[med-svn] [khmer] 02/02: new upstream version

Sat Oct 7 17:04:07 UTC 2017

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to tag debian/2.1.2+dfsg-1
in repository khmer.

commit d70b37c37a380eafa016b7b82d8ee680cd4bc035
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Thu Oct 5 09:13:39 2017 -0700

    new upstream version
---
 debian/changelog                |  6 ++++++
 debian/clean                    |  8 ++++++++
 debian/control                  |  3 ++-
 debian/docs                     |  2 +-
 debian/khmer-common.install     |  2 +-
 debian/liboxli-dev.install      |  8 ++++----
 debian/liboxli1.install         |  2 +-
 debian/patches/amend-skip       |  2 +-
 debian/patches/install-prefix   | 15 +++++++++++++--
 debian/patches/local-libs       | 11 +++++------
 debian/patches/older-setuptools |  4 ++--
 debian/patches/python3          | 18 +++++++++---------
 debian/patches/setup.py-py3     |  2 +-
 debian/rules                    | 15 +++++++--------
 14 files changed, 61 insertions(+), 37 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 2f3783c..1bef44e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+khmer (2.1.2+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 2.1.2
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sat, 07 Oct 2017 05:47:31 -0700
+
 khmer (2.1.1+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..c8af2af
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,8 @@
+fakehome/
+debian/*.1
+.pybuild/
+khmer.egg-info/
+khmer/_oxli/*.cp*
+khmer/_khmer.cpython*
+debian/files
+src/debian/
diff --git a/debian/control b/debian/control
index 22d6816..8d4c822 100644
--- a/debian/control
+++ b/debian/control
@@ -17,10 +17,11 @@ Build-Depends: debhelper (>= 9),
                python3-pytest-runner,
                python3-sphinx,
                python3-sphinxcontrib.autoprogram,
+               cython3 (>= 0.26.1),
                zlib1g-dev,
                libbz2-dev,
                asciidoctor
-Standards-Version: 4.0.0
+Standards-Version: 4.1.1
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/khmer.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/khmer.git
 Homepage: http://khmer.readthedocs.org
diff --git a/debian/docs b/debian/docs
index 053763d..8921722 100644
--- a/debian/docs
+++ b/debian/docs
@@ -3,4 +3,4 @@ CITATION
 README.rst
 debian/README.test
 debian/tests/run-unit-test
-lib/test-compile.cc
+src/oxli/test-compile.cc
diff --git a/debian/khmer-common.install b/debian/khmer-common.install
index a582dd5..e2890a7 100644
--- a/debian/khmer-common.install
+++ b/debian/khmer-common.install
@@ -1 +1 @@
-lib/magic        usr/share/file/khmer
+include/oxli/magic        usr/share/file/khmer
diff --git a/debian/liboxli-dev.install b/debian/liboxli-dev.install
index 7ef9843..ba339dc 100755
--- a/debian/liboxli-dev.install
+++ b/debian/liboxli-dev.install
@@ -1,6 +1,6 @@
 #!/usr/bin/dh-exec
-lib/liboxli.a       usr/lib/${DEB_HOST_MULTIARCH}
-lib/oxli.pc         usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig
-lib/liboxli.so      usr/lib/${DEB_HOST_MULTIARCH}
+src/oxli/liboxli.a       usr/lib/${DEB_HOST_MULTIARCH}
+src/oxli/oxli.pc         usr/lib/${DEB_HOST_MULTIARCH}/pkgconfig
+src/oxli/liboxli.so      usr/lib/${DEB_HOST_MULTIARCH}
 # NB: we install the headers to the oxli subdir.
-lib/*.hh            usr/include/oxli
+include/oxli/*.hh            usr/include/oxli
diff --git a/debian/liboxli1.install b/debian/liboxli1.install
index 05f9d57..78ec87a 100755
--- a/debian/liboxli1.install
+++ b/debian/liboxli1.install
@@ -1,2 +1,2 @@
 #!/usr/bin/dh-exec
-lib/liboxli.so.1  usr/lib/${DEB_HOST_MULTIARCH}
+src/oxli/liboxli.so.1  usr/lib/${DEB_HOST_MULTIARCH}
diff --git a/debian/patches/amend-skip b/debian/patches/amend-skip
index 52f4736..eb39dc4 100644
--- a/debian/patches/amend-skip
+++ b/debian/patches/amend-skip
@@ -2,7 +2,7 @@ From: Michael R. Crusoe <michael.crusoe at gmail.com>
 Subject: Fix fatal pytest.skip usage
 --- khmer.orig/tests/khmer_tst_utils.py
 +++ khmer/tests/khmer_tst_utils.py
-@@ -187,7 +187,7 @@
+@@ -188,7 +188,7 @@
              status = _runscript(scriptname, sandbox=sandbox)
          except SystemExit as err:
              status = err.code
diff --git a/debian/patches/install-prefix b/debian/patches/install-prefix
index bbb5e77..82bf80e 100644
--- a/debian/patches/install-prefix
+++ b/debian/patches/install-prefix
@@ -1,6 +1,17 @@
 Description: Use correct library version etc. (fixed by upstream #1240, remove for 2.0)
---- khmer.orig/lib/Makefile
-+++ khmer/lib/Makefile
+--- khmer.orig/Makefile
++++ khmer/Makefile
+@@ -38,7 +38,7 @@
+ # `SHELL=bash` Will break Titus's laptop, so don't use BASH-isms like
+ # `[[` conditional expressions.
+ #
+-PREFIX=/usr/local
++PREFIX ?= /usr/local
+ CPPSOURCES=$(wildcard src/oxli/*.cc include/oxli/*.hh src/khmer/_cpy_*.cc include/khmer/_cpy_*.hh) setup.py
+ CYSOURCES=$(wildcard khmer/_oxli/*.pxd khmer/_oxli/*.pyx)
+ PYSOURCES=$(filter-out khmer/_version.py, \
+--- khmer.orig/src/oxli/Makefile
++++ khmer/src/oxli/Makefile
 @@ -63,7 +63,7 @@
  # when optimization is turned on).
  WANT_DEBUGGING=false
diff --git a/debian/patches/local-libs b/debian/patches/local-libs
index 4535584..fc84fb9 100644
--- a/debian/patches/local-libs
+++ b/debian/patches/local-libs
@@ -3,17 +3,16 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 
 --- khmer.orig/setup.cfg
 +++ khmer/setup.cfg
-@@ -1,10 +1,10 @@
+@@ -1,9 +1,10 @@
  [build_ext]
  define = SEQAN_HAS_BZIP2,SEQAN_HAS_ZLIB
  undef = NO_UNIQUE_RC
 -# libraries = z,bz2
 +libraries = z,bz2
  ## if using system libraries
--include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher
--# include-dirs = lib
-+#include-dirs = lib:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher
-+include-dirs = lib:third-party/seqan/core/include:third-party/smhasher
+-include-dirs = include:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher
++#include-dirs = include:third-party/zlib:third-party/bzip2:third-party/seqan/core/include:third-party/smhasher
++include-dirs = include:third-party/seqan/core/include:third-party/smhasher
+ # include-dirs = lib
  ## if using system libraries (broken)
  
