)
-+                pass
- test_seqs = """>test_set1_0
- GGTAGATGGGACTACCTCATGACATGAAACTGCAGTCTGTTCTTTTATAGAAGCTTCATACTTGGAGATGTATACTATTA
- CTTAGGACTATGGAGGTATA

debian/patches/fix_python_shebang_line.patch

-Author: Steffen Moeller <moeller@debian.org>
-Description: fix path to python interpreter
---- PyCogent-1.5.3.orig/cogent/align/dp_calculation.py
-+++ PyCogent-1.5.3/cogent/align/dp_calculation.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env/python
-+#!/usr/bin/python
- 
- from cogent.maths.markov import SiteClassTransitionMatrix
- from cogent.recalculation.definition import PositiveParamDefn, \
---- PyCogent-1.5.3.orig/cogent/data/molecular_weight.py
-+++ PyCogent-1.5.3/cogent/data/molecular_weight.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env Python
-+#!/usr/bin/python
- """Data for molecular weight calculations on proteins and nucleotides."""
- 
- __author__ = "Rob Knight"
---- PyCogent-1.5.3.orig/cogent/format/text_tree.py
-+++ PyCogent-1.5.3/cogent/format/text_tree.py
-@@ -1,4 +1,4 @@
--#!/bin/env python
-+#!/usr/bin/python
- # file text_tree.py
- """Simple base text representation of phylo tree."""
- 
---- PyCogent-1.5.3.orig/cogent/recalculation/__init__.py
-+++ PyCogent-1.5.3/cogent/recalculation/__init__.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/envthon
-+#!/usr/bin/python
- __all__ = ['array', 'calculation', 'definition', 'scope', 'setting']
- 
- __author__ = "Peter Maxwell"
---- PyCogent-1.5.3.orig/cogent/recalculation/setting.py
-+++ PyCogent-1.5.3/cogent/recalculation/setting.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python'
-+#!/usr/bin/python
- """Instances of these classes are assigned to different parameter/scopes
- by a parameter controller"""
- 
---- PyCogent-1.5.3.orig/cogent/phylo/maximum_likelihood.py
-+++ PyCogent-1.5.3/cogent/phylo/maximum_likelihood.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/env python'
-+#!/usr/bin/python
- from tree_space import TreeEvaluator, ancestry2tree
- from least_squares import WLS
- from math import exp

debian/patches/ignore_numpy_test_issue.patch

-Description: Skip test featuring wrong numpy usage
- Traceback (most recent call last):
-   File "/<<PKGBUILDDIR>>/tests/test_util/test_array.py", line 596, in test_split_dimension
-     a = split_dimension(m, 0)
-   File "/<<PKGBUILDDIR>>/cogent/util/array.py", line 504, in split_dimension
-     return reshape(m, new_dim)
- ...
- TypeError: 'numpy.float64' object cannot be interpreted as an index
- .
- The issue occurred after upgrading from Numpy 1.11.2 to 1.12.0~b1 which
- has cause also other packages test suites failures.  Since this version
- of Cogent is in low maintenance mode it will probably not be adapted to
- any new Numpy versions so skipping two tests might be the most appropriate
- step to deal with this issue
-Bug-Debian: https://bugs.debian.org/848746
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Tue, 20 Dec 2016 09:36:34 +0100
-
-
---- a/tests/test_util/test_array.py
-+++ b/tests/test_util/test_array.py
-@@ -591,12 +591,6 @@ class ArrayMathTests(TestCase):
-         self.assertEqual(a.shape, (3,4,12,12))
-         #should fail with IndexError for invalid dimension
-         self.assertRaises(IndexError, split_dimension, m, 5, (3,4))
--        #should assume even split if not supplied
--        m = reshape(arange(16**3), (16,16,16))
--        a = split_dimension(m, 0)
--        self.assertEqual(a.shape, (4,4,16,16))
--        a = split_dimension(m, 1)
--        self.assertEqual(a.shape, (16,4,4,16))
- 
-     def test_non_diag(self):
-         """non_diag should return non-diag elements from flattened matrices"""
---- a/tests/test_draw/test_distribution_plots.py
-+++ b/tests/test_draw/test_distribution_plots.py
-@@ -233,12 +233,6 @@ class DistributionPlotsTests(TestCase):
-         result = _plot_bar_data(ax, [], 'red', 0.5, 3.75, 1.5, 'sem')
-         self.assertTrue(result is None)
- 
--    def test_plot_scatter_data(self):
--        """_plot_scatter_data() should return a Collection instance."""
--        fig, ax = _create_plot()
--        result = _plot_scatter_data(ax, [1, 2, 3], '^', 0.77, 1, 1.5, 'stdv')
--        self.assertFloatEqual(result.get_sizes(), 20)
--
-     def test_plot_scatter_data_empty(self):
-         """_plot_scatter_data() should not error when given empty list of data,
-         but should not plot anything."""

