This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to tag debian/2.1.1+dfsg-1 in repository khmer.
commit 56fff0a1261d5db120019258379162970b7b4b27 Author: Michael R. Crusoe <[email protected]> Date: Tue Aug 29 23:30:24 2017 -0700 new upstream release --- debian/changelog | 5 ++- debian/clean | 2 - debian/control | 5 ++- debian/khmer-common.lintian-overrides | 2 +- debian/khmer.install | 2 +- debian/patches/older-setuptools | 7 ++-- debian/patches/python3 | 72 +++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + debian/patches/setup.py-py3 | 9 ++--- debian/tests/run-unit-test | 3 +- 10 files changed, 89 insertions(+), 19 deletions(-) diff --git a/debian/changelog b/debian/changelog index a52c4f9..2f3783c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -5,9 +5,10 @@ khmer (2.1.1+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] * New upstream version 2.1.1 - * Incorporate patch from Ubuntu, thank you Michael Hudson-Doyle. Closes: #862380 + * Incorporate patch from Ubuntu, thank you Michael Hudson-Doyle. + Closes: #862380 - -- Michael R. Crusoe <[email protected]> Mon, 20 Feb 2017 01:50:56 -0800 + -- Michael R. Crusoe <[email protected]> Tue, 29 Aug 2017 23:30:09 -0700 khmer (2.0+dfsg-10ubuntu1) artful; urgency=medium diff --git a/debian/clean b/debian/clean deleted file mode 100644 index fe4e972..0000000 --- a/debian/clean +++ /dev/null @@ -1,2 +0,0 @@ -.pybuild/ -fakehome/ diff --git a/debian/control b/debian/control index 9c7ae9f..22d6816 100644 --- a/debian/control +++ b/debian/control @@ -16,10 +16,11 @@ Build-Depends: debhelper (>= 9), python3-pytest, python3-pytest-runner, python3-sphinx, + python3-sphinxcontrib.autoprogram, zlib1g-dev, libbz2-dev, asciidoctor -Standards-Version: 3.9.8 +Standards-Version: 4.0.0 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 @@ -44,7 +45,7 @@ Architecture: amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64el any-s Multi-Arch: same Depends: khmer-common, python3 (>= 3.3), - python3-screed (<< 1.0), + python3-screed (>= 1.0), ${shlibs:Depends}, ${misc:Depends}, ${python3:Depends} diff --git a/debian/khmer-common.lintian-overrides b/debian/khmer-common.lintian-overrides index 5686645..2c7adaa 100644 --- a/debian/khmer-common.lintian-overrides +++ b/debian/khmer-common.lintian-overrides @@ -1 +1 @@ -khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.txt +khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt diff --git a/debian/khmer.install b/debian/khmer.install index f84dbe4..1de24e4 100644 --- a/debian/khmer.install +++ b/debian/khmer.install @@ -1,2 +1,2 @@ debian/bin/* usr/bin/ -debian/khmer.metainfo.xml /usr/share/appdata +debian/khmer.metainfo.xml /usr/share/metainfo/ diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools index a986fe4..89b9a5e 100644 --- a/debian/patches/older-setuptools +++ b/debian/patches/older-setuptools @@ -3,16 +3,15 @@ Author: Michael R. Crusoe <[email protected]> --- khmer.orig/setup.py +++ khmer/setup.py -@@ -36,8 +36,6 @@ +@@ -36,7 +36,6 @@ # Contact: [email protected] """Setup for khmer project.""" -import ez_setup -- + import os import sys - from os import listdir as os_listdir -@@ -56,7 +54,6 @@ +@@ -56,7 +55,6 @@ from distutils.errors import DistutilsPlatformError import versioneer diff --git a/debian/patches/python3 b/debian/patches/python3 new file mode 100644 index 0000000..5c80b81 --- /dev/null +++ b/debian/patches/python3 @@ -0,0 +1,72 @@ +Author: Michael R. Crusoe <[email protected]> +Description: s/python/python3/ as appropriate + +--- khmer.orig/Makefile ++++ khmer/Makefile +@@ -79,7 +79,7 @@ + TESTATTR ?