This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer.
commit 282f3fd598e2bff1466e7c42358ccfe1f87ebbd5 Author: Michael R. Crusoe <[email protected]> Date: Fri Jul 31 07:12:22 2015 -0700 clean up d/changelog, drop patch, fix tests & install --- debian/changelog | 18 +-- debian/control | 6 +- debian/liboxli1.install | 2 +- debian/patches/install-prefix | 11 ++ debian/patches/pr-1148-changes | 358 ----------------------------------------- debian/patches/series | 2 +- debian/rules | 11 +- 7 files changed, 24 insertions(+), 384 deletions(-) diff --git a/debian/changelog b/debian/changelog index 5954430..5983c59 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,19 +1,5 @@ -khmer (2.0rc1+dfsg-1) UNRELEASED; urgency=low - - * Updated to 2.0rc1 release - - -- Michael R. Crusoe <[email protected]> Wed, 08 Jul 2015 20:02:36 -0700 - -khmer (1.3+dfsg-2) UNRELEASED; urgency=low - - * Remove 'module' infix from CPython extension which allows dh_python2 to - add the multiarch triplet infix without affecting module loading. Removed - symlink workaround now that it is no longer needed. - - -- Michael R. Crusoe <[email protected]> Thu, 12 Feb 2015 06:02:36 -0500 - -khmer (1.3+dfsg-1) unstable; urgency=medium +khmer (2.0~rc2+dfsg-1) UNRELEASED; urgency=low * Initial upload (Closes: #777688) - -- Michael R. Crusoe <[email protected]> Tue, 27 Jan 2015 16:07:19 -0500 + -- Michael R. Crusoe <[email protected]> Tue, 27 Jan 2015 16:07:19 -0500 diff --git a/debian/control b/debian/control index 5e40aca..9b223b3 100644 --- a/debian/control +++ b/debian/control @@ -29,7 +29,7 @@ Architecture: any Multi-Arch: same Depends: ${misc:Depends}, ${shlibs:Depends} -Description: in-memory DNA sequence kmer counting, filtering & graph traversal +Description: common files for the khmer project tools khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to @@ -63,7 +63,7 @@ Depends: khmer-common, ${shlibs:Depends}, ${misc:Depends} Pre-Depends: ${misc:Pre-Depends} -Description: in-memory DNA sequence kmer counting, filtering & graph traversal +Description: in-memory DNA sequence analysis library from the khmer project khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to @@ -79,7 +79,7 @@ Depends: khmer-common, ${shlibs:Depends}, ${misc:Depends} Pre-Depends: ${misc:Pre-Depends} -Description: in-memory DNA sequence kmer counting, filtering & graph traversal +Description: in-memory DNA sequence analysis dev library khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to diff --git a/debian/liboxli1.install b/debian/liboxli1.install index b0934fa..3bec701 100755 --- a/debian/liboxli1.install +++ b/debian/liboxli1.install @@ -1,2 +1,2 @@ #!