debian/README.Debian

-pbalign
-=======
-
-Some good soul needs to add a Python3 package.

debian/changelog

+pbalign (0.3.2-2) UNRELEASED; urgency=medium
+
+  * Afif removed himself as Uploader
+  * Add myself as Uploader
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #937252
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove trailing whitespace in debian/rules
+  * Trim trailing whitespace.
+  * Set upstream metadata fields: Repository, Repository-Browse.
+  TODO:
+    - Sphinx has import failures
+    - python3-pbh5tools not yet available
+
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Dec 2019 10:59:33 +0100
+
 pbalign (0.3.2-1) unstable; urgency=medium
 
   * Team upload

debian/compat

-11

debian/control

 Source: pbalign
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: python
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all,
-               python-setuptools,
-               python-pbcore,
-               python-pbcommand,
+               python3,
+               python3-setuptools,
+               python3-pbcore,
+               python3-pbcommand,
                python3-sphinx,
-               python-nose
-Standards-Version: 4.3.0
+               python3-nose
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/pbalign
 Vcs-Git: https://salsa.debian.org/med-team/pbalign.git
 Homepage: https://github.com/PacificBiosciences/pbalign
@@ -19,11 +20,11 @@ Homepage: https://github.com/PacificBiosciences/pbalign
 Package: pbalign
 Architecture: all
 Depends: ${misc:Depends},
-         ${python:Depends},
-         python-pbalign (= ${source:Version}),
-         python-pkg-resources,
-         blasr (>= 5.3+0)
-Recommends: python-pbh5tools,
+         ${python3:Depends},
+         python3-pbalign (= ${source:Version}),
+         python3-pkg-resources,
+         blasr
+Recommends: python3-pbh5tools,
             hdf5-tools
 Suggests: bowtie2,
           gmap,
@@ -36,12 +37,12 @@ Description: map Pacific Biosciences reads to reference DNA sequences
  .
  This package is part of the SMRTAnalysis suite.
 
-Package: python-pbalign
+Package: python3-pbalign
 Architecture: all
 Depends: ${misc:Depends},
-         ${python:Depends},
-         blasr (>= 5.3+0)
-Recommends: python-pbh5tools,
+         ${python3:Depends},
+         blasr
+Recommends: python3-pbh5tools,
             hdf5-tools
 Suggests: bowtie2,
           gmap,

