diff -Nru python-bx-0.8.8/debian/changelog python-bx-0.8.9/debian/changelog --- python-bx-0.8.8/debian/changelog 2020-12-07 17:24:28.000000000 +0000 +++ python-bx-0.8.9/debian/changelog 2021-02-24 20:46:03.000000000 +0000 @@ -1,20 +1,16 @@ -python-bx (0.8.8-1build3) hirsute; urgency=medium +python-bx (0.8.9-1) unstable; urgency=medium - * No-change rebuild to drop python3.8 extensions. + * New upstream version + * Fixed d/watch to find the latest version. + * Fixed Python 2.4 shebang lines + * Standards-Version: 4.5.1 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * No tab in license text (routine-update) + * Set upstream metadata fields: Bug-Submit. - -- Matthias Klose Mon, 07 Dec 2020 18:24:28 +0100 - -python-bx (0.8.8-1build2) hirsute; urgency=medium - - * No-change rebuild to build with python3.9 as supported. - - -- Matthias Klose Mon, 26 Oct 2020 14:02:39 +0100 - -python-bx (0.8.8-1build1) focal; urgency=medium - - * No-change rebuild to drop python3.7. - - -- Matthias Klose Tue, 18 Feb 2020 09:38:39 +0100 + -- Steffen Moeller Wed, 24 Feb 2021 21:46:03 +0100 python-bx (0.8.8-1) unstable; urgency=medium diff -Nru python-bx-0.8.8/debian/control python-bx-0.8.9/debian/control --- python-bx-0.8.8/debian/control 2020-02-14 15:04:46.000000000 +0000 +++ python-bx-0.8.9/debian/control 2021-02-24 20:46:02.000000000 +0000 @@ -1,24 +1,25 @@ Source: python-bx Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , - Michael R. Crusoe + Michael R. Crusoe Section: python Testsuite: autopkgtest-pkg-python Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, zlib1g-dev, python3-setuptools, - python3-all-dev, + python3-all-dev:any, python3-lzo, - python3-nose, - python3-numpy, + python3-nose , + python3-numpy , python3-six, cython3 -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/python-bx Vcs-Git: https://salsa.debian.org/med-team/python-bx.git Homepage: https://github.com/bxlab/bx-python +Rules-Requires-Root: no Package: python3-bx Architecture: any diff -Nru python-bx-0.8.8/debian/copyright python-bx-0.8.9/debian/copyright --- python-bx-0.8.8/debian/copyright 2020-02-14 14:13:04.000000000 +0000 +++ python-bx-0.8.9/debian/copyright 2021-02-24 20:46:02.000000000 +0000 @@ -6,7 +6,7 @@ Copyright: 2005-2015 The Pennsylvania State University James Taylor Bob Harris - 2013-2015 The Johns Hopkins University + 2013-2015 The Johns Hopkins University License: MIT Files: lib/bx_extras/fpconst.py diff -Nru python-bx-0.8.8/debian/patches/series python-bx-0.8.9/debian/patches/series --- python-bx-0.8.8/debian/patches/series 2019-12-18 11:30:43.000000000 +0000 +++ python-bx-0.8.9/debian/patches/series 2021-02-24 20:46:03.000000000 +0000 @@ -1,2 +1,3 @@ +shebang.patch no-download.patch fix_BIN_OFFSETS_MAX diff -Nru python-bx-0.8.8/debian/patches/shebang.patch python-bx-0.8.9/debian/patches/shebang.patch --- python-bx-0.8.8/debian/patches/shebang.patch 1970-01-01 00:00:00.000000000 +0000 +++ python-bx-0.8.9/debian/patches/shebang.patch 2021-02-24 20:46:03.000000000 +0000 @@ -0,0 +1,130 @@ +Index: python-bx/scripts/bed_build_windows.py +=================================================================== +--- python-bx.orig/scripts/bed_build_windows.py ++++ python-bx/scripts/bed_build_windows.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + Build windows of length `window_size` over the sequences defined by +Index: python-bx/scripts/bed_complement.py +=================================================================== +--- python-bx.orig/scripts/bed_complement.py ++++ python-bx/scripts/bed_complement.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + Complement the regions of a bed file. Requires a file that maps source names +Index: python-bx/scripts/bed_count_by_interval.py +=================================================================== +--- python-bx.orig/scripts/bed_count_by_interval.py ++++ python-bx/scripts/bed_count_by_interval.