[med-svn] [Git][med-team/pbalign][master] 9 commits: Add myself as Uploader
Andreas Tille
gitlab at salsa.debian.org
Fri Dec 13 10:19:12 GMT 2019
Andreas Tille pushed to branch master at Debian Med / pbalign
Commits:
f12bd4e0 by Andreas Tille at 2019-12-13T10:00:06Z
Add myself as Uploader
- - - - -
8ff56925 by Andreas Tille at 2019-12-13T10:02:31Z
Use 2to3 to port from Python2 to Python3
- - - - -
a83c7c4d by Andreas Tille at 2019-12-13T10:02:59Z
routine-update: debhelper-compat 12
- - - - -
179cd363 by Andreas Tille at 2019-12-13T10:03:03Z
routine-update: Standards-Version: 4.4.1
- - - - -
8c2378cd by Andreas Tille at 2019-12-13T10:03:03Z
R-U: Trailing whitespace in debian/rules
- - - - -
517498f6 by Andreas Tille at 2019-12-13T10:03:04Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
8cd30c0d by Andreas Tille at 2019-12-13T10:03:09Z
Set upstream metadata fields: Repository, Repository-Browse.
- - - - -
e87bb50f by Andreas Tille at 2019-12-13T10:12:54Z
Python3 in packaging
- - - - -
fdbf75c3 by Andreas Tille at 2019-12-13T10:18:46Z
Add TODO
- - - - -
9 changed files:
- − debian/README.Debian
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/pbalign.docs
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/README.Debian deleted
=====================================
@@ -1,4 +0,0 @@
-pbalign
-=======
-
-Some good soul needs to add a Python3 package.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+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 at debian.org> Fri, 13 Dec 2019 10:59:33 +0100
+
pbalign (0.3.2-1) unstable; urgency=medium
* Team upload
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -1,17 +1,18 @@
Source: pbalign
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at 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
=====================================
@@ -0,0 +1,601 @@
+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/937252
+Author: Andreas Tille <tille at 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
=====================================
@@ -1 +1,2 @@
find_definitions_from_pbcore.patch
+2to3.patch
=====================================
debian/pbalign.docs
=====================================
@@ -1,2 +1 @@
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
@@ -40,7 +40,7 @@ override_dh_install:
mv $(BINDIR)/* $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
no_override_dh_installmanpages: SHELL=bash
-no_override_dh_installmanpages:
+no_override_dh_installmanpages:
# Create manpages - this is deactivated in favour of debian/createmanpages script which is executed before creating the package
mkdir -p $(MANDIR)
declare -A description; \
@@ -52,7 +52,7 @@ no_override_dh_installmanpages:
[extractUnmappedSubreads.py]="Extract unmapped subreads from a fasta file" \
); \
set -x \
- export PYTHONPATH=$(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
=====================================
@@ -1,9 +1,11 @@
Registry:
- - Name: OMICtools
- Entry: OMICS_18565
- - Name: SciCrunch
- Entry: NA
- - Name: bio.tools
- Entry: NA
- - Name: conda:bioconda
- Entry: pbalign
+- Name: OMICtools
+ Entry: OMICS_18565
+- Name: SciCrunch
+ Entry: NA
+- Name: bio.tools
+ Entry: NA
+- Name: conda:bioconda
+ Entry: pbalign
+Repository: https://github.com/PacificBiosciences/pbalign.git
+Repository-Browse: https://github.com/PacificBiosciences/pbalign
View it on GitLab: https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c
--
View it on GitLab: https://salsa.debian.org/med-team/pbalign/compare/9db0d533f4ed00062e321314b467bf64d8647b96...fdbf75c3577ed02122704966069f19edd7eceb1c
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