debian/patches/2to3.patch

+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/937252
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 13 Dec 2019 10:59:33 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -3,25 +3,25 @@ SHELL = /bin/bash -e
+ all: build install
+ 
+ build:
+-	python setup.py build --executable="/usr/bin/env python"
++	python3 setup.py build --executable="/usr/bin/python3"
+ 
+ bdist:
+-	python setup.py build --executable="/usr/bin/env python"
+-	python setup.py bdist --formats=egg
++	python3 setup.py build --executable="/usr/bin/python3"
++	python3 setup.py bdist --formats=egg
+ 
+ install:
+-	python setup.py install
++	python3 setup.py install
+ 
+ develop:
+-	python setup.py develop
++	python3 setup.py develop
+ 
+ pylint:
+-	pylint --errors-only pbalign
++	pylint3 --errors-only pbalign
+ 
+ test: pylint
+ 	# Unit tests
+ 	#find tests/unit -name "*.py" | xargs nosetests
+-	python setup.py test
++	python3 setup.py test
+ 	# End-to-end tests
+ 	@echo pbalign cram tests require blasr installed.
+ 	find tests/cram -name "*.t" | xargs cram 
+@@ -29,7 +29,7 @@ test: pylint
+ h5test:
+ 	# Tests for pre-3.0 smrtanalysis when default file formats are *.h5
+ 	@echo pbalign h5 tests require blasr, samtoh5, loadPulses, samFilter and etc installed.
+-	nosetests --verbose tests/unit_h5/*.py
++	nosetests3 --verbose tests/unit_h5/*.py
+ 	find tests/cram_h5 -name "*.t" | xargs cram -v
+ 
+ doc:
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -40,8 +40,8 @@ source_suffix = '.rst'
+ master_doc = 'index'
+ 
+ # General information about the project.
+-project = u'pbalign'
+-copyright = u'2013, 2013, pbiDevNet'
++project = 'pbalign'
++copyright = '2013, 2013, pbiDevNet'
+ 
+ # The version info for the project you're documenting, acts as replacement for
+ # |version| and |release|, also used in various other places throughout the
+@@ -183,8 +183,8 @@ latex_elements = {
+ # Grouping the document tree into LaTeX files. List of tuples
+ # (source start file, target name, title, author, documentclass [howto/manual]).
+ latex_documents = [
+-  ('index', 'pbalign.tex', u'pbalign Documentation',
+-   u'2013, pbiDevNet', 'manual'),
++  ('index', 'pbalign.tex', 'pbalign Documentation',
++   '2013, pbiDevNet', 'manual'),
+ ]
+ 
+ # The name of an image file (relative to this directory) to place at the top of
+@@ -213,8 +213,8 @@ latex_documents = [
+ # One entry per manual page. List of tuples
+ # (source start file, name, description, authors, manual section).
+ man_pages = [
+-    ('index', 'pbalign', u'pbalign Documentation',
+-     [u'2013, pbiDevNet'], 1)
++    ('index', 'pbalign', 'pbalign Documentation',
++     ['2013, pbiDevNet'], 1)
+ ]
+ 
+ # If true, show URL addresses after external links.
+@@ -227,8 +227,8 @@ man_pages = [
+ # (source start file, target name, title, author,
+ #  dir menu entry, description, category)
+ texinfo_documents = [
+-  ('index', 'pbalign', u'pbalign Documentation',
+-   u'2013, pbiDevNet', 'pbalign', 'One line description of project.',
++  ('index', 'pbalign', 'pbalign Documentation',
++   '2013, pbiDevNet', 'pbalign', 'One line description of project.',
+    'Miscellaneous'),
+ ]
+ 
+--- a/pbalign/__init__.py
++++ b/pbalign/__init__.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -32,7 +32,7 @@
+ # Author: Yuan Li
+ """Initialization."""
+ 
+-from __future__ import absolute_import
++
+ 
+ _changelist = "$Change: 173392 $"
+ 
+--- a/pbalign/alignservice/__init__.py
++++ b/pbalign/alignservice/__init__.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -31,4 +31,4 @@
+ 
+ # Author: Yuan Li
+ """Initialization."""
+-from __future__ import absolute_import
++
+--- a/pbalign/alignservice/align.py
++++ b/pbalign/alignservice/align.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -32,7 +32,7 @@
+ # Author: Yuan Li
+ """This script defines class AlignService."""
+ 
+-from __future__ import absolute_import
++
+ import logging
+ from copy import copy
+ from pbalign.options import importDefaultOptions
+--- a/pbalign/alignservice/blasr.py
++++ b/pbalign/alignservice/blasr.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -33,7 +33,7 @@
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import
++
+ from pbalign.alignservice.align import AlignService
+ from pbalign.utils.fileutil import FILE_FORMATS, real_upath, getFileFormat
+ import logging
+--- a/pbalign/alignservice/bowtie.py
++++ b/pbalign/alignservice/bowtie.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -33,7 +33,7 @@
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import
++
+ from pbalign.alignservice.fastabasedalign import FastaBasedAlignService
+ from os import path
+ from pbcore.util.Process import backticks
+--- a/pbalign/alignservice/fastabasedalign.py
++++ b/pbalign/alignservice/fastabasedalign.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -34,7 +34,7 @@ which converts PacBio reads in BASE/PULS
+ align."""
+ 
+ # Author: Yuan Li
+-from __future__ import absolute_import
++
+ from pbalign.alignservice.align import AlignService
+ from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS
+ from pbcore.util.Process import backticks
+--- a/pbalign/alignservice/gmap.py
++++ b/pbalign/alignservice/gmap.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -33,7 +33,7 @@
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import
++
+ from os import path
+ from pbalign.alignservice.fastabasedalign import FastaBasedAlignService
+ from pbalign.utils.fileutil import isExist
+--- a/pbalign/bampostservice.py
