debian/NEWS.Debian

+jellyfish (2.2.10-1) unstable; urgency=medium
+
+ The the binary package python3-dna-jellyfish containing the Python module
+ was dropped due to issues in the build process which is documented in this
+ mail to the developers list
+ 
+    https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-September/065549.html
+
+ I'd happily re-introduce the Python module if anybody will provide a
+ patch for a successful build.
+
+ -- Andreas Tille <tille@debian.org>  Mon, 03 Sep 2018 11:57:00 +0200

debian/changelog

-jellyfish (2.2.10-1) UNRELEASED; urgency=medium
+jellyfish (2.2.10-1) unstable; urgency=medium
 
   * New upstream version
   * Point Vcs fields to salsa.debian.org
@@ -8,8 +8,10 @@ jellyfish (2.2.10-1) UNRELEASED; urgency=medium
   * Catch exceptions by reference
   * Do not replace random '-L' strings in command line
     Closes: #907819
+  * Drop python3-dna-jellyfish package since the Python module had issues in
+    build process and nobody seemed to be interested to help solving theses
 
- -- Andreas Tille <tille@debian.org>  Mon, 03 Sep 2018 08:34:22 +0200
+ -- Andreas Tille <tille@debian.org>  Fri, 21 Sep 2018 08:45:53 +0200
 
 jellyfish (2.2.8-3) unstable; urgency=medium
 

debian/control

@@ -92,28 +92,28 @@ Description: count k-mers in DNA sequences (development files of jellyfish)
  This package contains the development files (static library and
  header files)
 
-Package: python3-dna-jellyfish
-Architecture: any
-Section: python
-Depends: ${python3:Depends},
-         ${misc:Depends},
-         ${shlibs:Depends}
-Description: count k-mers in DNA sequences (Python bindings of jellyfish)
- 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 the Python bindings of jellyfish.
+#Package: python3-dna-jellyfish
+#Architecture: any
+#Section: python
+#Depends: ${python3:Depends},
+#         ${misc:Depends},
+#         ${shlibs:Depends}
+#Description: count k-mers in DNA sequences (Python bindings of jellyfish)
+# 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 the Python bindings of jellyfish.
 
 Package: libjellyfish-perl
 Architecture: any

debian/rules

@@ -14,22 +14,22 @@ export PERL_MM_OPT=INSTALLDIRS=vendor
 export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"
 
 %:
-	dh $@ --with python3
+	dh $@ # --with python3
 
 override_dh_auto_install:
 	dh_auto_install -- install-data
 
 override_dh_install:
 	# dh_install -X*.a -X*.la -Xpkgconfig
-	dh_install -ppython3-dna-jellyfish
-	pybuild -d swig/python --name dna-jellyfish
-#	pybuild -d swig/python --name dna-jellyfish --disable test/python3
-#	pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py"
-#	pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py"
-	chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so
+#	dh_install -ppython3-dna-jellyfish
+#	pybuild -d swig/python --name dna-jellyfish
+##	pybuild -d swig/python --name dna-jellyfish --disable test/python3
+##	pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_string_mers.py"
+##	pybuild -d swig/python --name dna-jellyfish --test --test-args "${CURDIR}/swig/python/ test_hash_counter.py"
+#	chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so
 	
 	dh_auto_configure --sourcedirectory=swig/perl5
-#	dh_auto_configure --sourcedirectory=swig/python
+##	dh_auto_configure --sourcedirectory=swig/python
 	dh_auto_build --sourcedirectory=swig/perl5
 	dh_auto_install --sourcedirectory=swig/perl5
 	chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so