debian/patches/matplotlib-2.2.3.patch

-Description: Ignore test with matplotlib 2.2.3 where a warning message
-  is different than expected
-Bug-Debian: https://bugs.debian.org/915908
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 17 Dec 2018 08:21:47 +0100
-
---- a/tests/test_draw/test_distribution_plots.py
-+++ b/tests/test_draw/test_distribution_plots.py
-@@ -507,12 +507,12 @@ class DistributionPlotsTests(TestCase):
-             _set_figure_size(fig, 3, 3)
-             self.assertFloatEqual(fig.get_size_inches(), (3, 3))
-             output = out.getvalue().strip()
--            self.assertEqual(output,
--            "Warning: could not automatically resize plot to make room for "
--            "axes labels and plot title. This can happen if the labels or "
--            "title are extremely long and the plot size is too small. Your "
--            "plot may have its labels and/or title cut-off. To fix this, "
--            "try increasing the plot's size (in inches) and try again.")
-+#            self.assertEqual(output,
-+#            "Warning: could not automatically resize plot to make room for "
-+#            "axes labels and plot title. This can happen if the labels or "
-+#            "title are extremely long and the plot size is too small. Your "
-+#            "plot may have its labels and/or title cut-off. To fix this, "
-+#            "try increasing the plot's size (in inches) and try again.")
-         finally:
-             sys.stdout = saved_stdout
- 

debian/patches/numpy-doctests.patch

-Description: Ensure doctests pass with different numpy versions
- The numpy output format changed with numpy 1.14 and this causes doctests to
- fail if raw numerical output is compared. See
- https://wiki.debian.org/ContinuousIntegration/TriagingTips/numpy-1.14-doctests
-Author: Stuart Prescott <stuart@debian.org>
-Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)
-Origin: https://github.com/pycogent/pycogent/files/2072985/numpy-doctests.patch
-Bug-Debian: https://bugs.debian.org/899205
-
---- a/tests/alltests.py
-+++ b/tests/alltests.py
-@@ -6,6 +6,14 @@
- import doctest, cogent.util.unit_test as unittest, sys, os
- from cogent.util.misc import app_path
- 
-+# Whitespace changes between numpy 1.13 and 1.14 will cause the doctests
-+# to fail; when doctests are updated to 1.14 format, this can be removed.
-+try:    # CRUFT
-+    import numpy as np
-+    np.set_printoptions(legacy='1.13')
-+except TypeError:
-+    pass
-+
- __author__ = "Peter Maxwell and Gavin Huttley"
- __copyright__ = "Copyright 2007-2016, The Cogent Project"
- __credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight",

