debian/changelog

-jellyfish (2.3.0-1) UNRELEASED; urgency=medium
+jellyfish (2.3.0-1) unstable; urgency=medium
 
+  * Team upload
+
+  [Andreas Tille]
   * Install config.h which is needed by sailfish package
   * New upstream version
   * debhelper-compat 12
 
+  [Steffen Moeller]
+  * Standards-Version: 4.4.0
+  * d/u/metadata: Added ref to conda
+  * deactivated installation of examples, which have changed considerably
+  * removed build-dependency on python2 (prime reason to upload)
+
  -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 13:37:07 +0200
 
 jellyfish (2.2.10-2) unstable; urgency=medium

debian/control

@@ -14,11 +14,10 @@ Build-Depends: debhelper-compat (= 12),
                procps,
                swig,
                python3-all-dev,
-               python-all-dev,
                dh-python,
                perl,
                chrpath
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
 Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
 Homepage: http://www.cbcb.umd.edu/software/jellyfish/
@@ -138,24 +137,24 @@ Description: count k-mers in DNA sequences (Perl bindings of jellyfish)
  .
  This package contains the Perl bindings of jellyfish.
 
-Package: jellyfish-examples
-Architecture: any
-Depends: jellyfish,
-         ${shlibs:Depends},
-         ${misc:Depends}
-Description: count k-mers in DNA sequences (examples for testing)
- JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
- DNA. A k-mer is a substring of length k, and counting the occurrences
- of all such substrings is a central step in many analyses of DNA
- sequence. JELLYFISH can count k-mers using an order of magnitude less
- memory and an order of magnitude faster than other k-mer counting
- packages by using an efficient encoding of a hash table and by
- exploiting the "compare-and-swap" CPU instruction to increase
- parallelism.
- .
- JELLYFISH is a command-line program that reads FASTA and multi-FASTA
- files containing DNA sequences. It outputs its k-mer counts in an
- binary format, which can be translated into a human-readable text
- format using the "jellyfish dump" command.
- .
- This package contains examples to test the package
+#Package: jellyfish-examples
+#Architecture: any
+#Depends: jellyfish,
+#         ${shlibs:Depends},
+#         ${misc:Depends}
+#Description: count k-mers in DNA sequences (examples for testing)
+# JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+# DNA. A k-mer is a substring of length k, and counting the occurrences
+# of all such substrings is a central step in many analyses of DNA
+# sequence. JELLYFISH can count k-mers using an order of magnitude less
+# memory and an order of magnitude faster than other k-mer counting
+# packages by using an efficient encoding of a hash table and by
+# exploiting the "compare-and-swap" CPU instruction to increase
+# parallelism.
+# .
+# JELLYFISH is a command-line program that reads FASTA and multi-FASTA
+# files containing DNA sequences. It outputs its k-mer counts in an
+# binary format, which can be translated into a human-readable text
+# format using the "jellyfish dump" command.
+# .
+# This package contains examples to test the package

debian/patches/fix_replacement_of_-L_option.patch

@@ -3,8 +3,10 @@ Bug-Debian: https://bugs.debian.org/907819
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
 
---- a/examples/count_in_file/Makefile
-+++ b/examples/count_in_file/Makefile
+Index: jellyfish/examples/count_in_file/Makefile
+===================================================================
+--- jellyfish.orig/examples/count_in_file/Makefile
++++ jellyfish/examples/count_in_file/Makefile
 @@ -1,6 +1,6 @@
  CC = g++
  CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3
@@ -13,8 +15,10 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
  LDLIBS = $(shell pkg-config --libs jellyfish-2.0)
  
  all: count_in_file
---- a/examples/jf_count_dump/Makefile
-+++ b/examples/jf_count_dump/Makefile
+Index: jellyfish/examples/jf_count_dump/Makefile
+===================================================================
+--- jellyfish.orig/examples/jf_count_dump/Makefile
++++ jellyfish/examples/jf_count_dump/Makefile
 @@ -1,6 +1,6 @@
  CC = g++
  CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3
@@ -23,8 +27,10 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
  LDLIBS = $(shell pkg-config --libs jellyfish-2.0)
  
