[med-svn] [Git][med-team/khmer][master] 7 commits: Fix liboxli-dev autopkgtest.
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Jan 8 14:18:23 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / khmer
Commits:
0b94e119 by Michael R. Crusoe at 2019-01-08T09:48:59Z
Fix liboxli-dev autopkgtest.
- - - - -
254ca62b by Michael R. Crusoe at 2019-01-08T10:43:45Z
skip the noroot tests
- - - - -
0474ea70 by Michael R. Crusoe at 2019-01-08T13:14:53Z
fix metainfo-validation-issue
- - - - -
82539b6a by Michael R. Crusoe at 2019-01-08T13:15:18Z
Symlink to files in python3-guzzle-sphinx-theme
Instead of shipping them ourselves; thanks rdfind!
- - - - -
f0ad030a by Michael R. Crusoe at 2019-01-08T13:47:39Z
Debian Buster's cython is > 0.26.1
- - - - -
7428ae9d by Michael R. Crusoe at 2019-01-08T14:09:23Z
keep both copies of the CITATION file
- - - - -
2132761e by Michael R. Crusoe at 2019-01-08T14:16:43Z
upload to unstable
- - - - -
12 changed files:
- debian/README.source
- debian/changelog
- debian/clean
- debian/control
- − debian/khmer-common.lintian-overrides
- debian/khmer.lintian-overrides
- debian/khmer.metainfo.xml
- + debian/patches/fix_liboxli_test
- debian/patches/series
- debian/rules
- debian/tests/run-unit-test
- debian/tests/test-liboxli-dev
Changes:
=====================================
debian/README.source
=====================================
@@ -3,7 +3,3 @@ khmer with changes they made. See third-party/seqan/ChangeLog for details. The
most important change is a bugfix which was acknowledged by the SeqAn developers
but will not be fixed until the version 2.0 release of SeqAn:
https://github.com/seqan/seqan/issues/720
-
-Skip packaging khmer v2.1.2 until cython version 0.26.1 in in Debian or
-https://github.com/cython/cython/commit/18bba8ff0261206db9243c2b1721633cb798af54
-is patched in
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+khmer (2.1.2+dfsg-5) unstable; urgency=medium
+
+ * Fix liboxli-dev autopkgtest.
+ * debian/khmer.metainfo.xml: Use a component ID in reverse domain-name
+ format.
+ * shrink khmer-common and silence many lintian warnings by symlinking to the
+ relevant files in python3-guzzle-sphinx-theme
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 08 Jan 2019 06:16:30 -0800
+
khmer (2.1.2+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/clean
=====================================
@@ -1,6 +1,7 @@
fakehome/
debian/*.1
.pybuild/
+.pytest_cache/
khmer.egg-info/
khmer/_oxli/*.cp*
khmer/_khmer.cpython*
=====================================
debian/control
=====================================
@@ -21,8 +21,7 @@ Build-Depends: debhelper (>= 11~),
zlib1g-dev,
libbz2-dev,
asciidoctor,
- libjs-jquery,
- libjs-twitter-bootstrap
+ rdfind
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/khmer
Vcs-Git: https://salsa.debian.org/med-team/khmer.git
@@ -33,7 +32,8 @@ Architecture: all
Multi-Arch: foreign
Depends: file,
${misc:Depends},
- ${sphinxdoc:Depends}
+ ${sphinxdoc:Depends},
+ python3-guzzle-sphinx-theme
Description: common files for the khmer project tools
khmer is a library and suite of command line tools for working with DNA
sequence. It is primarily aimed at short-read sequencing data such as
=====================================
debian/khmer-common.lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-khmer-common: extra-license-file usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt
=====================================
debian/khmer.lintian-overrides
=====================================
@@ -1,13 +1,3 @@
-# These files are unchanged files from upstream tarball. There is no problem for a reproducible build
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz
-khmer: gzip-file-is-not-multi-arch-same-safe usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz
-