= 'not known_failing and not jenkins and not huge and not linux' + endif + +-MODEXT=$(shell python -c \ ++MODEXT=$(shell python3 -c \ + "import sysconfig;print(sysconfig.get_config_var('SO'))") + EXTENSION_MODULE = khmer/_khmer$(MODEXT) + +@@ -138,7 +138,7 @@ + + debug: FORCE + export CFLAGS="-pg -fprofile-arcs -D_GLIBCXX_DEBUG_PEDANTIC \ +- -D_GLIBCXX_DEBUG -DDEBUG_ASSEMBLY=1 -DDEBUG_FILTERS=1"; python setup.py build_ext --debug \ ++ -D_GLIBCXX_DEBUG -DDEBUG_ASSEMBLY=1 -DDEBUG_FILTERS=1"; python3 setup.py build_ext --debug \ + --inplace + + ## doc : render documentation in HTML +@@ -254,7 +254,7 @@ + --html-report diff-cover.html + + pytests.xml: FORCE +- py.test --junitxml=$@ -m ${TESTATTR} ++ py.test-3 --junitxml=$@ -m ${TESTATTR} + + ## doxygen : generate documentation of the C++ and Python code + # helpful packages: doxygen graphviz +@@ -294,7 +294,7 @@ + ## test : run the khmer test suite + test: FORCE + ./setup.py develop +- py.test -m ${TESTATTR} ++ py.test-3 -m ${TESTATTR} + + sloccount.sc: $(CPPSOURCES) $(PYSOURCES) $(wildcard tests/*.py) Makefile + sloccount --duplicates --wide --details lib khmer scripts tests \ +@@ -310,7 +310,7 @@ + export PATH=${PATH}:${cov_analysis_dir}/bin; \ + cov-build --dir cov-int --c-coverage gcov \ + --disable-gcov-arg-injection make coverage-debug; \ +- cov-capture --dir cov-int --c-coverage gcov python -m pytest \ ++ cov-capture --dir cov-int --c-coverage gcov python3 -m pytest \ + -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 @@ + + list-citation: + git log --format='%aN,%aE' | sort -u | grep -v -F -f author-skips.txt > authors.csv +- python sort-authors-list.py ++ python3 sort-authors-list.py + + ## cpp-demos : run programs demonstrating access to the (unstable) C++ API + cpp-demos: sharedobj +@@ -371,9 +371,9 @@ + + ## py-demos : run programs demonstrating access to the Python API + py-demos: sharedobj +- python examples/python-api/exact-counting.py +- python examples/python-api/bloom.py +- python examples/python-api/consume.py examples/c++-api/reads.fastq ++ python3 examples/python-api/exact-counting.py ++ python3 examples/python-api/bloom.py ++ python3 examples/python-api/consume.py examples/c++-api/reads.fastq + + FORCE: + diff --git a/debian/patches/series b/debian/patches/series index 0b16d07..6194b19 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -9,3 +9,4 @@ cpython-bug-empty-exceptions #silence-mt-bug amend-skip setup.py-py3 +python3 diff --git a/debian/patches/setup.py-py3 b/debian/patches/setup.py-py3 index ee2fcf2..0a6f1ad 100644 --- a/debian/patches/setup.py-py3 +++ b/debian/patches/setup.py-py3 @@ -3,11 +3,9 @@ Date: Fri Jun 23 06:19:31 2017 -0700 Forwarded: https://github.com/dib-lab/khmer/pull/1333 Subject: fix py3 compat for setup.py -diff --git a/setup.py b/setup.py -index ef9b6c12..46fba6fa 100755 ---- a/setup.py -+++ b/setup.py -@@ -244,7 +244,11 @@ else: +--- khmer.orig/setup.py ++++ khmer/setup.py +@@ -197,7 +197,11 @@ # 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 @@ -20,4 +18,3 @@ index ef9b6c12..46fba6fa 100755 authors = csv.reader(csvin) authorstr = ', '.join([row[0] for row in authors]) authorstr = 'Daniel Standage, ' + authorstr + ', C. Titus Brown' - diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test index 62f5745..336750c 100644 --- a/debian/tests/run-unit-test +++ b/debian/tests/run-unit-test @@ -5,4 +5,5 @@ if [ "$ADTTMP" = "" ] ; then ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` fi cd $ADTTMP -PATH=/usr/lib/khmer/bin/:$PATH python3 -m nose --attr '!known_failing,!huge' khmer +PATH=/usr/lib/khmer/bin/:$PATH python3 -m pytest --pyarg khmer \ + -m 'not known_failing and not huge' -- 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