debian/patches/numpy_xor.patch

-Description: Use xor rather than subtraction on booleans
- Numpy no longer accepts the ambiguous construction of a-b when a and b are bools.
- Normally, this can be replaced with XORs.
-Author: Stuart Prescott <stuart@debian.org>
-Last-Update: Tue, 05 Jun 2018 15:32:46 +0000 (UTC)
-Origin: https://github.com/pycogent/pycogent/files/2072984/numpy_xor.patch
-Bug-Debian: https://bugs.debian.org/899205
-
---- a/cogent/core/sequence.py
-+++ b/cogent/core/sequence.py
-@@ -1248,7 +1248,7 @@
-         gap_indices = map(self.Alphabet.index, self.MolType.Gaps)
-         valid_indices = self._data < len(self.Alphabet)
-         for i in gap_indices:
--            valid_indices -= self._data == i
-+            valid_indices ^= self._data == i
-         result = compress(valid_indices, self._data)
-         return self.__class__(result, Info=self.Info)
- 
---- a/cogent/maths/distance_transform.py
-+++ b/cogent/maths/distance_transform.py
-@@ -670,9 +670,9 @@
-         return zeros((0,0),'d')
-     dists = zeros((numrows,numrows),'d')
-     for i in range(numrows):
--        r1 = datamtx[i] # cache here
-+        r1 = datamtx[i].astype(dists.dtype) # cache here
-         for j in range(i):
--            dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j]))
-+            dists[i,j] = dists[j,i] = sum(abs(r1 - datamtx[j].astype(dists.dtype)))
-             
-     return dists
- 

debian/patches/parsinsert_not_in_caps.patch

-Author: Tim Booth <tbooth@ceh.ac.uk>
-Last-Update: Fri, 25 Apr 2014 17:27:42 +0100
-Description: make script compatible with spelling of Debian's
- parsinsert package
-
---- a/cogent/app/parsinsert.py
-+++ b/cogent/app/parsinsert.py
-@@ -28,7 +28,7 @@ from StringIO import StringIO
- class ParsInsert(CommandLineApplication):
-     """ParsInsert application Controller"""
- 
--    _command = 'ParsInsert'
-+    _command = 'parsinsert'
-     _input_handler = '_input_as_multiline_string'
-     _parameters = {
-                     # read mask from this file
---- a/tests/test_app/test_parsinsert.py
-+++ b/tests/test_app/test_parsinsert.py
-@@ -60,7 +60,7 @@ class ParsInsertTests(TestCase):
-         
-         app = ParsInsert()
-         self.assertEqual(app.BaseCommand, \
--                         ''.join(['cd "',getcwd(),'/"; ','ParsInsert']))
-+                         ''.join(['cd "',getcwd(),'/"; ','parsinsert']))
-         
-     def test_change_working_dir(self):
-         """Change working dir"""
-@@ -68,7 +68,7 @@ class ParsInsertTests(TestCase):
-         app = ParsInsert(WorkingDir='/tmp/ParsInsertTest')
-         self.assertEqual(app.BaseCommand, \
-                        ''.join(['cd "','/tmp/ParsInsertTest',\
--                                '/"; ','ParsInsert']))
-+                                '/"; ','parsinsert']))
-                                 
-         rmtree('/tmp/ParsInsertTest')
- 
---- a/tests/alltests.py
-+++ b/tests/alltests.py
-@@ -232,7 +232,7 @@ def suite():
-             ('mothur', 'test_mothur'),
-             ('muscle', 'test_muscle_v38'),
-             ('msms', 'test_msms'),
--            ('ParsInsert', 'test_parsinsert'),
-+            ('parsinsert', 'test_parsinsert'),
-             ('pplacer', 'test_pplacer'),
-             ('rdp_classifier-2.2.jar', 'test_rdp_classifier'),
-             ('rdp_classifier-2.0.jar', 'test_rdp_classifier20'),

debian/patches/privacy.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Tue, 05 Jun 2018 21:47:29 +0200
-Description: Avoid insertion of Google phone home code
-
---- a/doc/templates/layout.html
-+++ b/doc/templates/layout.html
-@@ -1,10 +1,5 @@
- {% extends "!layout.html" %}
-  
--{% block extrahead %}     
--<script type="text/javascript" src="http://www.google.com/jsapi?key=ABQIAAAAbW_pA971hrPgosv-Msv7hRQZ4X-jPDmWcshBrz2j7-fJvuUABRTGWmdiw2G89JpgztGlFGG8hDxRAw"></script>\
--<script type="text/javascript" src="{{ pathto("_static/google_feed.js",1)}}"></script>
--{% endblock %}
--
- {% block sidebartoc %}
- <div class="news">
- <table id="feed"><tr><td><h3><a href="http://pycogent.wordpress.com/">PyCogent News and Announcements</a></h3></td>

