[med-svn] [Git][med-team/python-bx][master] 12 commits: Fixed d/watch
Steffen Möller
gitlab at salsa.debian.org
Wed Feb 24 20:54:41 GMT 2021
Steffen Möller pushed to branch master at Debian Med / python-bx
Commits:
135c83c6 by Steffen Moeller at 2021-02-24T21:45:39+01:00
Fixed d/watch
- - - - -
079d1e35 by Steffen Moeller at 2021-02-24T21:45:54+01:00
New upstream version 0.8.9
- - - - -
baa96c6e by Steffen Moeller at 2021-02-24T21:45:54+01:00
routine-update: New upstream version
- - - - -
23925fd6 by Steffen Moeller at 2021-02-24T21:45:57+01:00
Update upstream source from tag 'upstream/0.8.9'
Update to upstream version '0.8.9'
with Debian dir 8434d22cc9df7a3fc855ac191cb2bcc39c789744
- - - - -
9fc3f312 by Steffen Moeller at 2021-02-24T21:45:57+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
586952b1 by Steffen Moeller at 2021-02-24T21:45:57+01:00
routine-update: debhelper-compat 13
- - - - -
16947359 by Steffen Moeller at 2021-02-24T21:46:00+01:00
routine-update: Add salsa-ci file
- - - - -
92ca70b7 by Steffen Moeller at 2021-02-24T21:46:00+01:00
routine-update: Rules-Requires-Root: no
- - - - -
31d3fdf0 by Steffen Moeller at 2021-02-24T21:46:01+01:00
routine-update: No tab in license text
- - - - -
18e6cc96 by Steffen Moeller at 2021-02-24T21:46:02+01:00
Set upstream metadata fields: Bug-Submit.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
b4f744f3 by Steffen Moeller at 2021-02-24T21:47:20+01:00
routine-update: Ready to upload to unstable
- - - - -
80c44543 by Steffen Moeller at 2021-02-24T21:54:03+01:00
Fixed shebang lines
- - - - -
19 changed files:
- .travis.yml
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/series
- + debian/patches/shebang.patch
- + debian/salsa-ci.yml
- debian/upstream/metadata
- debian/watch
- lib/bx/__init__.py
- lib/bx/intervals/operations/quicksect.py
- lib/bx/misc/cdb.py
- lib/bx/seq/twobit.py
- scripts/aggregate_scores_in_intervals.py
- scripts/axt_to_lav.py
- scripts/axt_to_maf.py
- scripts/bed_coverage.py
- scripts/bed_merge_overlapping.py
- setup.py
Changes:
=====================================
.travis.yml
=====================================
@@ -68,9 +68,9 @@ addons:
- 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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+python-bx (0.8.9-1) unstable; urgency=medium
+
+ * 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.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 24 Feb 2021 21:46:03 +0100
+
python-bx (0.8.8-1) unstable; urgency=medium
* Modernize debian/watch
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-python,
zlib1g-dev,
python3-setuptools,
@@ -15,10 +15,11 @@ Build-Depends: debhelper-compat (= 12),
python3-numpy <!nocheck>,
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
=====================================
debian/copyright
=====================================
@@ -6,7 +6,7 @@ Files: *
Copyright: 2005-2015 The Pennsylvania State University
James Taylor <james at bx.psu.edu>
Bob Harris <rsharris at bx.psu.edu>
- 2013-2015 The Johns Hopkins University
+ 2013-2015 The Johns Hopkins University
License: MIT
Files: lib/bx_extras/fpconst.py
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
+shebang.patch
no-download.patch
fix_BIN_OFFSETS_MAX
=====================================
debian/patches/shebang.patch
=====================================
@@ -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
=====================================
debian/salsa-ci.yml
=====================================
@@ -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
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Submit: https://github.com/bxlab/bx-python/issues/new
Registry:
- Name: OMICtools
Entry: OMICS_18239
=====================================
debian/watch
=====================================
@@ -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
=====================================
lib/bx/__init__.py
=====================================
@@ -1 +1 @@
-__version__ = '0.8.8'
+__version__ = '0.8.9'
=====================================
lib/bx/intervals/operations/quicksect.py
=====================================
@@ -6,7 +6,12 @@ from __future__ import print_function
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 @@ class IntervalNode(object):
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 @@ def main():
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):
=====================================
lib/bx/misc/cdb.py
=====================================
@@ -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,
=====================================
lib/bx/seq/twobit.py
=====================================
@@ -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 @@ class TwoBitFile(Mapping):
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)
=====================================
scripts/aggregate_scores_in_intervals.py
=====================================
@@ -16,7 +16,8 @@ from __future__ import division, print_function
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
=====================================
scripts/axt_to_lav.py
=====================================
@@ -153,7 +153,7 @@ def read_lengths(fileName):
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
=====================================
scripts/axt_to_maf.py
=====================================
@@ -155,7 +155,7 @@ def read_lengths(fileName):
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
=====================================
scripts/bed_coverage.py
=====================================
@@ -9,14 +9,14 @@ usage: %prog bed files ...
"""
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
=====================================
scripts/bed_merge_overlapping.py
=====================================
@@ -9,14 +9,14 @@ usage: %prog bed files ...
"""
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
=====================================
setup.py
=====================================
@@ -24,6 +24,8 @@ with open(version_file) as f:
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 @@ def main():
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 @@ def main():
author="James Taylor, Bob Harris, David King, Brent Pedersen, Kanwei Li, and others",
author_email="james at 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",
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/1d4133a73bac696675ccd04ca9e405ec673a26e8...80c44543898676b6f18134b417246de5e087d6d1
--
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/1d4133a73bac696675ccd04ca9e405ec673a26e8...80c44543898676b6f18134b417246de5e087d6d1
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