debian/changelog

+consensuscore (1.1.1+dfsg-2) UNRELEASED; urgency=medium
+
+  * Use 2to3 to convert from Python2 and Python3
+    Closes: #936328
+  * Add myself to Uploaders
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  TODO: Does not build
+
+ -- Andreas Tille <tille@debian.org>  Sat, 07 Dec 2019 12:44:55 +0100
+
 consensuscore (1.1.1+dfsg-1) unstable; urgency=medium
 
   * Team upload

debian/compat

-11

debian/control

 Source: consensuscore
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                dh-exec,
                libboost-dev,
                swig,
-# Python2
-               python-setuptools,
-               python-all-dev,
-               python-numpy,
 # Python3
                python3-setuptools,
                python3-all-dev,
                python3-numpy
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/consensuscore
 Vcs-Git: https://salsa.debian.org/med-team/consensuscore.git
 Homepage: https://github.com/PacificBiosciences/ConsensusCore
@@ -35,21 +32,6 @@ Description: algorithms for PacBio multiple sequence consensus -- development fi
  This package is part of the SMRT Analysis suite.
  It provides the header files and static library.
 
-Package: python-pbconsensuscore
-Architecture: any-amd64 any-i386
-Section: python
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         ${python:Depends}
-Description: algorithms for PacBio multiple sequence consensus -- Python 2
- ConsensusCore is a library of C++ algorithms for Pacific Biosciences
- multiple sequence consensus that powers Quiver (Python) and ConsensusTools
- (.NET). This library primarily exists as the backend for GenomicConsensus,
- which implements Quiver.
- .
- This package is part of the SMRT Analysis suite.
- It provides the Python2 bindings.
-
 Package: python3-pbconsensuscore
 Architecture: any-amd64 any-i386
 Section: python