/usr/bin/dh-exec -lib/liboxli.so.2.0rc1+dfsg usr/lib/${DEB_HOST_MULTIARCH} +lib/liboxli.so.2.0~rc2+dfsg usr/lib/${DEB_HOST_MULTIARCH} diff --git a/debian/patches/install-prefix b/debian/patches/install-prefix new file mode 100644 index 0000000..56745d2 --- /dev/null +++ b/debian/patches/install-prefix @@ -0,0 +1,11 @@ +--- khmer.orig/lib/Makefile ++++ khmer/lib/Makefile +@@ -28,7 +28,7 @@ + # when optimization is turned on). + WANT_DEBUGGING=false + +-PREFIX=/usr/local ++PREFIX ?= /usr/local + + ### NOTE: No user-serviceable parts below this line! ### + diff --git a/debian/patches/pr-1148-changes b/debian/patches/pr-1148-changes deleted file mode 100644 index 5882288..0000000 --- a/debian/patches/pr-1148-changes +++ /dev/null @@ -1,358 +0,0 @@ ---- khmer.orig/lib/Makefile -+++ khmer/lib/Makefile -@@ -1,3 +1,8 @@ -+# Should we use the standard system zlib and libbz2? -+ -+USE_SYSTEM_ZLIB ?= false -+USE_SYSTEM_LIBBZ2 ?= false -+ - # Profile? - # Set this variable to true if you wish to profile the codes. - WANT_PROFILING=false -@@ -29,47 +34,61 @@ - # and are willing to accept the overhead such instrumentation introduces. - WITH_INTERNAL_METRICS=false - -- - PREFIX=/usr/local - - ### NOTE: No user-serviceable parts below this line! ### - - INCLUDES= -I ../third-party/seqan/core/include/ \ -- -I ../third-party/zlib/ \ -- -I ../third-party/bzip2/ \ - -I ../third-party/smhasher/ - --CXXFLAGS=$(INCLUDES) --CXX_WARNING_FLAGS=-Wall --CXX_OPTIMIZATION_FLAGS=-O3 --CXX_SHARED_LIB_FLAGS=-fPIC --CXXFLAGS+= \ -- $(CXX_WARNING_FLAGS) \ -- $(CXX_OPTIMIZATION_FLAGS) \ -- $(CXX_SHARED_LIB_FLAGS) -- --CFLAGS=$(INCLUDES) --C_WARNING_FLAGS=-Wall --C_OPTIMIZATION_FLAGS=-O3 --C_SHARED_LIB_FLAGS=-fPIC --CFLAGS+= $(C_WARNING_FLAGS) $(C_OPTIMIZATION_FLAGS) $(C_SHARED_LIB_FLAGS) -+ifeq ($(USE_SYSTEM_ZLIB), false) -+INCLUDES += -I ../third-party/zlib/ -+endif -+ -+ifeq ($(USE_SYSTEM_LIBBZ2), false) -+INCLUDES += -I ../third-party/bzip2/ -+endif -+ -+# Warnings in common to C and C++ -+WARNINGS=-Wall - --LIBS= -+# Flags in common to C and C++ -+COMMON_FLAGS=-O3 -fPIC -+SEQAN_FLAGS=-DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -+ -+# Base C/CXXFLAGS -+CPPFLAGS ?= -+CPPFLAGS += $(SEQAN_FLAGS) -+ -+CXXFLAGS ?= -+CXXFLAGS += $(COMMON_FLAGS) $(WARNINGS) -+CXXFLAGS += -Wstrict-null-sentinel -+CXXFLAGS += $(INCLUDES) $(CPPFLAGS) -+ -+CFLAGS ?= -+CXXFLAGS += $(COMMON_FLAGS) $(WARNINGS) -+CFLAGS += -Wshadow -Wcast-align -Wstrict-prototypes -+CFLAGS += $(INCLUDES) $(CPPFLAGS) -+ -+LDFLAGS ?= -+ifneq ($(USE_SYSTEM_ZLIB), false) -+LDFLAGS += -lz -+endif -+ -+ifneq ($(USE_SYSTEM_LIBBZ2), false) -+LDFLAGS += -lbz2 -+endif - - ifeq ($(WANT_DEBUGGING), true) --CXX_DEBUG_FLAGS=-g --CXXFLAGS+= $(CXX_DEBUG_FLAGS) --CFLAGS+= $(CXX_DEBUG_FLAGS) --else --CXX_DEBUG_FLAGS= -+DEBUG_FLAGS=-g -+CXXFLAGS += $(DEBUG_FLAGS) -+CFLAGS += $(DEBUG_FLAGS) - endif - - ifeq ($(WANT_EXTRA_SANITY_CHECKING), true) - DEFINE_KHMER_EXTRA_SANITY_CHECKS=-DKHMER_EXTRA_SANITY_CHECKS --CXXFLAGS+= $(DEFINE_KHMER_EXTRA_SANITY_CHECKS) --CFLAGS+= $(DEFINE_KHMER_EXTRA_SANITY_CHECKS) --else --DEFINE_KHMER_EXTRA_SANITY_CHECKS= -+CXXFLAGS += $(DEFINE_KHMER_EXTRA_SANITY_CHECKS) -+CFLAGS += $(DEFINE_KHMER_EXTRA_SANITY_CHECKS) - endif - - ifeq ($(WANT_PROFILING), true) -@@ -77,19 +96,20 @@ - CXX=tau_cxx.sh - endif - ifeq ($(PROFILER_OF_CHOICE), gprof) --PROFILING_LIBS=-pg --CXXFLAGS+= -pg --LIBS+= $(PROFILING_LIBS) -+CXXFLAGS += -pg -+CFLAGS += -pg -+LDFLAGS += -pg - endif - endif - - ifeq ($(WITH_INTERNAL_METRICS), true) --CXXFLAGS+= -DWITH_INTERNAL_METRICS -+CXXFLAGS += -DWITH_INTERNAL_METRICS -+CFLAGS += -DWITH_INTERNAL_METRICS - endif - - # Place POSIX threads last in linking order, if needed. - ifneq ($(shell uname), Linux) --LIBS+= -pthread -+LDFLAGS += -pthread - endif - - -@@ -99,47 +119,50 @@ - rm -f chkomp) - - ifeq ($(HAVE_OPENMP), true) -- CFLAGS += -fopenmp -- CXXFLAGS += -fopenmp -+CXXFLAGS +=-fopenmp -+CFLAGS +=-fopenmp - endif - --VERSION = $(shell python get_version.py) -+ifneq ($(PACKAGE_VERSION),) -+VERSION = $(PACKAGE_VERSION) -+else -+VERSION = $(shell ./get_version.py) -+endif - --LIBVERSION = $(shell python get_version.py | sed -e 's/^\([^-]*\)-.*/\1/') --LIBKHMERSO=libkhmer.so.$(LIBVERSION) -+MAJOR_VERSION = $(shell echo $(VERSION) | sed -e 's/^\([^-\.]*\)\.\([^-\.]*\).*/\1/') -+MINOR_VERSION = $(shell echo $(VERSION) | sed -e 's/^\([^-\.]*\)\.\([^-\.]*\).*/\2/') - --CXXFLAGS+= -DVERSION=$(VERSION) -+LIB_VERSION = $(MAJOR_VERSION).$(MINOR_VERSION) -+ -+ifeq ($(shell uname), Darwin) -+SHARED_EXT = dylib -+SONAME = liboxli.$(SHARED_EXT).$(MAJOR_VERSION) -+SONAME_FLAGS = -install_name $(PREFIX)/lib/$(SONAME) -compatibility_version $(MAJOR_VERSION) -current_version $(VERSION) -+else -+SHARED_EXT = so -+SONAME = liboxli.$(SHARED_EXT).$(MAJOR_VERSION) -+SONAME_FLAGS = -Wl,-soname=$(SONAME) -+endif -+ -+LIBKHMERSO=liboxli.$(SHARED_EXT).$(LIB_VERSION) -+ -+CXXFLAGS += -DVERSION=$(VERSION) - - NO_UNIQUE_RC=0 --CXXFLAGS+= -DNO_UNIQUE_RC=$(NO_UNIQUE_RC) -+CXXFLAGS += -DNO_UNIQUE_RC=$(NO_UNIQUE_RC) -+CFLAGS += -DNO_UNIQUE_RC=$(NO_UNIQUE_RC) - - export CXX - export CFLAGS - export CXXFLAGS --export LIBS -+export LDFLAGS - export VERSION - - - #### Third party dependencies #### --# ZLIB -+# ZLIB, use .lo not .o, so we get -fPIC and other library-related flags - ZLIB_DIR=../third-party/zlib - ZLIB_OBJS_BASE=\ -- adler32.o \ -- crc32.o \ -- deflate.o \ -- infback.o \ -- inffast.o \ -- inflate.o \ -- inftrees.o \ -- trees.o \ -- zutil.o \ -- compress.o \ -- uncompr.o \ -- gzclose.o \ -- gzlib.o \ -- gzread.o \ -- gzwrite.o --ZLIB_PIC_OBJS_BASE=\ - adler32.lo \ - crc32.lo \ - deflate.lo \ -@@ -157,7 +180,6 @@ - gzwrite.lo - - ZLIB_OBJS=$(addprefix $(ZLIB_DIR)/, $(ZLIB_OBJS_BASE)) --ZLIB_PIC_OBJS=$(addprefix $(ZLIB_DIR)/, $(ZLIB_PIC_OBJS_BASE)) - - # BZ2 - BZIP2_DIR=../third-party/bzip2 -@@ -173,7 +195,7 @@ - BZIP2_OBJS=$(addprefix $(BZIP2_DIR)/, $(BZIP2_OBJS_BASE)) - - --#### khmer proper below here #### -+#### oxli proper below here #### - - LIBKHMER_OBJS= \ - counting.o \ -@@ -187,9 +209,22 @@ - read_parsers.o \ - subset.o \ - trace_logger.o \ -- murmur3.o \ -- $(BZIP2_OBJS) \ -- $(ZLIB_PIC_OBJS) -+ murmur3.o -+ -+PRECOMILE_OBJS ?