Clean up quilt patches

  * Point Vcs fields to salsa.debian.org

  * Standards-Version: 4.1.4

  * Adapt watch file to also catch v$VERSION tarball names

  * Clean up quilt patches

  * Try to enable swig Python bindings

  TODO: ... but failed

 -- Andreas Tille <tille@debian.org>  Thu, 26 Apr 2018 21:19:48 +0200

 -- Andreas Tille <tille@debian.org>  Mon, 03 Sep 2018 08:34:22 +0200

jellyfish (2.2.8-3) unstable; urgency=medium

From 6dfc57b516249454dc0a708ceb4833623cbf0ffd Mon Sep 17 00:00:00 2001

From: Guillaume Marcais <gmarcais@cs.cmu.edu>

Date: Wed, 14 Feb 2018 07:29:54 -0500

Subject: [PATCH] Fix testing on arm64.

---

 jellyfish/fastq2sam.cc | 2 +-

 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jellyfish/fastq2sam.cc b/jellyfish/fastq2sam.cc

index e152ccf..b0b6b0d 100644

--- a/jellyfish/fastq2sam.cc

+++ b/jellyfish/fastq2sam.cc

@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) {

     //    os << "@PG\tID:fastq2sam\tPN:fastq2sam\n";

     std::string name, seq, quals;

-    char c = is.get();

+    int c = is.get();

     while(c == '@') {

       std::getline(is, name);

       std::getline(is, seq);

From 0adb7ea223a6718bad4e82fc9813ae7708b59ee2 Mon Sep 17 00:00:00 2001

From: Guillaume Marcais <gmarcais@cs.cmu.edu>

Date: Mon, 12 Feb 2018 14:32:29 -0500

Subject: [PATCH] Added missing tests/small_mers.sh file.

---

 tests/small_mers.sh | 11 +++++++++++

 1 file changed, 11 insertions(+)

 create mode 100644 tests/small_mers.sh

diff --git a/tests/small_mers.sh b/tests/small_mers.sh

new file mode 100644

index 0000000..5eb7db0

--- /dev/null

+++ b/tests/small_mers.sh

@@ -0,0 +1,11 @@

+#! /bin/sh

+

+cd tests

+. ./compat.sh

+

+sort -k2,2 > ${pref}.md5sum <<EOF

+

+EOF

+

+$JF count -t $nCPUs -o ${pref}_m10_10M.jf -s 1M -m 7 -C seq10m.fa

+$JF histo ${pref}_m10_10M.jf > ${pref}_m10_10M.histo

Description: Don't compile using an rpath

Author: Michael R. Crusoe <crusoe@ucdavis.edu>

--- jellyfish.orig/swig/python/setup.py

+++ jellyfish/swig/python/setup.py

@@ -25,7 +25,6 @@

 jf_libs    = [re.sub(r'-l', '', x) for x in os.popen("pkg-config --libs-only-l jellyfish-2.0").read().rstrip().split()]

 jf_libdir  = [re.sub(r'-L', '', x) for x in os.popen("pkg-config --libs-only-L jellyfish-2.0").read().rstrip().split()]

-jf_rpath   = [re.sub(r'^', '-Wl,-rpath,', x) for x in jf_libdir]

 jf_ldflags = os.popen("pkg-config --libs-only-other jellyfish-2.0").read().rstrip().split()

@@ -35,7 +34,7 @@

                              libraries = jf_libs,

                              library_dirs = jf_libdir,

                              extra_compile_args = ["-std=c++0x"] + jf_cflags,

-                             extra_link_args = jf_ldflags + jf_rpath,

+                             extra_link_args = jf_ldflags,

                              language = "c++")

 setup(name = 'dna_jellyfish',

       version = '0.0.1',

--- jellyfish.orig/swig/Tuprules.tup

+++ jellyfish/swig/Tuprules.tup

@@ -77,12 +77,6 @@

   JELLYFISH_LIBS = `pkg-config --libs jellyfish-2.0` 

 endif

-ifdef JELLYFISH_RPATH

-  JELLYFISH_RPATH = @(JELLYFISH_RPATH)

-else

-  JELLYFISH_RPATH = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`

-endif

-

 ifdef RUBY_CFLAGS

   RUBY_CFLAGS = @(RUBY_CFLAGS)

 else

--- jellyfish.orig/swig/perl5/Makefile.PL

+++ jellyfish/swig/perl5/Makefile.PL

@@ -9,7 +9,6 @@

 my $jf_cflags = `pkg-config --cflags jellyfish-2.0`;

 my $jf_libs   = `pkg-config --libs jellyfish-2.0`;

-my $jf_rpath  = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`;

 WriteMakefile(NAME      => 'jellyfish',

               CC        => 'g++-4.4',

--- jellyfish.orig/swig/perl5/Tupfile

+++ jellyfish/swig/perl5/Tupfile

@@ -3,7 +3,7 @@

 export PKG_CONFIG_PATH

 SWIGFLAGS = -perl5

 CXXFLAGS += $(JELLYFISH_CFLAGS) $(PERL_CFLAGS) -fPIC

-LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(PERL_LIBS)

+LDFLAGS += -shared $(JELLYFISH_LIBS) $(PERL_LIBS)

 : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx | jellyfish.pm <jf>

 : jellyfish_wrap.cxx |> !cxx |>

--- jellyfish.orig/swig/python/Tupfile

+++ jellyfish/swig/python/Tupfile

@@ -3,7 +3,7 @@

 export PKG_CONFIG_PATH

 SWIGFLAGS = -python

 CXXFLAGS += $(JELLYFISH_CFLAGS) $(PYTHON_CFLAGS) -fPIC

-LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(PYTHON_LIBS)

+LDFLAGS += -shared $(JELLYFISH_LIBS) $(PYTHON_LIBS)

 : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx | jellyfish.py <jf>

 : jellyfish_wrap.cxx |> !cxx |>

--- jellyfish.orig/swig/ruby/Tupfile

+++ jellyfish/swig/ruby/Tupfile

@@ -3,7 +3,7 @@

 export PKG_CONFIG_PATH

 SWIGFLAGS = -ruby

 CXXFLAGS += $(JELLYFISH_CFLAGS) $(RUBY_CFLAGS) -fPIC

-LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(RUBY_LIBS)

+LDFLAGS += -shared $(JELLYFISH_LIBS) $(RUBY_LIBS)

 : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx

 : jellyfish_wrap.cxx |> !cxx |>

--- jellyfish.orig/swig/ruby/extconf.rb

+++ jellyfish/swig/ruby/extconf.rb

@@ -7,6 +7,5 @@

 $defs << `pkg-config --cflags jellyfish-2.0`.chomp << '-std=c++0x'

 $libs << `pkg-config --libs jellyfish-2.0`.chomp

-$libs << `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`.chomp

 create_makefile('jellyfish')

Description: Don't use -Werror

 The SWIG-generated swig/perl5/swig_wrap.cpp gives warnings with

 gcc 7, don't make these fatal with -Werror.

Author: Adrian Bunk <bunk@debian.org>

Last-Update: Tue, 15 Aug 2017 15:56:06 +0300

Bug-Debian: https://bugs.debian.org/872262

--- a/development.mk

+++ b/development.mk

@@ -1,4 +1,4 @@

-AM_CXXFLAGS += -Werror

+#AM_CXXFLAGS += -Werror

 # Count lines of code

 .PHONY: cloc cloc_jellyfish