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + """ + For each interval in `bed1` count the number of intersecting regions in `bed2`. + +Index: python-bx/scripts/bed_count_overlapping.py +=================================================================== +--- python-bx.orig/scripts/bed_count_overlapping.py ++++ python-bx/scripts/bed_count_overlapping.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + """ + For each interval in `bed1` count the number of intersecting regions in `bed2`. + +Index: python-bx/scripts/bed_rand_intersect.py +=================================================================== +--- python-bx.orig/scripts/bed_rand_intersect.py ++++ python-bx/scripts/bed_rand_intersect.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + From a set of regions and two sets of intervals inside those regions +Index: python-bx/scripts/div_snp_table_chr.py +=================================================================== +--- python-bx.orig/scripts/div_snp_table_chr.py ++++ python-bx/scripts/div_snp_table_chr.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + FIXME! +Index: python-bx/scripts/int_seqs_to_char_strings.py +=================================================================== +--- python-bx.orig/scripts/int_seqs_to_char_strings.py ++++ python-bx/scripts/int_seqs_to_char_strings.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python3 + + """ + Translate lists of space separated integers (magnitude less than 62) and print +Index: python-bx/scripts/interval_join.py +=================================================================== +--- python-bx.orig/scripts/interval_join.py ++++ python-bx/scripts/interval_join.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + Match up intersecting intervals from two files. This performs a "full join", +Index: python-bx/scripts/lzop_build_offset_table.py +=================================================================== +--- python-bx.orig/scripts/lzop_build_offset_table.py ++++ python-bx/scripts/lzop_build_offset_table.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + Read a compressed file as created by 'lzop' from stdin and write a table to +Index: python-bx/scripts/mMK_bitset.py +=================================================================== +--- python-bx.orig/scripts/mMK_bitset.py ++++ python-bx/scripts/mMK_bitset.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + from __future__ import print_function + + from optparse import OptionParser +Index: python-bx/scripts/maf_div_sites.py +=================================================================== +--- python-bx.orig/scripts/maf_div_sites.py ++++ python-bx/scripts/maf_div_sites.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + """ + Create a bed file listing all the divergent sites between two specific species + in a maf. +Index: python-bx/scripts/maf_interval_alignibility.py +=================================================================== +--- python-bx.orig/scripts/maf_interval_alignibility.py ++++ python-bx/scripts/maf_interval_alignibility.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + WARNING: bz2/bz2t support and file cache support are new and not as well +Index: python-bx/scripts/maf_species_in_all_files.py +=================================================================== +--- python-bx.orig/scripts/maf_species_in_all_files.py ++++ python-bx/scripts/maf_species_in_all_files.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.4 ++#!/usr/bin/python3 + + """ + Takes a list of maf filenames on the command line and prints a comma separated diff -Nru python-bx-0.8.8/debian/salsa-ci.yml python-bx-0.8.9/debian/salsa-ci.yml --- python-bx-0.8.8/debian/salsa-ci.yml 1970-01-01 00:00:00.000000000 +0000 +++ python-bx-0.8.9/debian/salsa-ci.yml 2021-02-24 20:46:00.000000000 +0000 @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff -Nru python-bx-0.8.8/debian/upstream/metadata python-bx-0.8.9/debian/upstream/metadata --- python-bx-0.8.8/debian/upstream/metadata 2019-12-18 09:44:00.000000000 +0000 +++ python-bx-0.8.9/debian/upstream/metadata 2021-02-24 20:46:02.000000000 +0000 @@ -1,3 +1,4 @@ +Bug-Submit: https://github.com/bxlab/bx-python/issues/new