debian/changelog

-jellyfish (2.3.0-2) UNRELEASED; urgency=medium
+jellyfish (2.3.0-2) unstable; urgency=medium
 
   * Restore jellyfish-examples, needed for the autopkgtest (Closes: #941262)
   * Enable an additional two test categories in the autopkgtests
   * Enabled htslib, to read SAM/BAM/CRAM files
+  * Restore python3-dna-jellyfish package
 
- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 27 Sep 2019 15:00:00 +0200
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 27 Sep 2019 18:29:29 +0200
 
 jellyfish (2.3.0-1) unstable; urgency=medium
 

debian/control

@@ -93,28 +93,28 @@ 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/patches/python3

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: forcibly avoid the deprecated module name
+--- jellyfish.orig/swig/Makefile.am
++++ jellyfish/swig/Makefile.am
+@@ -20,11 +20,6 @@
+ PYTHON_BUILT = swig/python/swig_wrap.cpp swig/python/dna_jellyfish.py
+ BUILT_SOURCES += $(PYTHON_BUILT)
+ 
+-if PYTHON_DEPRECATED
+-pythonglobaldir = $(PYTHON_SITE_PKG)
+-pythonglobal_SCRIPTS = swig/python/jellyfish.py
+-EXTRA_DIST += $(pythonglobal_SCRIPTS)
+-endif
+ pythonextdir = $(PYTHON_SITE_PKG)/dna_jellyfish
+ pythonext_SCRIPTS = swig/python/__init__.pyc
+ pythonext_LTLIBRARIES = swig/python/_dna_jellyfish.la

debian/patches/series

@@ -5,3 +5,4 @@ portability.patch
 #fix_catch.patch
 fix_replacement_of_-L_option.patch
 test_needs_bash
+python3

debian/rules

@@ -12,15 +12,13 @@ export PKG_CONFIG_ALLOW_SYSTEM_LIBS=true
 export PKG_CONFIG_SYSROOT_DIR=${CURDIR}/debian/tmp/
 export PKG_CONFIG_PATH=$(shell pkg-config --variable pc_path pkg-config)
 export PERL_MM_OPT=INSTALLDIRS=vendor
-export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"
+export PYBUILD_BUILD_ARGS=build_ext -L${CURDIR}/.libs
 
 export DEB_LDFLAGS_MAINT_APPEND = -lpthread
+export PYBUILD_NAME = dna_jellyfish
 
 %:
-	dh $@ # --with python3
-
-override_dh_auto_install:
-	dh_auto_install -- install-data
+	dh $@ --with python3
 
 #override_dh_installexamples:
 #	dh_installexamples
@@ -28,18 +26,10 @@ override_dh_auto_install:
 #	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
-#	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_build --sourcedirectory=swig/perl5
+override_dh_auto_install:
+	chrpath --delete bin/.libs/*
+	dh_auto_install -- install-data
+	dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild
 	dh_auto_install --sourcedirectory=swig/perl5
 	chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
 	dh_install
@@ -51,9 +41,12 @@ override_dh_install:
 		    --movedev config.h usr/include/$(DEB_SOURCE) \
 			debian/tmp/usr/lib/*/lib$(DEB_SOURCE)-*.so
 	sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/${DEB_HOST_MULTIARCH}/*.la
+	chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so
 
 override_dh_auto_configure:
-	dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib # --enable-python-binding
+	dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3
+	dh_auto_configure --sourcedirectory=swig/perl5
+	dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild
 
 override_dh_clean:
 	dh_clean
@@ -80,6 +73,9 @@ override_dh_auto_build:
 	mkdir -p debian/tmp_save_tests
 	cp -a tests/* debian/tmp_save_tests
 	dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam
+	dh_auto_install -- install-data
+	dh_auto_build --sourcedirectory=swig/perl5
+	dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild
 #	cd doc ;  RUBYLIB=$PWD PATH=$PATH:../bin make clean all ; cd ..
 #	broken
 

debian/tests/run-unit-test

@@ -10,6 +10,7 @@ mkdir tests
 cp -a /usr/share/doc/jellyfish-examples/examples/* tests
 mv tests/compat.sh ./
 sed -i "s#DIR=../bin#DIR=/usr/lib/${pkg}/bin#" compat.sh
+echo "#define HAVE_HTSLIB" > config.h
 tests/generate_sequence.sh
 sh tests/parallel_hashing.sh
 sh tests/merge.sh