= -+PRECLEAN_TARGS ?= -+ -+ifeq ($(USE_SYSTEM_ZLIB), false) -+LIBKHMER_OBJS += $(ZLIB_OBJS) -+PRECOMILE_OBJS += $(ZLIB_OBJS) -+PRECLEAN_TARGS += zlibclean -+endif -+ -+ifeq ($(USE_SYSTEM_LIBBZ2), false) -+LIBKHMER_OBJS += $(BZIP2_OBJS) -+PRECOMILE_OBJS += $(BZIP2_OBJS) -+PRECLEAN_TARGS += libbz2clean -+endif - - KHMER_HEADERS= \ - counting.hh \ -@@ -206,38 +241,35 @@ - subset.hh \ - trace_logger.hh - --TEST_PROGS = test-Colors test-read-aligner test-compile -- - # START OF RULES # - - # The all rule comes first! --all: $(LIBKHMERSO) libkhmer.a khmer.pc -+all: $(LIBKHMERSO) liboxli.a oxli.pc - --clean: -- rm -f *.o *.a *.so* khmer.pc $(TEST_PROGS) -+zlibclean: - (cd $(ZLIB_DIR) && make distclean) -+libbz2clean: - (cd $(BZIP2_DIR) && make -f Makefile-libbz2_so clean) - --test: $(TEST_PROGS) -+clean: $(PRECLEAN_TARGS) -+ rm -f *.o *.a *.$(SHARED_EXT)* oxli.pc $(TEST_PROGS) - --install: $(LIBKHMERSO) libkhmer.a khmer.pc $(KHMER_HEADERS) -- mkdir -p $(PREFIX)/lib $(PREFIX)/lib/pkgconfig $(PREFIX)/include/ -- cp -r $(KHMER_HEADERS) \ -- ../third-party/smhasher/MurmurHash3.h \ -- $(PREFIX)/include/ -- cp khmer.pc $(PREFIX)/lib/pkgconfig/ -- cp $(LIBKHMERSO) libkhmer.a $(PREFIX)/lib -- ln -sf $(PREFIX)/lib/$(LIBKHMERSO) $(PREFIX)/lib/libkhmer.so -+install: $(LIBKHMERSO) liboxli.a oxli.pc $(KHMER_HEADERS) -+ mkdir -p $(PREFIX)/lib $(PREFIX)/lib/pkgconfig $(PREFIX)/include/oxli -+ cp -r $(KHMER_HEADERS) \ -+ ../third-party/smhasher/MurmurHash3.h \ -+ $(PREFIX)/include/oxli/ -+ cp oxli.pc $(PREFIX)/lib/pkgconfig/ -+ cp $(LIBKHMERSO) liboxli.a $(PREFIX)/lib -+ ln -sf $(PREFIX)/lib/$(LIBKHMERSO) $(PREFIX)/lib/$(SONAME) -+ ln -sf $(PREFIX)/lib/$(SONAME) $(PREFIX)/lib/liboxli.$(SHARED_EXT) - --khmer.pc: khmer.pc.in -+oxli.pc: oxli.pc.in - sed -e 's,@prefix@,$(PREFIX),' -e 's,@VERSION@,$(VERSION),' $< >$@ - - $(ZLIB_OBJS): - (cd $(ZLIB_DIR) && ./configure && make $(ZLIB_OBJS_BASE)) - --$(ZLIB_PIC_OBJS): -- (cd $(ZLIB_DIR) && ./configure && make $(ZLIB_PIC_OBJS_BASE)) -- - $(BZIP2_OBJS): - (cd $(BZIP2_DIR) && make -f Makefile-libbz2_so $(BZIP2_OBJS_BASE)) - -@@ -245,17 +277,14 @@ - murmur3.o: ../third-party/smhasher/MurmurHash3.cc - $(CXX) $(CXXFLAGS) -c -o $@ $< - --%.o: %.cc $(ZLIB_OBJS) $(ZLIB_PIC_OBJS) $(BZIP2_OBJS) $(KHMER_HEADERS) -- $(CXX) $(CXXFLAGS) -c -o $@ $< -+%.o: %.cc $(PRECOMILE_OBJS) $(KHMER_HEADERS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -c -o $@ $< - - $(LIBKHMERSO): $(LIBKHMER_OBJS) -- $(CXX) $(CXXFLAGS) -shared -o $@ $(LIBKHMER_OBJS) -- ln -sf $(LIBKHMERSO) libkhmer.so -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $(SONAME_FLAGS) -shared -o $@ $^ -+ ln -sf $(LIBKHMERSO) $(SONAME) -+ ln -sf $(SONAME) liboxli.