[med-svn] [khmer] 02/02: clean up d/changelog, drop patch, fix tests & install
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jul 31 16:33:14 UTC 2015
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 <michael.crusoe at gmail.com>
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 <crusoe at ucdavis.edu> 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 <mcrusoe at msu.edu> 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 <mcrusoe at msu.edu> Tue, 27 Jan 2015 16:07:19 -0500
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> 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, at prefix@,$(PREFIX),' -e 's, at VERSION@,$(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
--
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