[med-svn] [Git][med-team/consensuscore][master] 7 commits: Use 2to3 to convert from Python2 and Python3
Andreas Tille
gitlab at salsa.debian.org
Sat Dec 7 12:08:18 GMT 2019
Andreas Tille pushed to branch master at Debian Med / consensuscore
Commits:
a828a3ba by Andreas Tille at 2019-12-07T11:46:51Z
Use 2to3 to convert from Python2 and Python3
- - - - -
363d6619 by Andreas Tille at 2019-12-07T11:47:46Z
Add myself to Uploaders
- - - - -
356b6167 by Andreas Tille at 2019-12-07T11:51:16Z
Packaging information for Python3 only
- - - - -
e7433a5a by Andreas Tille at 2019-12-07T11:53:50Z
routine-update: debhelper-compat 12
- - - - -
4af40806 by Andreas Tille at 2019-12-07T11:53:55Z
routine-update: Standards-Version: 4.4.1
- - - - -
08940cf9 by Andreas Tille at 2019-12-07T11:59:29Z
Remove duplicate
- - - - -
ccccc89e by Andreas Tille at 2019-12-07T12:07:21Z
Does not build
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+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 at debian.org> Sat, 07 Dec 2019 12:44:55 +0100
+
consensuscore (1.1.1+dfsg-1) unstable; urgency=medium
* Team upload
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -1,22 +1,19 @@
Source: consensuscore
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at 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},
- ${python:Depends}
-Description: algorithms for PacBio multiple sequence consensus -- Python 2
- ConsensusCore is a library of C++ algorithms for Pacific Biosciences
- multiple sequence consensus that powers Quiver (Python) and ConsensusTools
- (.NET). This library primarily exists as the backend for GenomicConsensus,
- which implements Quiver.
- .
- This package is part of the SMRT Analysis suite.
- It provides the Python2 bindings.
-
Package: python3-pbconsensuscore
Architecture: any-amd64 any-i386
Section: python
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,310 @@
+Description: Use 2to3 to convert from Python2 and Python3
+Bug-Debian: https://bugs.debian.org/936328
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 07 Dec 2019 12:44:55 +0100
+
+--- a/make/Python.mk
++++ b/make/Python.mk
+@@ -8,11 +8,11 @@ endif
+ include make/Defs.mk
+
+ ifeq (,$(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
=====================================
@@ -1,3 +1,4 @@
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
View it on GitLab: https://salsa.debian.org/med-team/consensuscore/compare/31ee63496bcc067dfc2251feb406be70c65ae16a...ccccc89e1271d7096d85503ca427b9c3982e0d3a
--
View it on GitLab: https://salsa.debian.org/med-team/consensuscore/compare/31ee63496bcc067dfc2251feb406be70c65ae16a...ccccc89e1271d7096d85503ca427b9c3982e0d3a
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