debian/patches/2to3.patch

+Description: Use 2to3 to convert from Python2 and Python3
+Bug-Debian: https://bugs.debian.org/936328
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 07 Dec 2019 12:44:55 +0100
+
+--- a/make/Python.mk
++++ b/make/Python.mk
+@@ -8,11 +8,11 @@ endif
+ include make/Defs.mk
+ 
+ ifeq (,$(wildcard $(PYTHON_INCLUDE)/Python.h))
+-$(error python include not configured properly, cannot build python module!)
++$(error python3 include not configured properly, cannot build python3 module!)
+ endif
+ 
+ ifeq (,$(wildcard $(NUMPY_INCLUDE)/numpy/arrayobject.h))
+-$(error numpy include not configured properly, cannot build python module!)
++$(error numpy include not configured properly, cannot build python3 module!)
+ endif
+ 
+ SWIG_CMD   := SWIG_LIB=$(SWIG_LIB) $(SWIG) -Wall -c++ -python -builtin
+@@ -27,6 +27,6 @@ $(PYTHON_DLL): $(SWIG_INTERFACES) $(CXX_
+ 	$(CXX) $(SHLIB_FLAGS) $(INCLUDES) -I $(PYTHON_INCLUDE) -I $(NUMPY_INCLUDE) $(GEN_CXX) $(CXX_LIB) -o $(PYTHON_DLL)
+ 
+ test-python: $(PYTHON_DLL)
+-	@PYTHONPATH=$(PYTHON_BUILD_DIR) python src/Demos/Demo.py && echo "Python build is OK!"
++	@PYTHONPATH=$(PYTHON_BUILD_DIR) python3 src/Demos/Demo.py && echo "Python3 build is OK!"
+ 
+ .PHONY: all test-python $(PYTHON_DLL)
+--- a/setup.py
++++ b/setup.py
+@@ -1,5 +1,5 @@
+-#!/usr/bin/env python
+-from __future__ import print_function
++#!/usr/bin/python3
++
+ 
+ from distutils.command.build import build as _build
+ from distutils.errors import CompileError
+--- a/src/Demos/Demo.py
++++ b/src/Demos/Demo.py
+@@ -1,4 +1,4 @@
+-from __future__ import print_function
++
+ import ConsensusCore as cc
+ 
+ print(cc.Version.VersionString())
+--- a/src/Tests/meson.build
++++ b/src/Tests/meson.build
+@@ -53,7 +53,7 @@ test(
+ 
+ if get_option('swig')
+   test(
+-    'quiver python import',
++    'quiver python3 import',
+     quiver_python,
+     args : [
+       files('test_import.py')],
+--- a/src/Tests/test_import.py
++++ b/src/Tests/test_import.py
+@@ -1,4 +1,4 @@
+-from __future__ import print_function
++
+ import ConsensusCore as cc
+ 
+ # basic test to verify that SWIG worked
+--- a/tools/cpplint.py
++++ b/tools/cpplint.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ #
+ # Copyright (c) 2009 Google Inc. All rights reserved.
+ #
+@@ -560,7 +560,7 @@ class _CppLintState(object):
+ 
+   def PrintErrorCounts(self):
+     """Print a summary of errors by category, and the total."""
+-    for category, count in self.errors_by_category.iteritems():
++    for category, count in list(self.errors_by_category.items()):
+       sys.stderr.write('Category \'%s\' errors found: %d\n' %
+                        (category, count))
+     sys.stderr.write('Total errors found: %d\n' % self.error_count)
+@@ -1007,7 +1007,7 @@ def CheckForCopyright(filename, lines, e
+ 
+   # We'll say it should occur by line 10. Don't forget there's a
+   # dummy line at the front.
+-  for line in xrange(1, min(len(lines), 11)):
++  for line in range(1, min(len(lines), 11)):
+     if re.search(r'Copyright', lines[line], re.I): break
+   else:                       # means no copyright line was found
+     error(filename, 0, 'legal/copyright', 5,
+@@ -1112,7 +1112,7 @@ def CheckForUnicodeReplacementCharacters
+     error: The function to call with any errors found.
+   """
+   for linenum, line in enumerate(lines):
+-    if u'\ufffd' in line:
++    if '\\ufffd' in line:
+       error(filename, linenum, 'readability/utf8', 5,
+             'Line contains invalid UTF-8 (or Unicode replacement character).')
+ 
+@@ -1602,7 +1602,7 @@ def CheckForFunctionLengths(filename, cl
+ 
+   if starting_func:
+     body_found = False
+-    for start_linenum in xrange(linenum, clean_lines.NumLines()):
++    for start_linenum in range(linenum, clean_lines.NumLines()):
+       start_line = lines[start_linenum]
+       joined_line += ' ' + start_line.lstrip()
+       if Search(r'(;|})', start_line):  # Declarations and trivial functions
+@@ -2136,7 +2136,7 @@ def GetLineWidth(line):
+     The width of the line in column positions, accounting for Unicode
+     combining characters and wide characters.
+   """
+-  if isinstance(line, unicode):
