[med-svn] [khmer] 01/02: new upstream release
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Aug 30 12:33:43 UTC 2017
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 <michael.crusoe at gmail.com>
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 <michael.crusoe at gmail.com> Mon, 20 Feb 2017 01:50:56 -0800
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> 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},
${python3:Depends}
diff --git a/debian/khmer-common.lintian-overrides b/debian/khmer-common.lintian-overrides
index 5686645..2c7adaa 100644
--- a/debian/khmer-common.lintian-overrides
+++ b/debian/khmer-common.lintian-overrides
@@ -1 +1 @@
-khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.txt
+khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt
diff --git a/debian/khmer.install b/debian/khmer.install
index f84dbe4..1de24e4 100644
--- a/debian/khmer.install
+++ b/debian/khmer.install
@@ -1,2 +1,2 @@
debian/bin/* usr/bin/
-debian/khmer.metainfo.xml /usr/share/appdata
+debian/khmer.metainfo.xml /usr/share/metainfo/
diff --git a/debian/patches/older-setuptools b/debian/patches/older-setuptools
index a986fe4..89b9a5e 100644
--- a/debian/patches/older-setuptools
+++ b/debian/patches/older-setuptools
@@ -3,16 +3,15 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
--- khmer.orig/setup.py
+++ khmer/setup.py
-@@ -36,8 +36,6 @@
+@@ -36,7 +36,6 @@
# Contact: khmer-project at idyll.org
"""Setup for khmer project."""
-import ez_setup
--
+
import os
import sys
- from os import listdir as os_listdir
-@@ -56,7 +54,6 @@
+@@ -56,7 +55,6 @@
from distutils.errors import DistutilsPlatformError
import versioneer
diff --git a/debian/patches/python3 b/debian/patches/python3
new file mode 100644
index 0000000..5c80b81
--- /dev/null
+++ b/debian/patches/python3
@@ -0,0 +1,72 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: s/python/python3/ as appropriate
+
+--- khmer.orig/Makefile
++++ khmer/Makefile
+@@ -79,7 +79,7 @@
+ TESTATTR ?= 'not known_failing and not jenkins and not huge and not linux'
+ endif
+
+-MODEXT=$(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'
--
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