  all: jf_count_dump
---- a/examples/query_per_sequence/Makefile
-+++ b/examples/query_per_sequence/Makefile
+Index: jellyfish/examples/query_per_sequence/Makefile
+===================================================================
+--- jellyfish.orig/examples/query_per_sequence/Makefile
++++ jellyfish/examples/query_per_sequence/Makefile
 @@ -1,6 +1,6 @@
  CC = g++
  CXXFLAGS = $(shell pkg-config --cflags jellyfish-2.0) -std=c++0x -Wall -O3
@@ -33,9 +39,11 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
  LDLIBS = $(shell pkg-config --libs jellyfish-2.0)
  
  all: query_per_sequence
---- a/swig/Tuprules.tup
-+++ b/swig/Tuprules.tup
-@@ -80,7 +80,7 @@ endif
+Index: jellyfish/swig/Tuprules.tup
+===================================================================
+--- jellyfish.orig/swig/Tuprules.tup
++++ jellyfish/swig/Tuprules.tup
+@@ -86,7 +86,7 @@ endif
  ifdef JELLYFISH_RPATH
    JELLYFISH_RPATH = @(JELLYFISH_RPATH)
  else
@@ -44,8 +52,10 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
  endif
  
  ifdef RUBY_CFLAGS
---- a/swig/perl5/Makefile.PL
-+++ b/swig/perl5/Makefile.PL
+Index: jellyfish/swig/perl5/Makefile.PL
+===================================================================
+--- jellyfish.orig/swig/perl5/Makefile.PL
++++ jellyfish/swig/perl5/Makefile.PL
 @@ -19,7 +19,7 @@ my $pkg = "jellyfish-2.0";
  my $jf_cflags = pkgconfig("--cflags $pkg");
  my $jf_libs   = pkgconfig("--libs $pkg");
@@ -55,9 +65,11 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
  
  print("$jf_cflags\n$jf_libs\n$jf_rpath\n");
  
---- a/swig/ruby/extconf.rb
-+++ b/swig/ruby/extconf.rb
-@@ -13,7 +13,7 @@ end
+Index: jellyfish/swig/ruby/extconf.rb
+===================================================================
+--- jellyfish.orig/swig/ruby/extconf.rb
++++ jellyfish/swig/ruby/extconf.rb
+@@ -19,7 +19,7 @@ end
  
  $defs << pkgconfig("--cflags jellyfish-2.0") << '-std=c++0x'
  libs = [pkgconfig("--libs jellyfish-2.0"),
@@ -66,9 +78,11 @@ Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
  
  if Array === $libs
    $libs += libs
---- a/swig/python/setup.py
-+++ b/swig/python/setup.py
-@@ -17,7 +17,7 @@ def pkgconfig(s):
+Index: jellyfish/swig/python/setup.py
+===================================================================
+--- jellyfish.orig/swig/python/setup.py
++++ jellyfish/swig/python/setup.py
+@@ -23,7 +23,7 @@ def pkgconfig(s):
  jf_libs    = [re.sub(r'-l', '', x) for x in pkgconfig("--libs-only-l jellyfish-2.0")]
  jf_include = [re.sub(r'-I', '', x) for x in pkgconfig("--cflags-only-I jellyfish-2.0")]
  jf_cflags  = pkgconfig("--cflags-only-other jellyfish-2.0")

debian/patches/manpage_whatis_entry.patch

@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Mon, 28 Aug 2017 14:10:27 +0200
 Description: Fix whatis entry in manpage (also fix some spelling issues)
 
---- a/doc/jellyfish.man
-+++ b/doc/jellyfish.man
+Index: jellyfish/doc/jellyfish.man
+===================================================================
+--- jellyfish.orig/doc/jellyfish.man
++++ jellyfish/doc/jellyfish.man
 @@ -12,11 +12,8 @@
  ..
  .TH "JELLYFISH" "1" "2010/10/1" "k\-mer counter " "k\-mer counter "

debian/patches/portability.patch

@@ -4,9 +4,11 @@ Bug-Debian: https://bugs.debian.org/871697
 Description: Replace asm statements by C code to increase portability
 Note: Does not work as described - needs verification
 
+Index: jellyfish/include/jellyfish/rectangular_binary_matrix.hpp
+===================================================================
 --- jellyfish.orig/include/jellyfish/rectangular_binary_matrix.hpp
 +++ jellyfish/include/jellyfish/rectangular_binary_matrix.hpp
-@@ -302,13 +302,20 @@
+@@ -296,13 +296,20 @@ namespace jellyfish {
  // #pragma GCC diagnostic pop
  