debian/patches/raxml_unsupported_version.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 21 May 2015 08:47:01 +0200
-Description: The test is checking for an old version of raxml
- for no good reason
-
---- a/tests/test_app/test_raxml_v730.py
-+++ b/tests/test_app/test_raxml_v730.py
-@@ -43,7 +43,8 @@ class GenericRaxml(TestCase):
-         version_string = stdout.strip().split(' ')[4].strip()
-         try:
-             version = tuple(map(int,version_string.split('.')))
--            pass_test = version == acceptable_version
-+# Debian has later versions than 7.3.0 and checking only a fixed version makes no sense at all
-+#            pass_test = version == acceptable_version
-         except ValueError:
-             pass_test = False
-             version_string = stdout

debian/patches/rdp_classifier.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 14 Sep 2016 21:48:35 +0200
-Description: Try to support rdp_classifier (but failed - no idea why)
-
---- a/cogent/app/rdp_classifier.py
-+++ b/cogent/app/rdp_classifier.py
-@@ -49,7 +49,7 @@ class RdpClassifier(CommandLineApplicati
-     '-training-data'.
-     """
-     _input_handler = '_input_as_lines'
--    _command = "rdp_classifier-2.2.jar"
-+    _command = "/usr/share/java/rdp_classifier.jar"
-     _options = {
-         # output file name for classification assignment
-         '-o': ValuedParameter('-', Name='o', Delimiter=' ', IsPath=True),
---- a/tests/test_app/test_rdp_classifier.py
-+++ b/tests/test_app/test_rdp_classifier.py
-@@ -30,7 +30,7 @@ class RdpClassifierTests(TestCase):
-         if 'RDP_JAR_PATH' in environ:
-             self.user_rdp_jar_path = environ['RDP_JAR_PATH']
-         else:
--            self.user_rdp_jar_path = 'rdp_classifier-2.2.jar'
-+            self.user_rdp_jar_path = '/usr/share/java/rdp_classifier.jar'
-         self.output_file = tempfile.NamedTemporaryFile()
- 
-     def test_default_java_vm_parameters(self):
---- a/tests/test_app/test_rdp_classifier20.py
-+++ b/tests/test_app/test_rdp_classifier20.py
-@@ -29,7 +29,7 @@ class RdpClassifier20Tests(TestCase):
-         if 'RDP_JAR_PATH' in environ:
-             self.user_rdp_jar_path = environ['RDP_JAR_PATH']
-         else:
--            self.user_rdp_jar_path = 'rdp_classifier-2.0.jar'
-+            self.user_rdp_jar_path = '/usr/share/java/rdp_classifier.jar'
- 
-     def test_default_java_vm_parameters(self):
-         """RdpClassifier should store default arguments to Java VM."""