- # define = NDEBUG
diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools
index 89b9a5e..e2d2e5a 100644
--- a/debian/patches/older-setuptools
+++ b/debian/patches/older-setuptools
@@ -9,9 +9,9 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
  
 -import ez_setup
  
+ import glob
  import os
- import sys
-@@ -56,7 +55,6 @@
+@@ -60,7 +59,6 @@
  from distutils.errors import DistutilsPlatformError
  
  import versioneer
diff --git a/debian/patches/python3 b/debian/patches/python3
index 5c80b81..e48aadd 100644
--- a/debian/patches/python3
+++ b/debian/patches/python3
@@ -3,7 +3,7 @@ Description: s/python/python3/ as appropriate
 
 --- khmer.orig/Makefile
 +++ khmer/Makefile
-@@ -79,7 +79,7 @@
+@@ -84,7 +84,7 @@
  	TESTATTR ?= 'not known_failing and not jenkins and not huge and not linux'
  endif
  
@@ -11,8 +11,8 @@ Description: s/python/python3/ as appropriate
 +MODEXT=$(shell python3 -c \
         "import sysconfig;print(sysconfig.get_config_var('SO'))")
  EXTENSION_MODULE = khmer/_khmer$(MODEXT)
- 
-@@ -138,7 +138,7 @@
+ CY_MODULES = $($(wildcard khmer/_oxli/*.pyx): .pyx=.$(MODEXT))
+@@ -147,7 +147,7 @@
  
  debug: FORCE
  	export CFLAGS="-pg -fprofile-arcs -D_GLIBCXX_DEBUG_PEDANTIC \
@@ -21,7 +21,7 @@ Description: s/python/python3/ as appropriate
  		--inplace
  
