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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> --- 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 <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
