Michael R. Crusoe pushed to branch master at Debian Med / jellyfish
Commits: b79d7cf1 by Michael R. Crusoe at 2019-09-27T14:33:03Z remove rpath - - - - - 71abcf60 by Michael R. Crusoe at 2019-09-27T14:59:52Z retry python3 package - - - - - dd72ffef by Michael R. Crusoe at 2019-09-27T15:50:20Z cleanups - - - - - 3b757c40 by Michael R. Crusoe at 2019-09-27T16:29:18Z document the restored python3 package - - - - - b183b49c by Michael R. Crusoe at 2019-09-27T16:29:41Z release - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/python3 - debian/patches/series - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,10 +1,11 @@ -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 <[email protected]> Fri, 27 Sep 2019 15:00:00 +0200 + -- Michael R. Crusoe <[email protected]> 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 ===================================== @@ -0,0 +1,16 @@ +Author: Michael R. Crusoe <[email protected]> +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 View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/f9bd3a805462e729a28442847950f29a0e76419c...b183b49c2e409f1951e909e1a28ba5e62aa5bae7 -- View it on GitLab: https://salsa.debian.org/med-team/jellyfish/compare/f9bd3a805462e729a28442847950f29a0e76419c...b183b49c2e409f1951e909e1a28ba5e62aa5bae7 You're receiving this email because of your account on salsa.debian.org.
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