[med-svn] [Git][med-team/ksw2][master] 5 commits: Cleanup templates, add watch file, enhance citation
Andreas Tille
gitlab at salsa.debian.org
Fri May 15 10:05:55 BST 2020
Andreas Tille pushed to branch master at Debian Med / ksw2
Commits:
20187b13 by Andreas Tille at 2020-05-15T08:21:22+02:00
Cleanup templates, add watch file, enhance citation
- - - - -
7d54606e by Andreas Tille at 2020-05-15T08:21:54+02:00
New upstream version 0.0+git20190429.f06f9b3
- - - - -
3ba79079 by Andreas Tille at 2020-05-15T08:21:54+02:00
Update upstream source from tag 'upstream/0.0+git20190429.f06f9b3'
Update to upstream version '0.0+git20190429.f06f9b3'
with Debian dir 69f2a84ea32462efae656dd1ba5b475284897616
- - - - -
a9a93147 by Andreas Tille at 2020-05-15T09:53:25+02:00
Use autoconf
- - - - -
283fc286 by Andreas Tille at 2020-05-15T11:05:28+02:00
Use autoconf to get a proper library package
- - - - -
16 changed files:
- + .gitignore
- debian/changelog
- debian/control
- − debian/libksw2-0.triggers
- − debian/libksw2-dev.dirs
- − debian/patches/Makefile.patch
- + debian/patches/autoconf.patch
- debian/patches/series
- − debian/postinst
- − debian/postrm
- debian/rules
- − debian/salsa-ci.yml.ex
- − debian/shlibs.local.ex
- debian/upstream/metadata
- + debian/watch
- − debian/watch.ex
Changes:
=====================================
.gitignore
=====================================
@@ -0,0 +1,4 @@
+.*.swp
+*.dSYM
+*.a
+*.o
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-ksw2 (0.0+20190429+gitf06f9b3-1) unstable; urgency=medium
+ksw2 (0.0+git20190429.f06f9b3-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #nnnn)
-- Steffen Moeller <moeller at debian.org> Thu, 14 May 2020 20:48:41 +0200
=====================================
debian/control
=====================================
@@ -2,7 +2,10 @@ Source: ksw2
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper-compat (= 12)
+Build-Depends: debhelper-compat (= 12),
+ autoconf-archive,
+ pkg-config,
+ zlib1g-dev
Standards-Version: 4.5.0
Section: libs
Homepage: https://github.com/lh3/ksw2
=====================================
debian/libksw2-0.triggers deleted
=====================================
@@ -1 +0,0 @@
-activate-noawait ldconfig
=====================================
debian/libksw2-dev.dirs deleted
=====================================
@@ -1 +0,0 @@
-usr/include/ksw2
=====================================
debian/patches/Makefile.patch deleted
=====================================
@@ -1,26 +0,0 @@
-Index: ksw2-0.0+20200514+gitf06f9b3/Makefile
-===================================================================
---- ksw2-0.0+20200514+gitf06f9b3.orig/Makefile
-+++ ksw2-0.0+20200514+gitf06f9b3/Makefile
-@@ -1,5 +1,7 @@
--CC= gcc
--CFLAGS= -g -Wall -Wextra -Wc++-compat -O2
-+CC ?= gcc
-+CFLAGS ?= -g -Wall -Wextra -O2
-+CFLAG += -Wc++-compat
-+CFLAGS += -fPIC
- CPPFLAGS= -DHAVE_KALLOC
- INCLUDES= -I.
- OBJS= ksw2_gg.o ksw2_gg2.o ksw2_gg2_sse.o ksw2_extz.o ksw2_extz2_sse.o \
-@@ -33,7 +35,10 @@ endif
- .c.o:
- $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
-
--all:$(PROG)
-+all:$(PROG) library
-+
-+library: $(OBJS) kalloc.o
-+ $(CC) -shared -o libksw2.so.0.0.20190429 -Wl,-soname,libksw2.so.0 $(OBJS) kalloc.o
-
- ksw2-test:cli.o kalloc.o $(OBJS)
- $(CC) $(CFLAGS) $^ -o $@ $(LIBS_MORE) $(LIBS)
=====================================
debian/patches/autoconf.patch
=====================================
@@ -0,0 +1,169 @@
+--- /dev/null
++++ b/Makefile.am
+@@ -0,0 +1,19 @@
++lib_LTLIBRARIES = libksw2.la
++
++libksw2dir=$(includedir)
++libksw2_HEADERS=kalloc.h kseq.h ksw2.h
++libksw2_la_SOURCES = ksw2_gg.c ksw2_gg2.c ksw2_gg2_sse.c ksw2_extz.c ksw2_extz2_sse.c \
++ ksw2_extd.c ksw2_extd2_sse.c ksw2_extf2_sse.c ksw2_exts2_sse.c \
++ kalloc.c
++libksw2_la_LDFLAGS = -version-info @LIB_VERSION@
++
++libksw2_la_CPPFLAGS = $(INCLUDES)
++
++bin_PROGRAMS = ksw2-test
++ksw2_test_SOURCES = cli.c
++ksw2_test_LDADD = libksw2.la
++
++pkgconfigdir=$(libdir)/pkgconfig
++pkgconfig_DATA = libksw2.pc
++
++
+--- /dev/null
++++ b/configure.ac
+@@ -0,0 +1,68 @@
++# -*- Autoconf -*-
++# Process this file with autoconf to produce a configure script.