++++ b/pbalign/bampostservice.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -37,7 +37,7 @@
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import, division, print_function
++
+ import logging
+ from pbalign.service import Service
+ from pbalign.utils.progutil import Execute
+--- a/pbalign/ccs.py
++++ b/pbalign/ccs.py
+@@ -13,7 +13,7 @@ import pbalign.options
+ 
+ class Constants(pbalign.options.Constants):
+     TOOL_ID = "pbalign.tasks.pbalign_ccs"
+-    DRIVER_EXE = "python -m pbalign.ccs --resolved-tool-contract"
++    DRIVER_EXE = "python3 -m pbalign.ccs --resolved-tool-contract"
+     INPUT_FILE_TYPE = FileTypes.DS_CCS
+     OUTPUT_FILE_TYPE = FileTypes.DS_ALIGN_CCS
+     # some modified defaults
+--- a/pbalign/filterservice.py
++++ b/pbalign/filterservice.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -34,7 +34,7 @@ in an input SAM file according to filter
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import
++
+ import logging
+ from pbalign.service import Service
+ from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS, isExist
+--- a/pbalign/options.py
++++ b/pbalign/options.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -32,7 +32,7 @@
+ # Author:Yuan Li
+ """This scripts defines functions for parsing PBAlignRunner options."""
+ 
+-from __future__ import absolute_import
++
+ import argparse
+ import logging
+ from copy import copy
+@@ -509,7 +509,7 @@ def importDefaultOptions(parsedOptions,
+     newOptions = copy(parsedOptions)
+     infoMsg = "Importing default options: "
+     optionsDictView = vars(newOptions)
+-    for k, v in additionalDefaults.iteritems():
++    for k, v in additionalDefaults.items():
+         if (k not in optionsDictView) or (optionsDictView[k] is None):
+             infoMsg += "{k}={v}, ".format(k=optionsDictView[k], v=v)
+             optionsDictView[k] = v
+--- a/pbalign/pbalignfiles.py
++++ b/pbalign/pbalignfiles.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -32,7 +32,7 @@
+ # Author: Yuan Li
+ """This script defines class PBALignFiles."""
+ 
+-from __future__ import absolute_import
++
+ from pbalign.utils.fileutil import checkInputFile, getRealFileFormat, \
+     checkOutputFile, checkReferencePath, checkRegionTableFile, \
+     getFileFormat, FILE_FORMATS
+--- a/pbalign/pbalignrunner.py
++++ b/pbalign/pbalignrunner.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+--- a/pbalign/service.py
++++ b/pbalign/service.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -30,7 +30,7 @@
+ ###############################################################################
+ 
+ """This script defines a virtual class Service."""
+-from __future__ import absolute_import
++
+ from pbalign.utils.progutil import Availability, \
+     CheckAvailability, Execute
+ 
+--- a/pbalign/tasks/align_minorvariants.py
++++ b/pbalign/tasks/align_minorvariants.py
+@@ -20,7 +20,7 @@ __version__ = "0.1"
+ 
+ class Constants(object):
+     TOOL_ID = "pbalign.tasks.align_minorvariants"
+-    DRIVER_EXE = "python -m pbalign.tasks.align_minorvariants --resolved-tool-contract "
++    DRIVER_EXE = "python3 -m pbalign.tasks.align_minorvariants --resolved-tool-contract "
+ 
+ 
+ def get_parser():
+--- a/pbalign/tools/__init__.py
++++ b/pbalign/tools/__init__.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -32,5 +32,5 @@
+ # Author: Yuan Li
+ """Migrate pbpy scripts to bioinformatics."""
+ 
+-from __future__ import absolute_import
++
+ 
+--- a/pbalign/tools/createChemistryHeader.py
++++ b/pbalign/tools/createChemistryHeader.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """createChemistryHeader.py gets chemistry triple information for movies in
+ a BLASR-produced SAM file. It writes a new SAM header file that contains the
+ chemisty information. This header can be used with samtools reheader. Most
+--- a/pbalign/tools/extractUnmappedSubreads.py
++++ b/pbalign/tools/extractUnmappedSubreads.py
+@@ -1,10 +1,10 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """
+ Starts with the filtered_reads.fa file. Reads in the control.cmp.h5 and
+ reference.cmp.h5, removing any subreads that map. Writes resulting fasta
+ entries to stdout.
+ """
+-from __future__ import print_function
++
+ 
+ import sys
+ import logging
+@@ -60,7 +60,7 @@ class ExtractRunner(PBToolRunner):
+         subread data structure."""
+         cmpFile = h5py.File(cmpH5FN, 'r')
+         movieInfo = cmpFile["/MovieInfo"]
+-        movieDict = dict(zip(movieInfo["ID"], movieInfo["Name"]))
++        movieDict = dict(list(zip(movieInfo["ID"], movieInfo["Name"])))
+ 
+         numAln = cmpFile["/AlnInfo/AlnIndex"].shape[0]
+         movieIdIdx, holeIdx, startIdx, endIdx = 2, 7, 11, 12
+--- a/pbalign/tools/loadChemistry.py
++++ b/pbalign/tools/loadChemistry.py
+@@ -1,6 +1,6 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
++
+ 
+-from __future__ import print_function
+ USAGE = \
+ """
+ loadChemistry.py
+@@ -38,7 +38,7 @@ def writeTriples(movieInfoGroup, triples
+     sequencingKit   = movieInfoGroup.create_dataset("SequencingKit"  , shape=shape, dtype=STRING_DTYPE, maxshape=(None,))
+     softwareVersion = movieInfoGroup.create_dataset("SoftwareVersion", shape=shape, dtype=STRING_DTYPE, maxshape=(None,))
+ 
+-    for (movieName, triple) in triplesByMovieName.items():
++    for (movieName, triple) in list(triplesByMovieName.items()):
+         if movieName in movieNamesInCmpH5:
+             idx = movieNamesInCmpH5.index(movieName)
+             bindingKit[idx]      = triple[0]
+--- a/pbalign/tools/mask_aligned_reads.py
