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commit a5cdb20d8179f0dd0981a307f15334571044f825 Author: Michael R. Crusoe <[email protected]> Date: Fri Jun 23 05:57:33 2017 -0700 new upstream release --- debian/changelog | 11 +++++++++-- debian/clean | 4 ++-- debian/control | 6 +++--- debian/patches/amend-skip | 20 +------------------- debian/patches/disable_google_analytics | 2 +- debian/patches/get_version | 6 +++--- debian/patches/older-setuptools | 2 +- debian/patches/series | 1 + debian/patches/setup.py-py3 | 23 +++++++++++++++++++++++ debian/patches/update-manifest | 6 +++--- debian/rules | 7 ++++--- 11 files changed, 51 insertions(+), 37 deletions(-) diff --git a/debian/changelog b/debian/changelog index 3e5aabc..a52c4f9 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,13 +1,20 @@ -khmer (2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12-1) experimental; urgency=medium +khmer (2.1.1+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * Remove empty field [ Michael R. Crusoe ] - * New upstream version 2.0~pre2.1-20170216-b2ab51575c2fa4c6bff078387ed8b67c4299df12 + * New upstream version 2.1.1 + * Incorporate patch from Ubuntu, thank you Michael Hudson-Doyle. Closes: #862380 -- Michael R. Crusoe <[email protected]> Mon, 20 Feb 2017 01:50:56 -0800 +khmer (2.0+dfsg-10ubuntu1) artful; urgency=medium + + * Fix build with Python 3.6. + + -- Michael Hudson-Doyle <[email protected]> Fri, 12 May 2017 13:15:00 +1200 + khmer (2.0+dfsg-10) unstable; urgency=medium * Team upload. diff --git a/debian/clean b/debian/clean index 0efb6f1..fe4e972 100644 --- a/debian/clean +++ b/debian/clean @@ -1,2 +1,2 @@ -.pybuild -fakehome +.pybuild/ +fakehome/ diff --git a/debian/control b/debian/control index 832b46e..9c7ae9f 100644 --- a/debian/control +++ b/debian/control @@ -7,15 +7,15 @@ Priority: optional Build-Depends: debhelper (>= 9), dh-python, dh-exec, + python3-guzzle-sphinx-theme, python3 (>= 3.3), python3-dev (>= 3.3), python3-all-dev (>= 3.3), python3-setuptools (>= 3.3), - python3-screed, - python3-sphinx, - python3-sphinxcontrib.autoprogram, + python3-screed (>= 1.0), python3-pytest, python3-pytest-runner, + python3-sphinx, zlib1g-dev, libbz2-dev, asciidoctor diff --git a/debian/patches/amend-skip b/debian/patches/amend-skip index 25a34ec..52f4736 100644 --- a/debian/patches/amend-skip +++ b/debian/patches/amend-skip @@ -1,26 +1,8 @@ From: Michael R. Crusoe <[email protected]> Subject: Fix fatal pytest.skip usage ---- khmer.orig/tests/test_sandbox_scripts.py -+++ khmer/tests/test_sandbox_scripts.py -@@ -61,11 +61,12 @@ - def teardown(): - utils.cleanup() - -- [email protected](not os.path.exists(os.path.join(os.path.dirname(__file__), -+ "../sandbox"))) - def _sandbox_scripts(): - sandbox_path = os.path.join(os.path.dirname(__file__), "../sandbox") -- if not os.path.exists(sandbox_path): -- pytest.skip("sandbox scripts are only tested in a repository") -+ #if not os.path.exists(sandbox_path): -+ # pytest.skip("sandbox scripts are only tested in a repository") - - path = os.path.join(sandbox_path, "*.py") - return [os.path.normpath(s) for s in glob.glob(path)] --- khmer.orig/tests/khmer_tst_utils.py +++ khmer/tests/khmer_tst_utils.py -@@ -186,7 +186,7 @@ +@@ -187,7 +187,7 @@ status = _runscript(scriptname, sandbox=sandbox) except SystemExit as err: status = err.code diff --git a/debian/patches/disable_google_analytics b/debian/patches/disable_google_analytics index 6351539..a6c3417 100644 --- a/debian/patches/disable_google_analytics +++ b/debian/patches/disable_google_analytics @@ -3,7 +3,7 @@ Author: Michael R. Crusoe <[email protected]> --- khmer.orig/doc/conf.py +++ khmer/doc/conf.py -@@ -184,7 +184,7 @@ +@@ -186,7 +186,7 @@ # Various settings