debian/patches/skip_weak_tests.patch

-Description: Skip some tests that do not create reproducible results at package
- build time
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 30 Nov 2016 07:33:20 +0100
-Bug-Debian: https://bugs.debian.org/846078
-
---- a/tests/test_struct/test_asa.py
-+++ b/tests/test_struct/test_asa.py
-@@ -142,21 +142,6 @@ class asaTest(TestCase):
-         x = residues[('2E12', 0, 'B', ('GLU', 77, ' '))].xtra.values()
-         self.assertTrue(x[0] != x[1])
- 
--    def test_uc2(self):
--        self.input_file = os.path.join('data', '1LJO.pdb')
--        self.input_structure = PDBParser(open(self.input_file))
--        asa.asa_xtra(self.input_structure, symmetry_mode='uc', xtra_key='ASA_XTAL')
--        asa.asa_xtra(self.input_structure)
--        self.input_structure.propagateData(sum, 'A', 'ASA', xtra=True)
--        self.input_structure.propagateData(sum, 'A', 'ASA_XTAL', xtra=True)
--        residues = einput(self.input_structure, 'R')
--        r1 = residues[('1LJO', 0, 'A', ('ARG', 65, ' '))]
--        r2 = residues[('1LJO', 0, 'A', ('ASN', 46, ' '))]
--        self.assertFloatEqual(r1.xtra.values(),
--                              [128.94081270529105, 22.807700865674093])
--        self.assertFloatEqual(r2.xtra.values(),
--                              [115.35738419425566, 115.35738419425566])
--
-     def test_crystal(self):
-         """compares asa within unit cell."""
-         self.input_file = os.path.join('data', '2E12.pdb')
---- a/tests/test_maths/test_optimisers.py
-+++ b/tests/test_maths/test_optimisers.py
-@@ -80,13 +80,6 @@ class OptimiserTestCase(TestCase):
-     #     """optimiser warning if max_evaluations exceeded"""
-     #     self._test_optimisation(max_evaluations=5, limit_action='warn')
-     
--    def test_get_max_eval_count(self):
--        """return the evaluation count from optimisation"""
--        f, last, evals = MakeF()
--        x, e = quiet(maximise, f, xinit=[1.0], bounds=([-10,10]),
--                    return_eval_count=True)
--        self.assertTrue(e > 500)
--    
-     def test_checkpointing(self):
-         filename = 'checkpoint.tmp.pickle'
-         if os.path.exists(filename):
---- a/tests/test_seqsim/test_tree.py
-+++ b/tests/test_seqsim/test_tree.py
-@@ -718,21 +718,6 @@ class OldPhyloNodeTests(TestCase):
-        result = [i.Q for i in t.traverse(self_after=True)]
-        self.assertEqual(result, ['c','b','c','c','c','a','a','a','c'])
-         
--
--    def test_assignP(self):
--        """RangeNode assignP should work when Qs set."""
--        t = self.t1
--        for i in t.traverse(self_before=True):
--            i.Length = random() * 0.5 #range 0 to 0.5
--        t.Q = Rates.random(DnaPairs)
--        t.assignQ()
--        t.assignP()
--        t.assignIds()
--        for node in t.traverse(self_after=True):
--            if node.Parent is not None:
--                self.assertFloatEqual(average(1-diag(node.P._data), axis=0), \
--                    node.Length)
--       
-     def test_assignLength(self):
-         """RangeNode assignLength should set branch length"""
-         t = self.t1
---- a/tests/test_seqsim/test_sequence_generators.py
-+++ b/tests/test_seqsim/test_sequence_generators.py
-@@ -465,45 +465,6 @@ class ConstantRegionTests(TestCase):
-         self.assertEqual(str(r.Current), 'ACGUUCGA')
-         self.assertEqual(len(r), len('ACGUUCGA'))
- 
--class UnpairedRegionTests(TestCase):
--    """Tests of unpaired region: should fill in w/ single-base frequencies."""
--    def test_init(self):
--        """Unpaired region should generate right freqs, even after change"""
--        freqs = Freqs({'C':10,'U':1, 'A':0})
--        r = UnpairedRegion('NN', freqs)
--        seq = r.Current
--        assert seq[0] in 'CU'
--        assert seq[1] in 'CU'
--        self.assertEqual(len(seq), 2)
--        fd = []
--        for i in range(1000):
--            r.refresh()
--            fd.append(str(seq))
--        fd = Freqs(''.join(fd))
--
--        observed = [fd['C'], fd['U']]
--        expected = [1800, 200]
--        self.assertSimilarFreqs(observed, expected)
--        self.assertEqual(fd['U'] + fd['C'], 2000)
--
--        freqs2 = Freqs({'A':5, 'U':5})
--        r.Composition = freqs2
--        r.Template = 'NNN'  #note that changing the Template changes seq ref
--        seq = r.Current
--        self.assertEqual(len(seq), 3)
--        assert seq[0] in 'AU'
--        assert seq[1] in 'AU'
--        assert seq[2] in 'AU'
--        fd = []
--        for i in range(1000):
--            r.refresh()
--            fd.append(str(seq))
--        fd = Freqs(''.join(fd))
--        observed = [fd['A'], fd['U']]
--        expected = [1500, 1500]
--        self.assertSimilarFreqs(observed, expected)
--        self.assertEqual(fd['A'] + fd['U'], 3000)
--
- class ShuffledRegionTests(TestCase):
-     """Shuffled region should randomize string"""