Registry: - Name: OMICtools Entry: OMICS_18239 diff -Nru python-bx-0.8.8/debian/watch python-bx-0.8.9/debian/watch --- python-bx-0.8.8/debian/watch 2020-02-14 14:11:49.000000000 +0000 +++ python-bx-0.8.9/debian/watch 2021-02-24 20:45:13.000000000 +0000 @@ -1,4 +1,3 @@ -# Compulsory line, this is a version 4 file version=4 opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-bx-$1.tar.gz%" \ - https://github.com/bxlab/bx-python/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@ + https://github.com/bxlab/bx-python/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz diff -Nru python-bx-0.8.8/lib/bx/__init__.py python-bx-0.8.9/lib/bx/__init__.py --- python-bx-0.8.8/lib/bx/__init__.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/lib/bx/__init__.py 2020-06-18 23:58:17.000000000 +0000 @@ -1 +1 @@ -__version__ = '0.8.8' +__version__ = '0.8.9' diff -Nru python-bx-0.8.8/lib/bx/intervals/operations/quicksect.py python-bx-0.8.9/lib/bx/intervals/operations/quicksect.py --- python-bx-0.8.8/lib/bx/intervals/operations/quicksect.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/lib/bx/intervals/operations/quicksect.py 2020-06-18 23:58:17.000000000 +0000 @@ -6,7 +6,12 @@ import math import random -import time + +try: + from time import process_time +except ImportError: + # For compatibility with Python < 3.3 + from time import clock as process_time class IntervalTree(object): @@ -130,7 +135,7 @@ def main(): test = None intlist = [] - for x in range(20000): + for _ in range(20000): start = random.randint(0, 1000000) end = start + random.randint(1, 1000) if test: @@ -138,19 +143,19 @@ else: test = IntervalNode(start, end) intlist.append((start, end)) - starttime = time.clock() + starttime = process_time() for x in range(5000): start = random.randint(0, 10000000) end = start + random.randint(1, 1000) result = [] test.intersect(start, end, lambda x: result.append(x.linenum)) - print("%f for tree method" % (time.clock() - starttime)) - starttime = time.clock() - for x in range(5000): + print("%f for tree method" % (process_time() - starttime)) + starttime = process_time() + for _ in range(5000): start = random.randint(0, 10000000) end = start + random.randint(1, 1000) bad_sect(intlist, start, end) - print("%f for linear (bad) method" % (time.clock() - starttime)) + print("%f for linear (bad) method" % (process_time() - starttime)) def test_func(node): diff -Nru python-bx-0.8.8/lib/bx/misc/cdb.py python-bx-0.8.9/lib/bx/misc/cdb.py --- python-bx-0.8.8/lib/bx/misc/cdb.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/lib/bx/misc/cdb.py 2020-06-18 23:58:17.000000000 +0000 @@ -1,8 +1,5 @@ - - -from collections import Mapping - from six.moves import reduce +from six.moves.collections_abc import Mapping from bx.misc.binary_file import ( BinaryFileReader, diff -Nru python-bx-0.8.8/lib/bx/seq/twobit.py python-bx-0.8.9/lib/bx/seq/twobit.py --- python-bx-0.8.8/lib/bx/seq/twobit.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/lib/bx/seq/twobit.py 2020-06-18 23:58:17.000000000 +0000 @@ -1,9 +1,10 @@ """ Access to files containing sequence data in 'twobit' format. """ -from collections import Mapping from struct import calcsize, unpack +from six.moves.collections_abc import Mapping + from . import _twobit TWOBIT_MAGIC_NUMBER = 0x1A412743 @@ -72,7 +73,7 @@ self.reserved = self.read("L") # Read index of sequence names to offsets index = dict() - for i in range(self.seq_count): + for _ in range(self.seq_count): name = self.read_p_string() offset = self.read("L") index[name] = TwoBitSequence(self, offset) diff -Nru python-bx-0.8.8/scripts/aggregate_scores_in_intervals.py python-bx-0.8.9/scripts/aggregate_scores_in_intervals.py --- python-bx-0.8.8/scripts/aggregate_scores_in_intervals.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/scripts/aggregate_scores_in_intervals.py 2020-06-18 23:58:17.000000000 +0000 @@ -16,7 +16,8 @@ import os import os.path import sys -from collections import Mapping + +from six.moves.collections_abc import Mapping import bx.wiggle from bx import misc diff -Nru python-bx-0.8.8/scripts/axt_to_lav.py python-bx-0.8.9/scripts/axt_to_lav.py --- python-bx-0.8.8/scripts/axt_to_lav.