      // i is the lower 2 bits of x, and an index into the smear array. Compute res ^= smear[i] & p[j].
@@ -29,7 +31,7 @@ Note: Does not work as described - needs verification
  
      uint64_t i, j = 0, x = 0;
      for(unsigned int w = 0; w < nb_words(); ++w) {
-@@ -320,16 +327,16 @@
+@@ -314,16 +321,16 @@ namespace jellyfish {
        }
        for( ; j > 7; j -= 8, p -= 8) {
          i = (x & (uint64_t)0x3) << 4;
@@ -50,7 +52,7 @@ Note: Does not work as described - needs verification
          x >>= 2;
        }
      }
-@@ -339,18 +346,19 @@
+@@ -333,18 +340,19 @@ namespace jellyfish {
      switch(j) {
      case 6:
        i = (x & (uint64_t)0x3) << 4;
@@ -73,7 +75,7 @@ Note: Does not work as described - needs verification
      uint64_t res1, res2;
      asm("movd %[acc], %[res1]\n\t"
          "psrldq $8, %[acc]\n\t"
-@@ -358,6 +366,10 @@
+@@ -352,6 +360,10 @@ namespace jellyfish {
          : [res1]"=r"(res1), [res2]"=r"(res2)
          : [acc]"x"(acc));
      return res1 ^ res2;

debian/patches/reproducible.patch

@@ -4,9 +4,11 @@ Bug-Debian: https://bugs.debian.org/863015
 Description: Enable reproducible build by avoiding the current
  date with time zone in json output
 
+Index: jellyfish/include/jellyfish/generic_file_header.hpp
+===================================================================
 --- jellyfish.orig/include/jellyfish/generic_file_header.hpp
 +++ jellyfish/include/jellyfish/generic_file_header.hpp
-@@ -180,6 +180,8 @@
+@@ -172,6 +172,8 @@ public:
  
  protected:
    std::string get_hostname() const {
@@ -15,7 +17,7 @@ Description: Enable reproducible build by avoiding the current
      struct utsname buf;
      if(uname(&buf) == -1)
        return "";
-@@ -187,6 +189,8 @@
+@@ -179,6 +181,8 @@ protected:
    }
  
    std::string get_pwd() const {
@@ -24,7 +26,7 @@ Description: Enable reproducible build by avoiding the current
  #ifdef PATH_MAX
      size_t len = PATH_MAX;
  #else
-@@ -202,6 +206,16 @@
+@@ -194,6 +198,16 @@ protected:
    std::string get_localtime() const {
      time_t t = time(0);
      std::string res(ctime(&t));

debian/patches/series

 manpage_whatis_entry.patch
 reproducible.patch
 portability.patch
-fix_catch.patch
+#Apparently fixed upstream
+#fix_catch.patch
 fix_replacement_of_-L_option.patch

debian/rules

@@ -21,11 +21,11 @@ export DEB_LDFLAGS_MAINT_APPEND = -lpthread
 override_dh_auto_install:
 	dh_auto_install -- install-data
 
-override_dh_installexamples:
-	dh_installexamples
-	sed '/SRCDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
-	sed '/BUILDDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
-	rm -f debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/swig*
+#override_dh_installexamples:
+#	dh_installexamples
+#	sed '/SRCDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
+#	sed '/BUILDDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
+#	rm -f debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/swig*
 
 override_dh_install:
 	# dh_install -X*.a -X*.la -Xpkgconfig
@@ -62,6 +62,18 @@ override_dh_clean:
 	fi
 	rm -f tests/compat.sh
 	rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py
+	rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so
+	rm -f swig/perl5/blib/bin/.exists
+	rm -f swig/perl5/blib/lib/.exists
+	rm -f swig/perl5/blib/lib/auto/jellyfish/.exists
+	rm -f swig/perl5/blib/man1/.exists
+	rm -f swig/perl5/blib/man3/.exists
+	rm -f swig/perl5/blib/script/.exists
+	rm -f swig/perl5/jellyfish.bs
+	rm -f swig/perl5/pm_to_blib
+	rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/
+
+
 
 override_dh_auto_build:
 	mkdir -p debian/tmp_save_tests