[med-svn] [Git][med-team/bowtie2][master] 4 commits: Update d/patches/2to3.patch, use importlib instead of deprecated imp module
Alexandre Mestiashvili
gitlab at salsa.debian.org
Fri Dec 6 22:42:36 GMT 2019
Alexandre Mestiashvili pushed to branch master at Debian Med / bowtie2
Commits:
edae9ad5 by Alexandre Mestiashvili at 2019-12-06T19:31:54Z
Update d/patches/2to3.patch, use importlib instead of deprecated imp module
- - - - -
3a2df740 by Alexandre Mestiashvili at 2019-12-06T20:16:05Z
Add patch silencing TBB deprecation warnings
- - - - -
ddf99c60 by Alexandre Mestiashvili at 2019-12-06T20:52:38Z
d/control: bump Policy to 4.4.1, add Rules-requires-root: no
- - - - -
88e9eb28 by Alexandre Mestiashvili at 2019-12-06T21:40:29Z
Update changelog
Gbp-Dch: Ignore
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/2to3.patch
- debian/patches/series
- + debian/patches/silence_tbb_deprecation_warning.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,21 @@
+bowtie2 (2.3.5.1-2) unstable; urgency=medium
+
+ [ Steffen Möller ]
+ * Added ref to conda
+
+ [ Andreas Tille ]
+ * SEQwiki is deprecated
+
+ [ Steffen Moeller ]
+ * d/u/metadata: yamllint
+
+ [ Alexandre Mestiashvili ]
+ * Update d/patches/2to3.patch, use importlib instead of deprecated imp module
+ * Add patch silencing TBB deprecation warnings
+ * d/control: bump Policy to 4.4.1, add Rules-requires-root: no
+
+ -- Alexandre Mestiashvili <mestia at debian.org> Fri, 06 Dec 2019 22:38:21 +0100
+
bowtie2 (2.3.5.1-1) unstable; urgency=medium
[ Michael R. Crusoe ]
=====================================
debian/control
=====================================
@@ -13,7 +13,8 @@ Build-Depends: debhelper-compat (= 12),
libclone-perl,
libfile-which-perl,
zlib1g-dev
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
+Rules-requires-root: no
Vcs-Browser: https://salsa.debian.org/med-team/bowtie2
Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git
Homepage: http://bowtie-bio.sourceforge.net/bowtie2
=====================================
debian/patches/2to3.patch
=====================================
@@ -5,7 +5,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
--- a/Makefile
+++ b/Makefile
-@@ -481,11 +481,11 @@ bowtie2.bat:
+@@ -481,11 +481,11 @@
bowtie2-build.bat:
echo "@echo off" > bowtie2-build.bat
@@ -27,7 +27,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
"""
sa.py
-@@ -15,7 +15,7 @@ import struct
+@@ -15,7 +15,7 @@
def loadBowtieSa(fh):
""" Load a .sa file from handle into an array of ints """
nsa = struct.unpack('I', fh.read(4))[0]
@@ -36,7 +36,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
def loadBowtieSaFilename(fn):
""" Load a .sa file from filename into an array of ints """
-@@ -58,7 +58,7 @@ if __name__ == "__main__":
+@@ -58,7 +58,7 @@
# Suffix array is in sas; note that $ is considered greater than all
# other characters
if ref is not None:
@@ -45,7 +45,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
sa1, sa2 = sas[i-1], sas[i]
assert sa1 != sa2
# Sanity check that suffixes are really in order
-@@ -76,4 +76,4 @@ if __name__ == "__main__":
+@@ -76,4 +76,4 @@
assert sas[-1] == len(ref)
go()
@@ -54,7 +54,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
+
--- a/scripts/test/README.md
+++ b/scripts/test/README.md
-@@ -17,7 +17,7 @@ They use the Python infrastructure in th
+@@ -17,7 +17,7 @@
From root:
@@ -63,7 +63,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
Val Antonescu originally set these up.
-@@ -27,7 +27,7 @@ Builds an index consisting of both human
+@@ -27,7 +27,7 @@
From root:
@@ -80,7 +80,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
"""
A few items to deal with sets of benchmarks.