# The test data are provided in different compression methods intentionally to test different compression methods
# Since they are small anyway there is no reason to work around this
khmer: duplicated-compressed-file usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.bz2
=====================================
debian/khmer.metainfo.xml
=====================================
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<component>
- <id>oxli</id>
+ <id>io.readthedocs.khmer</id>
<metadata_license>MIT</metadata_license>
<name>khmer</name>
<summary>in-memory DNA sequence kmer counting, filtering & graph traversal</summary>
=====================================
debian/patches/fix_liboxli_test
=====================================
@@ -0,0 +1,17 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Fix liboxli sanity check test
+--- khmer.orig/src/oxli/test-compile.cc
++++ khmer/src/oxli/test-compile.cc
+@@ -39,10 +39,10 @@
+ // This file is used to test compilation with liboxli.a/liboxli.so, after
+ // installation
+
+-#include <oxli/hashtable.hh>
++#include <oxli/hashgraph.hh>
+
+ int main()
+ {
+- oxli::Countgraph test(1,1);
++ oxli::Countgraph test(1,{1});
+ return 0;
+ }
=====================================
debian/patches/series
=====================================
@@ -10,3 +10,4 @@ cpython-bug-empty-exceptions
amend-skip
setup.py-py3
python3
+fix_liboxli_test
=====================================
debian/rules
=====================================
@@ -28,7 +28,8 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$$PATH ; \
cd {build_dir}; export PYTHONPATH=$$(pwd); {interpreter} -m pytest \
- -m 'not known_failing and not jenkins and not huge'" dh_auto_test
+ -m 'not known_failing and not jenkins and not huge and not noroot'\
+ -q" dh_auto_test
endif
override_dh_auto_clean:
@@ -42,5 +43,10 @@ override_dh_install:
find debian/khmer -name .gitignore -delete
override_dh_sphinxdoc:
- dh_sphinxdoc -X jquery.js
-
+ dh_sphinxdoc
+ rdfind -makesymlinks true -followsymlinks true\
+ /usr/lib/python3/dist-packages/guzzle_sphinx_theme \
+ $(shell find debian/khmer-common | grep -i -v citation)
+ rm debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt
+ cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \
+ ln -s ../../CITATION citations.rst.txt
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,8 +2,8 @@
pkg=khmer
if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
-cd $ADTTMP
+cd "$ADTTMP"
PATH=/usr/lib/khmer/bin/:$PATH python3 -m pytest --pyarg khmer \
- -m 'not known_failing and not huge'
+ -m 'not known_failing and not huge and not noroot' -q
=====================================
debian/tests/test-liboxli-dev
=====================================
@@ -2,17 +2,20 @@
pkg=khmer
if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
-cd $ADTTMP
+cd "$ADTTMP"
-c++ -o test-prog-static -static -std=c++11 `pkg-config oxli --static --cflags` -I/usr/include/oxli/smhasher \
- /usr/share/doc/khmer-common/test-compile.cc `pkg-config oxli --static --libs`
+c++ -o test-prog-static -static -std=c++11 \
+ $(pkg-config oxli --static --cflags) -I/usr/include/oxli/smhasher \
+ /usr/share/doc/khmer-common/test-compile.cc \
+ $(pkg-config oxli --static --libs)
./test-prog-static
-c++ -o test-prog-dynamic -std=c++11 `pkg-config oxli --cflags` -I/usr/include/oxli/smhasher \
- /usr/share/doc/khmer-common/test-compile.cc `pkg-config oxli --libs`
+c++ -o test-prog-dynamic -std=c++11 $(pkg-config oxli --cflags) \
+ -I/usr/include/oxli/smhasher \
+ /usr/share/doc/khmer-common/test-compile.cc $(pkg-config oxli --libs)
./test-prog-dynamic
View it on GitLab: https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a
--
View it on GitLab: https://salsa.debian.org/med-team/khmer/compare/bfaee76542be628908ef3784d2f481afe604fac4...2132761eba7b69c19444c17f28a28d9c2173358a
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