to pass to templates: html_context = { diff --git a/debian/patches/get_version b/debian/patches/get_version index 93208f2..c04d91b 100644 --- a/debian/patches/get_version +++ b/debian/patches/get_version @@ -7,9 +7,9 @@ Description: Use debian package version instead of git version import os +import subprocess - # If extensions (or modules to document with autodoc) are in another directory, - # add these directories to sys.path here. If the directory is relative to the -@@ -57,9 +58,12 @@ + import guzzle_sphinx_theme + +@@ -56,9 +57,12 @@ # The full version, including alpha/beta/rc tags. diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools index c7ee1b6..a986fe4 100644 --- a/debian/patches/older-setuptools +++ b/debian/patches/older-setuptools @@ -12,7 +12,7 @@ Author: Michael R. Crusoe <[email protected]> import os import sys from os import listdir as os_listdir -@@ -55,7 +53,6 @@ +@@ -56,7 +54,6 @@ from distutils.errors import DistutilsPlatformError import versioneer diff --git a/debian/patches/series b/debian/patches/series index cad6753..0b16d07 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -8,3 +8,4 @@ install-prefix cpython-bug-empty-exceptions #silence-mt-bug amend-skip +setup.py-py3 diff --git a/debian/patches/setup.py-py3 b/debian/patches/setup.py-py3 new file mode 100644 index 0000000..ee2fcf2 --- /dev/null +++ b/debian/patches/setup.py-py3 @@ -0,0 +1,23 @@ +Author: Michael R. Crusoe <[email protected]> +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: + # 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 +-with open('authors.csv', 'r') as csvin: ++if sys.version_info[0] == 2: ++ author_opts = {} ++else: ++ author_opts = { "newline": '', "encoding": 'utf-8'} ++with open('authors.csv', 'r', **author_opts) as csvin: + authors = csv.reader(csvin) + authorstr = ', '.join([row[0] for row in authors]) + authorstr = 'Daniel Standage, ' + authorstr + ', C. Titus Brown' + diff --git a/debian/patches/update-manifest b/debian/patches/update-manifest index 182fddf..364e7de 100644 --- a/debian/patches/update-manifest +++ b/debian/patches/update-manifest @@ -3,9 +3,9 @@ Subject: CONTRIBUTING.md has moved and isn't installed anymore --- khmer.orig/MANIFEST.in +++ khmer/MANIFEST.in @@ -1,5 +1,5 @@ - include ChangeLog ez_setup.py IDEAS Makefile README.rst setup.cfg + include ChangeLog ez_setup.py IDEAS Makefile README.md setup.cfg -include versioneer.py MANIFEST.in CITATION CONTRIBUTING.md Doxyfile.in +include versioneer.py MANIFEST.in CITATION Doxyfile.in - include LICENSE TODO .ycm_extra_conf.py + include LICENSE TODO .ycm_extra_conf.py authors.csv recursive-include lib *.hh *.cc [Mm]akefile* get_version.py - recursive-include third-party *.cc *.1 *.xsl README* sample* words* *.sh *.c + recursive-include khmer *.hh diff --git a/debian/rules b/debian/rules index e24d02b..8a96cfc 100755 --- a/debian/rules +++ b/debian/rules @@ -8,8 +8,6 @@ export PYBUILD_DESTDIR_python3=debian/khmer export USE_SYSTEM_ZLIB=true export USE_SYSTEM_LIBBZ2=true -export PACKAGE_VERSION := $(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ') - export HOME=$(shell echo $$PWD"/fakehome") %: @@ -26,7 +24,7 @@ override_dh_auto_test: dh_auto_install PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$$PATH ; \ - cd {build_dir}; {interpreter} -m pytest \ + cd {build_dir}; export PYTHONPATH=$$(pwd); {interpreter} -m pytest \ -m 'not known_failing and not jenkins and not huge'" dh_auto_test @@ -42,5 +40,8 @@ override_dh_install: dh_install find debian/khmer -name .gitignore -delete +override_dh_sphinxdoc: + dh_sphinxdoc -X jquery.js + get-orig-source: uscan --verbose --force-download --repack --compression xz -- 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