-     def test_init(self):
---- a/tests/test_cluster/test_nmds.py
-+++ b/tests/test_cluster/test_nmds.py
-@@ -43,59 +43,6 @@ class NMDSTests(TestCase):
-         self.assertEqual(size(pts, 0), 4)
-         self.assertEqual(size(pts, 1), 2)
- 
--    def test_2(self):
--        """l19 data should give stress below .13"""
--        ptmtx = array(
--            [[7,1,0,0,0,0,0,0,0],
--            [4,2,0,0,0,1,0,0,0],
--            [2,4,0,0,0,1,0,0,0],
--            [1,7,0,0,0,0,0,0,0],
--            [0,8,0,0,0,0,0,0,0],
--            [0,7,1,0,0,0,0,0,0],#idx 5
--            [0,4,2,0,0,0,2,0,0],
--            [0,2,4,0,0,0,1,0,0],
--            [0,1,7,0,0,0,0,0,0],
--            [0,0,8,0,0,0,0,0,0],
--            [0,0,7,1,0,0,0,0,0],#idx 10
--            [0,0,4,2,0,0,0,3,0],
--            [0,0,2,4,0,0,0,1,0],
--            [0,0,1,7,0,0,0,0,0],
--            [0,0,0,8,0,0,0,0,0],
--            [0,0,0,7,1,0,0,0,0],#idx 15
--            [0,0,0,4,2,0,0,0,4],
--            [0,0,0,2,4,0,0,0,1],
--            [0,0,0,1,7,0,0,0,0]], 'float')
--        distmtx = dist_euclidean(ptmtx)
--        nm = NMDS(distmtx, verbosity=0)
--        self.assertLessThan(nm.getStress(), .13)
--    
--    def test_3(self):
--        """l19 data should give stress below .13 in multi-D"""
--        ptmtx = array(
--            [[7,1,0,0,0,0,0,0,0],
--            [4,2,0,0,0,1,0,0,0],
--            [2,4,0,0,0,1,0,0,0],
--            [1,7,0,0,0,0,0,0,0],
--            [0,8,0,0,0,0,0,0,0],
--            [0,7,1,0,0,0,0,0,0],#idx 5
--            [0,4,2,0,0,0,2,0,0],
--            [0,2,4,0,0,0,1,0,0],
--            [0,1,7,0,0,0,0,0,0],
--            [0,0,8,0,0,0,0,0,0],
--            [0,0,7,1,0,0,0,0,0],#idx 10
--            [0,0,4,2,0,0,0,3,0],
--            [0,0,2,4,0,0,0,1,0],
--            [0,0,1,7,0,0,0,0,0],
--            [0,0,0,8,0,0,0,0,0],
--            [0,0,0,7,1,0,0,0,0],#idx 15
--            [0,0,0,4,2,0,0,0,4],
--            [0,0,0,2,4,0,0,0,1],
--            [0,0,0,1,7,0,0,0,0]], 'float')
--        distmtx = dist_euclidean(ptmtx)
--        for dim in range(3,18):
--            nm = NMDS(distmtx, verbosity=0, dimension=dim)
--            self.assertLessThan(nm.getStress(), .13)
--
-     def test_metaNMDS(self):
-         """l19 data should give stress below .13"""
-         ptmtx = array(
---- a/tests/test_align/test_weights/test_methods.py
-+++ b/tests/test_align/test_weights/test_methods.py
-@@ -177,48 +177,6 @@ class VoronoiTests(GeneralTests):
-             if x > 0:
-                 self.assertNotEqual(results[x], results[x-1])
-     
--    def test_mVOR(self):
--        """mVOR: should return weights closer to the 'True' weights"""
--        #err=5e-2 #original error value
--        # Raised the error value to prevent occasional failure of the test.
--        # The mVOR method takes a sample from a distribution and the outcome
--        # will depend on this sample. Every now and then, one of the weights
--        # was more than 0.05 away from the expected weight. Raised the 
--        # allowed error value to prevent that. To use the method on real
--        # data, a larger sample should be taken (e.g. 10000?), but increasing
--        # the sample size here would make the test too slow.
--        err=0.075
--        aln3_exp = {'seq1':.25, 'seq2':.25, 'seq3':.5}
--        aln4_exp = {'seq1':.1667, 'seq2':.1667,'seq3':.1667,'seq4':.1667,\
--            'seq5':.3333}       
--        aln6_exp = dict(zip(map(str,[1,2,3,4,5,6,7,8,9,10]),
--            [0.09021,0.08039,0.113560,0.10399,0.092370,0.097130,
--            0.09198,0.09538,0.10927,0.12572]))
--
--        # the following assertSimilarMeans statements were added to replace 
--        # stochastic assertFloatEqualAbs calls below
--        self.assertSimilarMeans(mVOR(self.aln3,order="ABC").values(),
--                                 aln3_exp.values())
--        self.assertSimilarMeans(mVOR(self.aln4,order="ABC").values(),
--                                 aln4_exp.values())
--        self.assertSimilarMeans(mVOR(self.aln6,order=DNA_ORDER,n=3000)\
--                                 .values(), aln6_exp.values())
--
--        #self.assertFloatEqualAbs(mVOR(self.aln3,order="ABC").values(),\
--        #    aln3_exp.values(),eps=err)
--        #self.assertFloatEqualAbs(mVOR(self.aln4,order="ABC").values(),\
--        #    aln4_exp.values(),eps=err)
--        #self.assertFloatEqualAbs(mVOR(self.aln6,order=DNA_ORDER,n=3000)\
--        #    .values(), aln6_exp.values(),eps=err)
--        
--        #the results vary with runs, because the sample of random profiles
--        #is different each time
--        results = []
--        for x in range(5):
--            results.append(mVOR(self.aln4,order="ABC"))
--            if x > 0:
--                self.assertNotEqual(results[x], results[x-1])
--
- class PositionBasedTests(GeneralTests):
-     """Contains tests for PB (=position-based) method"""
-     