++  if isinstance(line, str):
+     width = 0
+     for uc in unicodedata.normalize('NFC', line):
+       if unicodedata.east_asian_width(uc) in ('W', 'F'):
+@@ -2472,7 +2472,7 @@ def _GetTextInside(text, start_pattern):
+ 
+   # Give opening punctuations to get the matching close-punctuations.
+   matching_punctuation = {'(': ')', '{': '}', '[': ']'}
+-  closing_punctuation = set(matching_punctuation.itervalues())
++  closing_punctuation = set(matching_punctuation.values())
+ 
+   # Find the position to start extracting text.
+   match = re.search(start_pattern, text, re.M)
+@@ -3022,7 +3022,7 @@ def CheckForIncludeWhatYouUse(filename,
+   required = {}  # A map of header name to linenumber and the template entity.
+                  # Example of required: { '<functional>': (1219, 'less<>') }
+ 
+-  for linenum in xrange(clean_lines.NumLines()):
++  for linenum in range(clean_lines.NumLines()):
+     line = clean_lines.elided[linenum]
+     if not line or line[0] == '#':
+       continue
+@@ -3070,7 +3070,7 @@ def CheckForIncludeWhatYouUse(filename,
+ 
+   # include_state is modified during iteration, so we iterate over a copy of
+   # the keys.
+-  header_keys = include_state.keys()
++  header_keys = list(include_state.keys())
+   for header in header_keys:
+     (same_module, common_path) = FilesBelongToSameModule(abs_filename, header)
+     fullpath = common_path + header
+@@ -3186,7 +3186,7 @@ def ProcessFileData(filename, file_exten
+ 
+   RemoveMultiLineComments(filename, lines, error)
+   clean_lines = CleansedLines(lines)
+-  for line in xrange(clean_lines.NumLines()):
++  for line in range(clean_lines.NumLines()):
+     ProcessLine(filename, file_extension, clean_lines, line,
+                 include_state, function_state, class_state, error,
+                 extra_check_functions)
+--- a/tools/find_boost
++++ b/tools/find_boost
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, re, sys
+ from glob import glob
+@@ -55,8 +55,8 @@ if __name__ == '__main__':
+     else:
+         boost = find_boost()
+     if boost_version(boost) < BOOST_MINIMUM_VERSION:
+-        print >> sys.stderr, "Boost version at least %s required!" \
+-            % str_version(BOOST_MINIMUM_VERSION)
+-        print >> sys.stderr, "Use --boost=<path> to specify boost location."
++        print("Boost version at least %s required!" \
++            % str_version(BOOST_MINIMUM_VERSION), file=sys.stderr)
++        print("Use --boost=<path> to specify boost location.", file=sys.stderr)
+         sys.exit(1)
+     print(boost)
+--- a/tools/find_swig
++++ b/tools/find_swig
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, re, sys
+ from glob import glob
+@@ -42,9 +42,9 @@ if __name__ == '__main__':
+         swig = find_swig()
+ 
+     if swig is None or swig_version(swig) < SWIG_MINIMUM_VERSION:
+-        print >> sys.stderr, "SWIG version at least %s required!" \
+-            % str_version(SWIG_MINIMUM_VERSION)
+-        print >> sys.stderr, "Use --swig=<path> to specify SWIG location."
++        print("SWIG version at least %s required!" \
++            % str_version(SWIG_MINIMUM_VERSION), file=sys.stderr)
++        print("Use --swig=<path> to specify SWIG location.", file=sys.stderr)
+         sys.exit(1)
+     else:
+         print(swig)
+--- a/tools/git-clang-format
++++ b/tools/git-clang-format
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ #
+ #===- git-clang-format - ClangFormat Git Integration ---------*- python -*--===#
+ #
+@@ -128,15 +128,15 @@ def main():
+   if opts.verbose >= 1:
+     ignored_files.difference_update(changed_lines)
+     if ignored_files:
+-      print 'Ignoring changes in the following files (wrong extension):'
++      print('Ignoring changes in the following files (wrong extension):')
+       for filename in ignored_files:
+-        print '   ', filename
++        print('   ', filename)
+     if changed_lines:
+-      print 'Running clang-format on the following files:'
++      print('Running clang-format on the following files:')
+       for filename in changed_lines:
+-        print '   ', filename
++        print('   ', filename)
+   if not changed_lines:
+-    print 'no modified files to format'