++
++AC_INIT(ksw2, 0.0, lh3 at me.com)
++AC_CONFIG_HEADERS([config.h])
++dnl AC_CONFIG_MACRO_DIR([/usr/share/aclocal]) - this does not help to find ax_check_zlib.m4
++
++AC_PREREQ(2.57)
++
++# Directory that contains install-sh and other auxiliary files
++AC_CONFIG_AUX_DIR([config])
++
++################################################################################
++# According to (http://www.mail-archive.com/autoconf@gnu.org/msg14232.html)
++# this macro should be after AC_INIT but before AM_INIT_AUTOMAKE
++################################################################################
++AC_CONFIG_MACRO_DIR(config)
++
++AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
++
++LIB_VERSION=0:0
++
++AC_SUBST([VERSION])
++AC_SUBST([LIB_VERSION])
++
++AC_SUBST([VERSION])
++
++# Checks for programs.
++AC_PROG_LN_S
++AC_PROG_INSTALL
++AC_PROG_LIBTOOL
++
++################################################################################
++# calling AC_PROG_CXX resets CXXFLAGS, we use our own flags set in the
++# the AX_CXXFLAGS macro below.
++# So we cache the argument to configure
++# here in ARG_CXX_FLAGS (so that our macro does not override them)
++################################################################################
++ARG_CXX_FLAGS="$CXXFLAGS"
++AC_PROG_CXX
++
++#Ranlib handled by check for libtool
++CXXFLAGS="$ARG_CXX_FLAGS"
++dnl AX_CXXFLAGS
++
++AC_SUBST(CXXFLAGS)
++
++CPPFLAGS="-I\$(top_srcdir) $CPPFLAGS"
++# Checks for libraries.
++
++m4_include([ax_check_zlib.m4])
++AX_CHECK_ZLIB()
++
++# Checks for header files.
++AC_HEADER_STDC
++AC_CHECK_HEADERS([stdlib.h])
++
++AC_PROG_MAKE_SET
++
++AC_DEFINE([HAVE_KALLOC], [], [Use ksw2's own malloc functions])
++
++AC_CONFIG_FILES([
++ Makefile
++ libksw2.pc
++ ])
++AC_OUTPUT
++
++
+--- /dev/null
++++ b/libksw2.pc.in
+@@ -0,0 +1,12 @@
++prefix=@prefix@
++exec_prefix=${prefix}
++libdir=${exec_prefix}/lib
++includedir=${prefix}/include
++
++
++Name: libksw
++Version: @VERSION@
++Description: globl alignment and alignment extension library
++Libs: -L${libdir} -lksw2
++Cflags: -I${includedir}
++
+--- a/Makefile
++++ /dev/null
+@@ -1,58 +0,0 @@
+-CC= gcc
+-CFLAGS= -g -Wall -Wextra -Wc++-compat -O2
+-CPPFLAGS= -DHAVE_KALLOC
+-INCLUDES= -I.
+-OBJS= ksw2_gg.o ksw2_gg2.o ksw2_gg2_sse.o ksw2_extz.o ksw2_extz2_sse.o \
+- ksw2_extd.o ksw2_extd2_sse.o ksw2_extf2_sse.o ksw2_exts2_sse.o
+-PROG= ksw2-test
+-LIBS= -lz
+-
+-ifneq ($(gaba),) # gaba source code directory
+- CPPFLAGS += -DHAVE_GABA
+- INCLUDES += -I$(gaba)
+- LIBS_MORE += -L$(gaba)/build -lgaba
+- CFLAGS += -msse4
+-endif
+-
+-ifneq ($(parasail),) # parasail install prefix
+- CPPFLAGS += -DHAVE_PARASAIL
+- INCLUDES += -I$(parasail)/include
+- LIBS_MORE += $(parasail)/lib/libparasail.a # don't link against the dynamic library
+-endif
+-
+-ifeq ($(sse2),)
+- CFLAGS += -march=native
+-endif
+-
+-ifneq ($(avx2),)
+- CFLAGS += -mavx2
+-endif
+-
+-.SUFFIXES:.c .o
+-
+-.c.o:
+- $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
+-
+-all:$(PROG)
+-
+-ksw2-test:cli.o kalloc.o $(OBJS)
+- $(CC) $(CFLAGS) $^ -o $@ $(LIBS_MORE) $(LIBS)
+-
+-clean:
+- rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM session*
+-
+-depend:
+- (LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c)
+-
+-# DO NOT DELETE
+-
+-cli.o: ksw2.h kseq.h
+-kalloc.o: kalloc.h
+-ksw2_extd.o: ksw2.h
+-ksw2_extd2_sse.o: ksw2.h
+-ksw2_extf2_sse.o: ksw2.h
+-ksw2_extz.o: ksw2.h
+-ksw2_extz2_sse.o: ksw2.h
+-ksw2_gg.o: ksw2.h
+-ksw2_gg2.o: ksw2.h
+-ksw2_gg2_sse.o: ksw2.h
=====================================
debian/patches/series
=====================================
@@ -1 +1 @@
-Makefile.patch
+autoconf.patch
=====================================
debian/postinst deleted
=====================================
@@ -1,19 +0,0 @@
-#!/bin/sh
-set -e
-
-case "$1" in
- configure)
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-#DEBHELPER#
-
-exit 0
=====================================
debian/postrm deleted
=====================================
@@ -1,16 +0,0 @@
-#!/bin/sh
-set -e
-
-case "$1" in
- purge|remove|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
- ;;
-
- *)
- echo "postrm called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-#DEBHELPER#
-
-exit 0
=====================================
debian/rules
=====================================
@@ -7,6 +7,11 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
-override_dh_auto_clean:
- dh_auto_clean
- rm -f lib*so*
+# FIXME: I'd love to get rid of this dirty hack - but I have no better idea how to check for zlib
+override_dh_autoreconf:
+ ln -s /usr/share/aclocal/ax_check_zlib.m4 .