debian/patches/sphinx.ext.pngmath.patch

-Description: Enable building with sphinx1.8
-Bug-Debian: https://bugs.debian.org/918829
-Author: Andreas Tille <tille@debian.org>
-Last-Changed: Thu, 10 Jan 2019 14:56:55 +0100
-
---- a/doc/conf.py
-+++ b/doc/conf.py
-@@ -22,7 +22,7 @@ import sys, os
- 
- # Add any Sphinx extension module names here, as strings. They can be extensions
- # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
--extensions = ['sphinx.ext.todo', 'sphinx.ext.doctest', 'sphinx.ext.pngmath']
-+extensions = ['sphinx.ext.todo', 'sphinx.ext.doctest', 'sphinx.ext.imgmath']
- 
- # todo_include_todos=True # to expose the TODOs, uncomment this line
- 

debian/patches/usr_bin_ls.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 16 Jun 2017 13:30:22 +0200
-Description: ls will be moved from /bin/ls to /usr/bin/ls - lets skip
- this test which does not make real sense anyway.
-
---- a/tests/test_util/test_misc.py
-+++ b/tests/test_util/test_misc.py
-@@ -1626,7 +1626,7 @@ class reverse_complementTests(TestCase):
- 
-     def test_app_path(self):
-         """app_path should return correct paths"""
--        self.assertEqual(app_path('ls'), '/bin/ls')
-+        # self.assertEqual(app_path('ls'), '/usr/bin/ls')
-         self.assertEqual(app_path('lsxxyyx'), False)
- 
- class CommandLineParserTests(TestCase):

debian/rules

@@ -8,46 +8,12 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 
 export PYBUILD_BEFORE_TEST=cp -r {dir}/tests/data {build_dir}
 
-BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-
-FAILED_TESTS := test_infernal \
-                test_mothur \
-                test_parsinsert \
-                test_raxml_v730 \
-                test_rtax \
-                test_clustalw \
-                test_mafft \
-                test_unifrac \
-                test_seqsim.test_analysis \
-                test_seqsim.test_usage
-
-ONLYAMD64_TESTS := test_bwa
-
-# There are tests failing on certain architectures
-# We need to decide between not shipping cogent there or hiding
-# our eyes from these failures.  See README.source for further
-# explanation.
-FAIL_ON_ARMEL_TESTS := test_core.test_profile
-
-
-FAIL_ON_PPC64_MIPS64EL := test_core.test_tree
-
-FAIL_ON_I386_TESTS := test_maths.test_stats.test_test \
-                      test_seqsim.test_sequence_generators
-
-FAIL_ON_PPC64_TESTS := test_app.test_util
-
-FAIL_ON_S390X_TESTS := test_maths.test_optimisers \
-                       test_format.test_pdb_color.PdbColorTests
-
-FAIL_ON_MIPS_TESTS := test_seqsim.test_sequence_generators
-
 export PYBUILD_NAME=cogent3
 
 include /usr/share/dpkg/default.mk
 
 %:
-	dh $@ --with python3,sphinxdoc --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_clean:
 	#These files are rebuilt on-the-fly
@@ -58,7 +24,7 @@ override_dh_clean:
 	rm -rf doc/_build
 	dh_clean
 
-__override_dh_auto_build:
+override_dh_auto_build:
 	dh_auto_build
 	set -x; cd doc; PYTHONPATH=$(CURDIR) http_proxy='127.0.0.1:9' $(MAKE) html
 	# remove superfluous files and dirs
@@ -79,38 +45,3 @@ override_dh_installdocs:
 	dh_installdocs
 	rm -rf debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/html/_sources
 	find debian -name doctrees -type d | xargs rm -rf
-
-___override_dh_auto_test:
-ifeq (,$(filter nocheck, $(DEB_BUILD_OPTIONS)))
-	cp -a tests/alltests.py tests/alltests.py~
-	# exclude tests known to fail
-	for tst in $(FAILED_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-# avoid amd64 only tools on other architectures
-ifeq ($(BUILDARCH),amd64)
-	echo "bwa can be tested on amd64 arch"
-else
-	for tst in $(ONLYAMD64_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-ifeq ($(BUILDARCH),$(filter $(BUILDARCH), mips64el ppc64el ppc64))
-	for tst in $(FAIL_ON_PPC64_MIPS64EL) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-endif
-ifeq ($(BUILDARCH),armel)
-	for tst in $(FAIL_ON_ARMEL_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-endif
-ifeq ($(BUILDARCH),ppc64)
-	for tst in $(FAIL_ON_PPC64_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-endif
-ifeq ($(BUILDARCH),s390x)
-	for tst in $(FAIL_ON_S390X_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-endif
-ifeq ($(BUILDARCH),mips)
-	for tst in $(FAIL_ON_MIPS_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-endif
-ifeq ($(BUILDARCH),$(filter $(BUILDARCH), i386 kfreebsd-i386))
-	for tst in $(FAIL_ON_I386_TESTS) ; do sed -i "/$${tst}/d" tests/alltests.py ; done
-endif
-endif
-	BLASTMAT=/usr/share/ncbi/data/ RDP_JAR_PATH=/usr/share/java/rdp_classifier.jar $(CURDIR)/run_tests -v # --debug
-	# restore original tests file
-	mv tests/alltests.py~ tests/alltests.py
-	find tests -name "*.pyc" -delete
-endif