debian/changelog

+bowtie2 (2.3.5.1-2) unstable; urgency=medium
+
+  [ Steffen Möller ]
+  * Added ref to conda
+
+  [ Andreas Tille ]
+  * SEQwiki is deprecated
+
+  [ Steffen Moeller ]
+  * d/u/metadata: yamllint
+
+  [ Alexandre Mestiashvili ]
+  * Update d/patches/2to3.patch, use importlib instead of deprecated imp module
+  * Add patch silencing TBB deprecation warnings
+  * d/control: bump Policy to 4.4.1, add Rules-requires-root: no
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Fri, 06 Dec 2019 22:38:21 +0100
+
 bowtie2 (2.3.5.1-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]

debian/control

@@ -13,7 +13,8 @@ Build-Depends: debhelper-compat (= 12),
                libclone-perl,
                libfile-which-perl,
                zlib1g-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
+Rules-requires-root: no
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie2
 Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git
 Homepage: http://bowtie-bio.sourceforge.net/bowtie2

debian/patches/2to3.patch

@@ -5,7 +5,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
 
 --- a/Makefile
 +++ b/Makefile
-@@ -481,11 +481,11 @@ bowtie2.bat:
+@@ -481,11 +481,11 @@
  
  bowtie2-build.bat:
  	echo "@echo off" > bowtie2-build.bat
@@ -27,7 +27,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  
  """
  sa.py
-@@ -15,7 +15,7 @@ import struct
+@@ -15,7 +15,7 @@
  def loadBowtieSa(fh):
  	""" Load a .sa file from handle into an array of ints """
  	nsa = struct.unpack('I', fh.read(4))[0]
@@ -36,7 +36,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  
  def loadBowtieSaFilename(fn):
  	""" Load a .sa file from filename into an array of ints """
-@@ -58,7 +58,7 @@ if __name__ == "__main__":
+@@ -58,7 +58,7 @@
  		# Suffix array is in sas; note that $ is considered greater than all
  		# other characters
  		if ref is not None:
@@ -45,7 +45,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  				sa1, sa2 = sas[i-1], sas[i]
  				assert sa1 != sa2
  				# Sanity check that suffixes are really in order
-@@ -76,4 +76,4 @@ if __name__ == "__main__":
+@@ -76,4 +76,4 @@
  			assert sas[-1] == len(ref)
  	
  	go()
@@ -54,7 +54,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
 +	
 --- a/scripts/test/README.md
 +++ b/scripts/test/README.md
-@@ -17,7 +17,7 @@ They use the Python infrastructure in th
+@@ -17,7 +17,7 @@
  
  From root:
  
@@ -63,7 +63,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  
  Val Antonescu originally set these up.
  
-@@ -27,7 +27,7 @@ Builds an index consisting of both human
+@@ -27,7 +27,7 @@
  
  From root:
  
@@ -80,7 +80,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  """
  A few items to deal with sets of benchmarks.
  """
-@@ -57,7 +57,7 @@ class Benchmarks(object):
+@@ -57,7 +57,7 @@
          self.set_idx = 0
          return self
  
@@ -89,7 +89,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
          if self.set_idx == len(self.values):
              raise StopIteration
  
-@@ -250,7 +250,7 @@ class TestAccuracy(Runable):
+@@ -250,7 +250,7 @@
                      delta = [0, 1]
                      logging.debug("%s: missed (pos:%d vs %d)" % (q_name, orig[1], rec.pos))
                  try:
@@ -114,7 +114,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  """
  A reader of SAM format.
  
-@@ -49,7 +49,7 @@ class SamHeader(object):
+@@ -49,7 +49,7 @@
          self.curr_idx = 0
          return self
  
@@ -123,7 +123,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
          if self.curr_idx == len(self.header_lines):
              raise StopIteration
              
-@@ -114,7 +114,7 @@ class SamReader(object):
+@@ -114,7 +114,7 @@
          self._source_fh.seek(self.header.end_header_pointer)
          return self
  
@@ -148,7 +148,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  """
  Note: This would look so much better replaced by XML or at least JSON. But 
        is not worth to do it for now.
-@@ -6,7 +6,7 @@ Note: This would look so much better rep
+@@ -6,7 +6,7 @@
  
  import os
  import gzip
@@ -157,7 +157,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  import logging
  
  
-@@ -66,14 +66,14 @@ class LargeTestsData(object):
+@@ -66,14 +66,14 @@
      def init_data(self):
          """ Try and init the data we need.
          """
@@ -174,7 +174,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
              gn_path  = os.path.join(self.data_dir_path,genome)
              gn_fasta = os.path.join(gn_path,gdata['ref_name'])
              if not os.path.exists(gn_fasta):
-@@ -103,7 +103,7 @@ class LargeTestsData(object):
+@@ -103,7 +103,7 @@
              
              try:
                  f = open(fname,'wb')
@@ -204,7 +204,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  import inspect
  import unittest
  import logging
-@@ -69,7 +69,7 @@ class TestLargeIndex(unittest.TestCase):
+@@ -69,7 +69,7 @@
     
  def get_suite():
      tests = ['test_human','test_mouse','test_large_index']
@@ -237,3 +237,12 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
  
  """
   Copyright 2014, Ben Langmead <langmea@cs.jhu.edu>
+@@ -21,7 +21,7 @@
+ 
+ 
+ import os
+-import imp
++import importlib
+ import sys
+ import inspect
+ import logging

debian/patches/series

@@ -5,3 +5,4 @@ reproducible.patch
 skip_test_requiring_non-free_libmath-random-perl.patch
 do-not-rebuild-during-test.patch
 2to3.patch
+silence_tbb_deprecation_warning.patch

debian/patches/silence_tbb_deprecation_warning.patch

+Subject: Silence TBB deprecation warnings, including specific headers only
+From: Alex Mestiashvili <amestia@rsh2.donotuse.de>
+--- bowtie2.orig/bt2_search.h
++++ bowtie2/bt2_search.h
+@@ -21,7 +21,6 @@
+ #define BT2_SEARCH_H_
+ #ifdef WITH_TBB
+ 
+-#include <tbb/tbb.h>
+ #include <tbb/task_group.h>
+ 
+ class multiseedSearchWorker {
+--- bowtie2.orig/blockwise_sa.h
++++ bowtie2/blockwise_sa.h
+@@ -21,7 +21,6 @@
+ #define BLOCKWISE_SA_H_
+ 
+ #ifdef WITH_TBB
+-#include <tbb/tbb.h>
+ #include <tbb/task_group.h>
+ #endif
+ 
+--- bowtie2.orig/diff_sample.h
++++ bowtie2/diff_sample.h
+@@ -21,7 +21,6 @@
+ #define DIFF_SAMPLE_H_
+ 
+ #ifdef WITH_TBB
+-#include <tbb/tbb.h>
+ #include <tbb/task_group.h>
+ #endif
+