[med-svn] [Git][med-team/khmer][master] 10 commits: Simplify autopkgtest. Closes: #955566
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Apr 7 16:36:52 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / khmer
Commits:
8653e925 by Michael R. Crusoe at 2020-04-07T17:24:02+02:00
Simplify autopkgtest. Closes: #955566
- - - - -
3f8d3a15 by Michael R. Crusoe at 2020-04-07T17:25:58+02:00
s/ADTTMP/AUTOPKGTEST_TMP/g
- - - - -
18e4e36f by Michael R. Crusoe at 2020-04-07T17:26:36+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
d92e62c2 by Michael R. Crusoe at 2020-04-07T17:26:37+02:00
routine-update: debhelper-compat 12
- - - - -
9331453b by Michael R. Crusoe at 2020-04-07T17:27:26+02:00
R-U: Trailing whitespace in debian/changelog
- - - - -
a45c973a by Michael R. Crusoe at 2020-04-07T17:27:26+02:00
routine-update: Add salsa-ci file
- - - - -
3059ec52 by Michael R. Crusoe at 2020-04-07T17:27:27+02:00
routine-update: Rules-Requires-Root: no
- - - - -
a8a29b75 by Michael R. Crusoe at 2020-04-07T17:27:33+02:00
Use secure URI in Homepage field.
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
8335a455 by Michael R. Crusoe at 2020-04-07T17:27:34+02:00
Remove obsolete fields Contact, Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -
d484922c by Michael R. Crusoe at 2020-04-07T17:28:17+02:00
release 2.1.2+dfsg-7 to unstable
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/salsa-ci.yml
- debian/tests/control
- debian/tests/run-unit-test
- debian/tests/test-liboxli-dev
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+khmer (2.1.2+dfsg-7) unstable; urgency=medium
+
+ * Simplify autopkgtest. Closes: #955566
+ * s/ADTTMP/AUTOPKGTEST_TMP/g
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 12 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Use secure URI in Homepage field.
+ * Remove obsolete fields Contact, Name from debian/upstream/metadata
+ (already present in machine-readable debian/copyright).
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 07 Apr 2020 17:27:50 +0200
+
khmer (2.1.2+dfsg-6) unstable; urgency=medium
* Fix building arch-independent packages separately.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,14 +4,14 @@ Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
Kevin Murray <spam at kdmurray.id.au>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
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,
+ python3-dev,
+ python3-all-dev,
+ python3-setuptools,
python3-screed (>= 1.0),
python3-pytest,
python3-pytest-runner,
@@ -21,20 +21,21 @@ Build-Depends: debhelper (>= 11~),
zlib1g-dev,
libbz2-dev,
asciidoctor,
- rdfind
-Standards-Version: 4.3.0
+ rdfind
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/khmer
Vcs-Git: https://salsa.debian.org/med-team/khmer.git
-Homepage: http://khmer.readthedocs.org
+Homepage: https://khmer.readthedocs.org
+Rules-Requires-Root: no
Package: khmer-common
Architecture: all
Multi-Arch: foreign
-Built-Using: ${sphinxdoc:Built-Using}
Depends: file,
${misc:Depends},
${sphinxdoc:Depends},
- python3-guzzle-sphinx-theme
+ python3-guzzle-sphinx-theme
+Built-Using: ${sphinxdoc:Built-Using}
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
@@ -47,7 +48,7 @@ Package: khmer
Architecture: amd64 any-arm64 any-ia64 any-sparc64
Multi-Arch: foreign
Depends: khmer-common,
- python3 (>= 3.3),
+ python3,
python3-screed (>= 1.0),
${shlibs:Depends},
${misc:Depends},
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/tests/control
=====================================
@@ -1,4 +1,3 @@
Tests: run-unit-test
- test-liboxli-dev
Depends: khmer,python3-pytest,python3-pytest-runner,build-essential,pkg-config,zlib1g-dev,libbz2-dev,liboxli-dev
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,9 +1,9 @@
#!/bin/sh -e
pkg=khmer
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
-cd "$ADTTMP"
+cd "$AUTOPKGTEST_TMP"
PATH=/usr/lib/khmer/bin/:$PATH python3 -m pytest --pyarg khmer \
-m 'not known_failing and not huge and not noroot' -q
=====================================
debian/tests/test-liboxli-dev
=====================================
@@ -2,9 +2,9 @@
pkg=khmer
if [ "$ADTTMP" = "" ] ; then
- ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
-cd "$ADTTMP"
+cd "$AUTOPKGTEST_TMP"
c++ -o test-prog-static -static -std=c++11 \
$(pkg-config oxli --static --cflags) -I/usr/include/oxli/smhasher \
@@ -13,11 +13,4 @@ c++ -o test-prog-static -static -std=c++11 \
./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)
-
-./test-prog-dynamic
-
-
rm -f test-prog-*
=====================================
debian/upstream/metadata
=====================================
@@ -1,12 +1,10 @@
Bug-Database: https://github.com/dib-lab/khmer/issues
Bug-Submit: https://github.com/dib-lab/khmer/issues/new
Changelog: https://raw.githubusercontent.com/dib-lab/khmer/master/ChangeLog
-Contact: khmer-project at idyll.org
Funding: >
AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, National
Human Genome Research Institute of the National Institutes of Health
under Award Number R01HG007513
-Name: khmer
Reference:
- Author: >
Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine and
View it on GitLab: https://salsa.debian.org/med-team/khmer/-/compare/f378b99327ffdf3b72f6c7bd09379c5bf888fd99...d484922c24d2dfa718172818311121ff084c8039
--
View it on GitLab: https://salsa.debian.org/med-team/khmer/-/compare/f378b99327ffdf3b72f6c7bd09379c5bf888fd99...d484922c24d2dfa718172818311121ff084c8039
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