  ## doc         : render documentation in HTML
-@@ -254,7 +254,7 @@
+@@ -263,7 +263,7 @@
  		--html-report diff-cover.html
  
  pytests.xml: FORCE
@@ -30,7 +30,7 @@ Description: s/python/python3/ as appropriate
  
  ## doxygen     : generate documentation of the C++ and Python code
  # helpful packages: doxygen graphviz
-@@ -294,7 +294,7 @@
+@@ -308,7 +308,7 @@
  ## test        : run the khmer test suite
  test: FORCE
  	./setup.py develop
@@ -38,8 +38,8 @@ Description: s/python/python3/ as appropriate
 +	py.test-3 -m ${TESTATTR}
  
  sloccount.sc: $(CPPSOURCES) $(PYSOURCES) $(wildcard tests/*.py) Makefile
- 	sloccount --duplicates --wide --details lib khmer scripts tests \
-@@ -310,7 +310,7 @@
+ 	sloccount --duplicates --wide --details include src khmer scripts tests \
+@@ -324,7 +324,7 @@
  		export PATH=${PATH}:${cov_analysis_dir}/bin; \
  		cov-build --dir cov-int --c-coverage gcov \
  			--disable-gcov-arg-injection make coverage-debug; \
@@ -48,7 +48,7 @@ Description: s/python/python3/ as appropriate
  			-m $(TESTATTR) ; \
  		cov-import-scm --dir cov-int --scm git 2>/dev/null; \
  	else echo 'bin/cov-build does not exist in $$cov_analysis_dir: '\
-@@ -363,7 +363,7 @@
+@@ -377,7 +377,7 @@
  
  list-citation:
  	git log --format='%aN,%aE' | sort -u | grep -v -F -f author-skips.txt > authors.csv
@@ -57,7 +57,7 @@ Description: s/python/python3/ as appropriate
  
  ## cpp-demos   : run programs demonstrating access to the (unstable) C++ API
  cpp-demos: sharedobj
-@@ -371,9 +371,9 @@
+@@ -385,9 +385,9 @@
  
  ## py-demos    : run programs demonstrating access to the Python API
  py-demos: sharedobj
diff --git a/debian/patches/setup.py-py3 b/debian/patches/setup.py-py3
index 0a6f1ad..fab4b72 100644
--- a/debian/patches/setup.py-py3
+++ b/debian/patches/setup.py-py3
@@ -5,7 +5,7 @@ Subject: fix py3 compat for setup.py
 
 --- khmer.orig/setup.py
 +++ khmer/setup.py
-@@ -197,7 +197,11 @@
+@@ -242,7 +242,11 @@
  #     correctly for the citation information, but this requires a non-standard
  #     library that we don't want to add as a dependency for `setup.py`.
  #     -- Daniel Standage, 2017-05-21
diff --git a/debian/rules b/debian/rules
index 8a96cfc..8367714 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,9 @@ export DH_VERBOSE=1
 export PYBUILD_NAME=khmer
 export PYBUILD_INSTALL_ARGS='--install-scripts=/usr/lib/khmer/bin'
 export PYBUILD_DESTDIR_python3=debian/khmer
-
+export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
+export DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
 # Force C++ library build to use Debian zlib1g-dev/libbz2-dev
 export USE_SYSTEM_ZLIB=true
 export USE_SYSTEM_LIBBZ2=true
@@ -18,7 +20,7 @@ override_dh_auto_build:
 	ln -sf "`pwd`"/.pybuild/pythonX.Y_*/build/khmer/*.so khmer && \
 		./setup.py develop --user && ./setup.py build_sphinx
 	asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc
-	cd lib && $(MAKE) clean all
+	cd src/oxli && $(MAKE) clean all
 
 override_dh_auto_test:
 	dh_auto_install
@@ -29,14 +31,11 @@ override_dh_auto_test:
 
 
 override_dh_auto_clean:
-	#dh_auto_clean
-	rm -f khmer/*.so
-	rm -f debian/*.1
-	cd lib && $(MAKE) clean
-	rm -Rf fakehome
+	dh_auto_clean || /bin/true
+	cd src/oxli && $(MAKE) clean
 
 override_dh_install:
-	cd lib && $(MAKE) PREFIX=../debian/tmp install
+	cd src/oxli && $(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