+ dh_autoreconf
+
+override_dh_auto_install:
+ dh_auto_install
+ rm ax_check_zlib.m4
=====================================
debian/salsa-ci.yml.ex deleted
=====================================
@@ -1,11 +0,0 @@
-# For more information on what jobs are run see:
-# https://salsa.debian.org/salsa-ci-team/pipeline
-#
-# To enable the jobs, go to your repository (at salsa.debian.org)
-# and click over Settings > CI/CD > Expand (in General pipelines).
-# In "Custom CI config path" write debian/salsa-ci.yml and click
-# in "Save Changes". The CI tests will run after the next commit.
----
-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/shlibs.local.ex deleted
=====================================
@@ -1 +0,0 @@
-libksw2 0.0+20200514+gitf06f9b3 ksw2 (>> 0.0+20200514+gitf06f9b3-0), ksw2 (<< 0.0+20200514+gitf06f9b3-99)
=====================================
debian/upstream/metadata
=====================================
@@ -1,14 +1,18 @@
Reference:
- - Author: Suzuki, H. and Kasahara, M.
- Year: 2018
- Title: Introducing difference recurrence relations for faster semi-global alignment of long sequences.
+ - Author: H. Suzuki and M. Kasahara
+ Title: Introducing difference recurrence relations for faster semi-global alignment of long sequences
Journal: BMC Bioinformatics
+ Year: 2018
Volume: 19
Pages: 45
+ DOI: 10.1186/s12859-018-2014-8
+ PMID: 29504909
+ PMCID: PMC5836832
+ URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2014-8
+ eprint: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2014-8
- Author: Li, H.
Year: 2018
Title: Minimap2: pairwise alignment for nucleotide sequences.
Journal: Bioinformatics
Volume: 34
Pages: 3094-3100
-
=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+
+opts="mode=git,pretty=0.0+git%cd.%h" \
+ https://github.com/lh3/ksw2.git HEAD
=====================================
debian/watch.ex deleted
=====================================
@@ -1,38 +0,0 @@
-# Example watch control file for uscan
-# Rename this file to "watch" and then you can run the "uscan" command
-# to check for upstream updates and more.
-# See uscan(1) for format
-
-# Compulsory line, this is a version 4 file
-version=4
-
-# PGP signature mangle, so foo.tar.gz has foo.tar.gz.sig
-#opts="pgpsigurlmangle=s%$%.sig%"
-
-# HTTP site (basic)
-#http://example.com/downloads.html \
-# files/ksw2-([\d\.]+)\.tar\.gz debian uupdate
-
-# Uncomment to examine an FTP server
-#ftp://ftp.example.com/pub/ksw2-(.*)\.tar\.gz debian uupdate
-
-# SourceForge hosted projects
-# http://sf.net/ksw2/ ksw2-(.*)\.tar\.gz debian uupdate
-
-# GitHub hosted projects
-#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz%" \
-# https://github.com/<user>/ksw2/tags \
-# (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate
-
-# PyPI
-# https://pypi.debian.net/ksw2/ksw2-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
-
-# Direct Git
-# opts="mode=git" http://git.example.com/ksw2.git \
-# refs/tags/v([\d\.]+) debian uupdate
-
-
-
-
-# Uncomment to find new files on GooglePages
-# http://example.googlepages.com/foo.html ksw2-(.*)\.tar\.gz
View it on GitLab: https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4
--
View it on GitLab: https://salsa.debian.org/med-team/ksw2/-/compare/328b6a20fdcaf6fc871913887a8265bb22231f11...283fc286a1f27a345cecd9f31e5201e12f6716b4
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