"""
-@@ -57,7 +57,7 @@ class Benchmarks(object):
+@@ -57,7 +57,7 @@
self.set_idx = 0
return self
@@ -89,7 +89,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
if self.set_idx == len(self.values):
raise StopIteration
-@@ -250,7 +250,7 @@ class TestAccuracy(Runable):
+@@ -250,7 +250,7 @@
delta = [0, 1]
logging.debug("%s: missed (pos:%d vs %d)" % (q_name, orig[1], rec.pos))
try:
@@ -114,7 +114,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
"""
A reader of SAM format.
-@@ -49,7 +49,7 @@ class SamHeader(object):
+@@ -49,7 +49,7 @@
self.curr_idx = 0
return self
@@ -123,7 +123,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
if self.curr_idx == len(self.header_lines):
raise StopIteration
-@@ -114,7 +114,7 @@ class SamReader(object):
+@@ -114,7 +114,7 @@
self._source_fh.seek(self.header.end_header_pointer)
return self
@@ -148,7 +148,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
"""
Note: This would look so much better replaced by XML or at least JSON. But
is not worth to do it for now.
-@@ -6,7 +6,7 @@ Note: This would look so much better rep
+@@ -6,7 +6,7 @@
import os
import gzip
@@ -157,7 +157,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
import logging
-@@ -66,14 +66,14 @@ class LargeTestsData(object):
+@@ -66,14 +66,14 @@
def init_data(self):
""" Try and init the data we need.
"""
@@ -174,7 +174,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
gn_path = os.path.join(self.data_dir_path,genome)
gn_fasta = os.path.join(gn_path,gdata['ref_name'])
if not os.path.exists(gn_fasta):
-@@ -103,7 +103,7 @@ class LargeTestsData(object):
+@@ -103,7 +103,7 @@
try:
f = open(fname,'wb')
@@ -204,7 +204,7 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
import inspect
import unittest
import logging
-@@ -69,7 +69,7 @@ class TestLargeIndex(unittest.TestCase):
+@@ -69,7 +69,7 @@
def get_suite():
tests = ['test_human','test_mouse','test_large_index']
@@ -237,3 +237,12 @@ Last-Update: Wed, 04 Sep 2019 15:18:29 +0200
"""
Copyright 2014, Ben Langmead <langmea at cs.jhu.edu>
+@@ -21,7 +21,7 @@
+
+
+ import os
+-import imp
++import importlib
+ import sys
+ import inspect
+ import logging
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ reproducible.patch
skip_test_requiring_non-free_libmath-random-perl.patch
do-not-rebuild-during-test.patch
2to3.patch
+silence_tbb_deprecation_warning.patch
=====================================
debian/patches/silence_tbb_deprecation_warning.patch
=====================================
@@ -0,0 +1,32 @@
+Subject: Silence TBB deprecation warnings, including specific headers only
+From: Alex Mestiashvili <amestia at rsh2.donotuse.de>
+--- bowtie2.orig/bt2_search.h
++++ bowtie2/bt2_search.h
+@@ -21,7 +21,6 @@
+ #define BT2_SEARCH_H_
+ #ifdef WITH_TBB
+
+-#include <tbb/tbb.h>
+ #include <tbb/task_group.h>
+
+ class multiseedSearchWorker {
+--- bowtie2.orig/blockwise_sa.h
++++ bowtie2/blockwise_sa.h
+@@ -21,7 +21,6 @@
+ #define BLOCKWISE_SA_H_
+
+ #ifdef WITH_TBB
+-#include <tbb/tbb.h>
+ #include <tbb/task_group.h>
+ #endif
+
+--- bowtie2.orig/diff_sample.h
++++ bowtie2/diff_sample.h
+@@ -21,7 +21,6 @@
+ #define DIFF_SAMPLE_H_
+
+ #ifdef WITH_TBB
+-#include <tbb/tbb.h>
+ #include <tbb/task_group.h>
+ #endif
+
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20
--
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/compare/ea7fa13e8815cc911840992817d7740e3b6d873e...88e9eb282622223cb71dbe13df8fcbc472093a20
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191206/d2252d84/attachment-0001.html>
More information about the debian-med-commit
mailing list