++++ b/pbalign/tools/mask_aligned_reads.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """Takes in a rgn.fofn and corresponding cmp.h5. Uses the
+ alignments from the cmp.h5 to mask corresponding regions of
+ the rgn.h5s. Writes output to a new rgn.fofn."""
+@@ -37,7 +37,7 @@ class AlignedReadsMasker(object):
+         logging.debug("Log Level set to DEBUG")
+ 
+         alignedReads = self._extractAlignedReads()
+-        nreads = sum([len(v) for v in alignedReads.values()])
++        nreads = sum([len(v) for v in list(alignedReads.values())])
+         logging.info("Extracted {r} reads ({m} movies) from {f}".format(
+             r=nreads, m=len(alignedReads), f=self.inCmpFile))
+ 
+--- a/pbalign/utils/RgnH5IO.py
++++ b/pbalign/utils/RgnH5IO.py
+@@ -1,9 +1,9 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # Author: Yuan Li
+ """
+ Region table reader and writer.
+ """
+-from __future__ import print_function
++
+ __all__ = ["RgnH5Reader",
+            "RgnH5Writer"]
+ import h5py
+@@ -199,7 +199,7 @@ class RgnH5Reader(object):
+         else:
+             movieNameString = movieNameAttr
+ 
+-        if not isinstance(movieNameString, basestring):
++        if not isinstance(movieNameString, str):
+             raise TypeError("Unsupported movieName {m} of type {t}."
+                             .format(m=movieNameString,
+                                     t=type(movieNameString)))
+--- a/pbalign/utils/__init__.py
++++ b/pbalign/utils/__init__.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -31,4 +31,4 @@
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import
++
+--- a/pbalign/utils/fileutil.py
++++ b/pbalign/utils/fileutil.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -34,7 +34,7 @@
+ 
+ """This scripts defines functions for handling input and output files."""
+ 
+-from __future__ import absolute_import
++
+ import os
+ import os.path as op
+ import logging
+--- a/pbalign/utils/progutil.py
++++ b/pbalign/utils/progutil.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+@@ -33,7 +33,7 @@
+ 
+ # Author: Yuan Li
+ 
+-from __future__ import absolute_import
++
+ from pbcore.util.Process import backticks
+ import logging
+ 
+--- a/pbalign/utils/tempfileutil.py
++++ b/pbalign/utils/tempfileutil.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ ###############################################################################
+ # Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
+ #
+--- a/setup.py
++++ b/setup.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ # -*- coding: utf-8 -*-
+ 
+ from setuptools import setup, find_packages
+--- a/tests/unit/test_fileutil.py
++++ b/tests/unit/test_fileutil.py
+@@ -1,5 +1,5 @@
+ """Test pbalign.util/fileutil.py"""
+-from __future__ import print_function
++
+ 
+ import tempfile
+ import unittest
+--- a/tests/unit/test_options.py
++++ b/tests/unit/test_options.py
+@@ -1,4 +1,4 @@
+-from __future__ import print_function
++
+ 
+ import tempfile
+ from argparse import *
+--- a/tests/unit/test_setpath.py
++++ b/tests/unit/test_setpath.py
+@@ -1,6 +1,6 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ from os import path
+-import ConfigParser
++import configparser
+ 
+ """Define test data path for pbalign."""
+ 
+@@ -11,7 +11,7 @@ NOSE_CFG = path.join(THIS_DIR, "nose.cfg
+ def _get_data_std_dir():
+     """Get the data directory which contains all the unittests files.
+     """
+-    nosecfg = ConfigParser.SafeConfigParser()
++    nosecfg = configparser.SafeConfigParser()
+     nosecfg.readfp(open(NOSE_CFG), 'r')
+     if nosecfg.has_section('data'):
+         data_dir = path.abspath(nosecfg.get('data', 'dataDir'))
+--- a/tests/unit/test_tool_contract.py
++++ b/tests/unit/test_tool_contract.py
+@@ -34,7 +34,7 @@ class TestPbalign(pbcommand.testkit.PbTe
+ 
+ 
+ class TestPbalignCCS(pbcommand.testkit.PbTestApp):
+-    DRIVER_BASE = "python -m pbalign.ccs"
++    DRIVER_BASE = "python3 -m pbalign.ccs"
+     INPUT_FILES = [
+         pbtestdata.get_file("rsii-ccs"),
+         pbtestdata.get_file("lambdaNEB")
+@@ -47,7 +47,7 @@ class TestPbalignCCS(pbcommand.testkit.P
+ 
+ 
+ class TestPbalignMinorVariants(pbcommand.testkit.PbTestApp):
+-    DRIVER_BASE = "python -m pbalign.tasks.align_minorvariants"
++    DRIVER_BASE = "python3 -m pbalign.tasks.align_minorvariants"
+     INPUT_FILES = [
+         pbtestdata.get_file("rsii-ccs"),
+         pbtestdata.get_file("lambdaNEB")
+--- a/tests/unit_h5/test_repackservice.py
++++ b/tests/unit_h5/test_repackservice.py
+@@ -1,5 +1,5 @@
+ """Test pbalign.forquiverservice.repack."""
+-from __future__ import print_function
++
+ import unittest
+ from os import path, remove
+ from shutil import copyfile
+--- a/tests/unit_h5/test_setpath.py
++++ b/tests/unit_h5/test_setpath.py
+@@ -1,6 +1,6 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+ from os import path
+-import ConfigParser
++import configparser
+ 
+ """Define test data path for pbalign."""
+ 
+@@ -11,7 +11,7 @@ NOSE_CFG = path.join(THIS_DIR, "nose.cfg
+ def _get_data_std_dir():
+     """Get the data directory which contains all the unittests files.
+     """
+-    nosecfg = ConfigParser.SafeConfigParser()
++    nosecfg = configparser.SafeConfigParser()
+     nosecfg.readfp(open(NOSE_CFG), 'r')
+     if nosecfg.has_section('data'):
+         data_dir = path.abspath(nosecfg.get('data', 'dataDir'))
+--- a/tests/unit_h5/test_sortservice.py
++++ b/tests/unit_h5/test_sortservice.py
+@@ -1,5 +1,5 @@
+ """Test pbalign.forquiverservice.sort."""
+-from __future__ import print_function
++
+ import unittest
+ from os import path, remove
+ from shutil import copyfile

