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 <[email protected]> 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 <[email protected]>, Kevin Murray <[email protected]> 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: [email protected] 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 You're receiving this email because of your account on salsa.debian.org.
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