$(SHARED_EXT) - --libkhmer.a: $(LIBKHMER_OBJS) -- ar rcs $@ $(LIBKHMER_OBJS) -+liboxli.a: $(LIBKHMER_OBJS) -+ ar rcs $@ $^ - ranlib $@ -- --# catch-all rule for test drivers --test-%: test-%.cc libkhmer.a -- $(CXX) $(CXXFLAGS) -I . -o $@ $< libkhmer.a ---- khmer.orig/lib/khmer.pc.in -+++ /dev/null -@@ -1,14 +0,0 @@ --prefix=@prefix@ --exec_prefix=${prefix} --libdir=${exec_prefix}/lib --sharedlibdir=${libdir} --includedir=${prefix}/include -- --Name: khmer --Description: The unsupported core C++ library from the khmer project --URL: http://khmer.readthedocs.org/ --Version: @VERSION@ -- --Requires: --Libs: -L${libdir} -L${sharedlibdir} -lkhmer --Cflags: -I${includedir} ---- /dev/null -+++ khmer/lib/oxli.pc.in -@@ -0,0 +1,14 @@ -+prefix=@prefix@ -+exec_prefix=${prefix} -+libdir=${exec_prefix}/lib -+sharedlibdir=${libdir} -+includedir=${prefix}/include -+ -+Name: khmer -+Description: The unsupported core C++ library from the khmer project -+URL: http://khmer.readthedocs.org/ -+Version: @VERSION@ -+ -+Requires: -+Libs: -L${libdir} -L${sharedlibdir} -lkhmer -+Cflags: -I${includedir} diff --git a/debian/patches/series b/debian/patches/series index f30874c..a9d55d6 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,6 +1,6 @@ setup-py-py3 -pr-1148-changes local-libs older-setuptools disable_google_analytics get_version +install-prefix diff --git a/debian/rules b/debian/rules index d309e42..8f8ed38 100755 --- a/debian/rules +++ b/debian/rules @@ -17,17 +17,17 @@ export PACKAGE_VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut override_dh_auto_build: dh_auto_build ln -sf "`pwd`"/.pybuild/pythonX.Y_*/build/khmer/*.so khmer && \ - ./setup.py build_sphinx + ./setup.py develop --user && ./setup.py build_sphinx ronn -r --manual=khmer --organization='Michigan State University' \ debian/khmer.1.ronn cd lib && $(MAKE) clean all override_dh_auto_test: PYBUILD_SYSTEM=custom \ - PYBUILD_TEST_ARGS="cd {build_dir}; \ - ln -s {build_dir}/../../../scripts khmer/; PYTHONPATH={build_dir} \ - {interpreter} -m nose --attr '!known_failing,!jenkins'; \ - rm khmer/scripts" dh_auto_test + PYBUILD_TEST_ARGS="cd {dir}; {interpreter} setup.py develop --user; \ + {interpreter} setup.py nosetests \ + --attr '!known_failing,!jenkins,!huge'" dh_auto_test + override_dh_auto_clean: dh_auto_clean @@ -36,6 +36,7 @@ override_dh_auto_clean: cd lib && $(MAKE) clean override_dh_install: + cd lib && $(MAKE) PREFIX=debian/tmp install dh_install find debian/khmer -name .gitignore -delete -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