debian/patches/series

 find_definitions_from_pbcore.patch
+2to3.patch

debian/pbalign.docs

 README.md
-debian/README.Debian

debian/rules

@@ -6,13 +6,13 @@ include /usr/share/dpkg/default.mk
 
 export PYBUILD_NAME = pbalign
 
-BUILDDIR = $(CURDIR)/debian/python-pbalign
+BUILDDIR = $(CURDIR)/debian/python3-$(PYBUILD_NAME)
 BINDIR=$(BUILDDIR)/usr/bin
 HELP2MAN = help2man --no-info --version-string $(DEB_VERSION_UPSTREAM)
 MANDIR = $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
 
 %:
-	dh $@ --with=python2 --buildsystem=pybuild
+	dh $@ --with=python3 --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
@@ -22,7 +22,7 @@ override_dh_auto_build:
 # (which are large) are not provided in the source distribution
 #override_dh_auto_test:
 #	export PYTHONPATH=$(CURDIR);	\
-#	cd tests/unit && python -m unittest discover
+#	cd tests/unit && python3 -m unittest discover
 
 override_dh_install:
 	dh_install
@@ -52,7 +52,7 @@ no_override_dh_installmanpages:
 	  [extractUnmappedSubreads.py]="Extract unmapped subreads from a fasta file" \
 	);								       \
 	set -x \
-	export PYTHONPATH=$(BUILDDIR)/usr/lib/python2.7/dist-packages;	       \
+	export PYTHONPATH=$(BUILDDIR)/usr/lib/python3.7/dist-packages;	       \
 	for executable in $(BUILDDIR)/usr/bin/*;			       \
 	do								       \
 	    $(HELP2MAN) --name="$${description[`basename $$executable`]}"      \
@@ -64,4 +64,3 @@ override_dh_auto_clean:
 	rm -rf doc/_build/
 	rm -f doc/pbalign.alignservice.rst doc/pbalign.rst doc/pbalign.tasks.rst doc/pbalign.tools.rst doc/pbalign.utils.rst
 	rm -rf pbalign.egg-info
-

debian/upstream/metadata

@@ -7,3 +7,5 @@ Registry:
   Entry: NA
 - Name: conda:bioconda
   Entry: pbalign
+Repository: https://github.com/PacificBiosciences/pbalign.git
+Repository-Browse: https://github.com/PacificBiosciences/pbalign