++    print('no modified files to format')
+     return
+   # The computed diff outputs absolute paths, so we must cd before accessing
+   # those files.
+@@ -146,20 +146,20 @@ def main():
+                                                binary=opts.binary,
+                                                style=opts.style)
+   if opts.verbose >= 1:
+-    print 'old tree:', old_tree
+-    print 'new tree:', new_tree
++    print('old tree:', old_tree)
++    print('new tree:', new_tree)
+   if old_tree == new_tree:
+     if opts.verbose >= 0:
+-      print 'clang-format did not modify any files'
++      print('clang-format did not modify any files')
+   elif opts.diff:
+     print_diff(old_tree, new_tree)
+   else:
+     changed_files = apply_changes(old_tree, new_tree, force=opts.force,
+                                   patch_mode=opts.patch)
+     if (opts.verbose >= 0 and not opts.patch) or opts.verbose >= 1:
+-      print 'changed files:'
++      print('changed files:')
+       for filename in changed_files:
+-        print '   ', filename
++        print('   ', filename)
+ 
+ 
+ def load_git_config(non_string_options=None):
+@@ -298,7 +298,7 @@ def filter_by_extension(dictionary, allo
+   `allowed_extensions` must be a collection of lowercase file extensions,
+   excluding the period."""
+   allowed_extensions = frozenset(allowed_extensions)
+-  for filename in dictionary.keys():
++  for filename in list(dictionary.keys()):
+     base_ext = filename.rsplit('.', 1)
+     if len(base_ext) == 1 or base_ext[1].lower() not in allowed_extensions:
+       del dictionary[filename]
+@@ -323,7 +323,7 @@ def run_clang_format_and_save_to_tree(ch
+ 
+   Returns the object ID (SHA-1) of the created tree."""
+   def index_info_generator():
+-    for filename, line_ranges in changed_lines.iteritems():
++    for filename, line_ranges in changed_lines.items():
+       mode = oct(os.stat(filename).st_mode)
+       blob_id = clang_format_to_blob(filename, line_ranges, binary=binary,
+                                      style=style)
+@@ -431,10 +431,10 @@ def apply_changes(old_tree, new_tree, fo
+   if not force:
+     unstaged_files = run('git', 'diff-files', '--name-status', *changed_files)
+     if unstaged_files:
+-      print >>sys.stderr, ('The following files would be modified but '
+-                           'have unstaged changes:')
+-      print >>sys.stderr, unstaged_files
+-      print >>sys.stderr, 'Please commit, stage, or stash them first.'
++      print(('The following files would be modified but '
++                           'have unstaged changes:'), file=sys.stderr)
++      print(unstaged_files, file=sys.stderr)
++      print('Please commit, stage, or stash them first.', file=sys.stderr)
+       sys.exit(2)
+   if patch_mode:
+     # In patch mode, we could just as well create an index from the new tree
+@@ -464,20 +464,20 @@ def run(*args, **kwargs):
+   if p.returncode == 0:
+     if stderr:
+       if verbose:
+-        print >>sys.stderr, '`%s` printed to stderr:' % ' '.join(args)
+-      print >>sys.stderr, stderr.rstrip()
++        print('`%s` printed to stderr:' % ' '.join(args), file=sys.stderr)
++      print(stderr.rstrip(), file=sys.stderr)
+     if strip:
+       stdout = stdout.rstrip('\r\n')
+     return stdout
+   if verbose:
+-    print >>sys.stderr, '`%s` returned %s' % (' '.join(args), p.returncode)
++    print('`%s` returned %s' % (' '.join(args), p.returncode), file=sys.stderr)
+   if stderr:
+-    print >>sys.stderr, stderr.rstrip()
++    print(stderr.rstrip(), file=sys.stderr)
+   sys.exit(2)
+ 
+ 
+ def die(message):
+-  print >>sys.stderr, 'error:', message
++  print('error:', message, file=sys.stderr)
+   sys.exit(2)
+ 
+ 

debian/patches/series

 spelling.patch
 compiler-flags.patch
 gcc-6.patch
+2to3.patch

debian/rules

@@ -9,7 +9,7 @@ export PYBUILD_NAME=pbconsensuscore
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@ --with python2,python3 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
@@ -20,10 +20,6 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 #	$(MAKE) test-python
 endif
 
-override_dh_python2:
-	dh_python2
-	dh_numpy
-
 override_dh_python3:
 	dh_python3
 	dh_numpy3