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/scripts/axt_to_lav.py 2020-06-18 23:58:17.000000000 +0000 @@ -153,7 +153,7 @@ raise ValueError("bad lengths line (%s:%d): %s" % (fileName, lineNumber, line)) if chrom in chromToLength: - raise ValueError("%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber)) + raise ValueError("%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber, line)) chromToLength[chrom] = length diff -Nru python-bx-0.8.8/scripts/axt_to_maf.py python-bx-0.8.9/scripts/axt_to_maf.py --- python-bx-0.8.8/scripts/axt_to_maf.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/scripts/axt_to_maf.py 2020-06-18 23:58:17.000000000 +0000 @@ -155,7 +155,7 @@ raise ValueError("bad lengths line (%s:%d): %s" % (fileName, lineNumber, line)) if (chrom in chromToLength): - raise ValueError("%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber)) + raise ValueError("%s appears more than once (%s:%d): %s" % (chrom, fileName, lineNumber, line)) chromToLength[chrom] = length diff -Nru python-bx-0.8.8/scripts/bed_coverage.py python-bx-0.8.9/scripts/bed_coverage.py --- python-bx-0.8.8/scripts/bed_coverage.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/scripts/bed_coverage.py 2020-06-18 23:58:17.000000000 +0000 @@ -9,14 +9,14 @@ """ from __future__ import print_function +import fileinput import sys -from itertools import chain from bx.bitset_builders import binned_bitsets_from_file bed_filenames = sys.argv[1:] if bed_filenames: - input = chain(* (open(_) for _ in bed_filenames)) + input = fileinput.input(bed_filenames) else: input = sys.stdin diff -Nru python-bx-0.8.8/scripts/bed_merge_overlapping.py python-bx-0.8.9/scripts/bed_merge_overlapping.py --- python-bx-0.8.8/scripts/bed_merge_overlapping.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/scripts/bed_merge_overlapping.py 2020-06-18 23:58:17.000000000 +0000 @@ -9,14 +9,14 @@ """ from __future__ import print_function +import fileinput import sys -from itertools import chain from bx.bitset_builders import binned_bitsets_from_bed_file bed_filenames = sys.argv[1:] if bed_filenames: - input = chain(* (open(_) for _ in bed_filenames)) + input = fileinput.input(bed_filenames) else: input = sys.stdin diff -Nru python-bx-0.8.8/setup.py python-bx-0.8.9/setup.py --- python-bx-0.8.8/setup.py 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/setup.py 2020-06-18 23:58:17.000000000 +0000 @@ -24,6 +24,8 @@ break else: raise Exception("Version not found in " + version_file) +with open('README.md') as f: + long_description = f.read() def main(): @@ -32,7 +34,9 @@ version=version, python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*', setup_requires=['numpy', 'cython'], - install_requires=['numpy', 'six'], + install_requires=[ + 'numpy', + 'six>=1.13.0'], py_modules=['psyco_full'], package_dir={'': 'lib'}, package_data={'': ['*.ps']}, @@ -42,7 +46,13 @@ author="James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others", author_email="james@jamestaylor.org", description="Tools for manipulating biological data, particularly multiple sequence alignments", + long_description=long_description, + long_description_content_type='text/markdown', url="https://github.com/bxlab/bx-python", + project_urls={ + "Bug Tracker": "https://github.com/bxlab/bx-python/issues", + "Source Code": "https://github.com/bxlab/bx-python", + }, license="MIT", classifiers=[ "Development Status :: 5 - Production/Stable", diff -Nru python-bx-0.8.8/.travis.yml python-bx-0.8.9/.travis.yml --- python-bx-0.8.8/.travis.yml 2020-02-13 11:52:37.000000000 +0000 +++ python-bx-0.8.9/.travis.yml 2020-06-18 23:58:17.000000000 +0000 @@ -68,9 +68,9 @@ - liblzo2-dev install: - - $PYTHON -m pip install Cython nose numpy python-lzo six + - $PYTHON -m pip install Cython nose numpy python-lzo - $PYTHON setup.py build_ext --inplace - - $PYTHON setup.py install + - $PYTHON -m pip install . script: - nosetests