This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository khmer.
commit 845c2d4bf1fb8632c5bd9e0abc86e6e10bd273c1 Author: Michael R. Crusoe <[email protected]> Date: Tue Sep 8 10:07:17 2015 -0700 update citations & upstream location `cme fix dpkg` changes Don't ship '.so' symlink in non-dev package --- debian/control | 17 ++++++------ debian/liboxli1.install | 1 - debian/liboxli1.lintian-overrides | 2 +- debian/patches/cpython-bug-empty-exceptions | 4 +-- debian/patches/get_version | 2 +- debian/patches/install-prefix | 2 +- debian/patches/setup-py-py3 | 2 +- debian/upstream/metadata | 41 ++++++++++++++++++++--------- debian/watch | 2 +- 9 files changed, 44 insertions(+), 29 deletions(-) diff --git a/debian/control b/debian/control index 3b6e8c1..8e09b6e 100644 --- a/debian/control +++ b/debian/control @@ -1,6 +1,7 @@ Source: khmer Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Michael R. Crusoe <[email protected]>, Kevin Murray <[email protected]> +Uploaders: Michael R. Crusoe <[email protected]>, + Kevin Murray <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 9), @@ -10,14 +11,14 @@ Build-Depends: debhelper (>= 9), python3-dev (>= 3.3), python3-all-dev (>= 3.3), python3-setuptools (>= 3.3), - python3-screed (>=0.9), - python3-screed (<<1.0), + python3-screed, + python3-screed (<< 1.0), python3-nose, python3-sphinx, python3-sphinxcontrib.autoprogram, zlib1g-dev, libbz2-dev, - ruby-ronn, + ruby-ronn Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/khmer.git Vcs-Git: git://anonscm.debian.org/debian-med/khmer.git @@ -28,7 +29,7 @@ Package: khmer-common Architecture: any Multi-Arch: same Depends: file, - ${misc:Depends}, + ${misc:Depends}, ${shlibs:Depends}, ${sphinxdoc:Depends} Description: common files for the khmer project tools @@ -44,8 +45,8 @@ Architecture: any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 ppc64 Multi-Arch: same Section: python Depends: khmer-common, - python3 (>= 3.3), - python3-screed (>= 0.9), + python3 (>= 3.3), + python3-screed, python3-screed (<< 1.0), ${misc:Depends}, ${shlibs:Depends}, @@ -61,7 +62,7 @@ Architecture: any Multi-Arch: same Section: libs Depends: khmer-common, - ${shlibs:Depends}, + ${shlibs:Depends}, ${misc:Depends} Pre-Depends: ${misc:Pre-Depends} Description: in-memory DNA sequence analysis library from the khmer project diff --git a/debian/liboxli1.install b/debian/liboxli1.install index 950db6f..05f9d57 100755 --- a/debian/liboxli1.install +++ b/debian/liboxli1.install @@ -1,3 +1,2 @@ #!/usr/bin/dh-exec -lib/liboxli.so usr/lib/${DEB_HOST_MULTIARCH} lib/liboxli.so.1 usr/lib/${DEB_HOST_MULTIARCH} diff --git a/debian/liboxli1.lintian-overrides b/debian/liboxli1.lintian-overrides index 26b12be..7977a36 100644 --- a/debian/liboxli1.lintian-overrides +++ b/debian/liboxli1.lintian-overrides @@ -1,4 +1,4 @@ # this library is experimental and will ABI/API often. Bump the SO name upon # every release -liboxli1: no-symbols-control-file usr/lib/x86_64-linux-gnu/liboxli.so +liboxli1: no-symbols-control-file usr/lib/x86_64-linux-gnu/liboxli.so.1 diff --git a/debian/patches/cpython-bug-empty-exceptions b/debian/patches/cpython-bug-empty-exceptions index 1f46b37..5fb9267 100644 --- a/debian/patches/cpython-bug-empty-exceptions +++ b/debian/patches/cpython-bug-empty-exceptions @@ -1,6 +1,6 @@ -Patch unit test asserts to work around a suspected CPython bug where execption -strings are empty. See upstream issues #885, #1190. +Description: Work around a suspected CPython bug +Occurs when exception strings are empty. See upstream issues #885, #1190. --- khmer.orig/tests/test_read_parsers.py +++ khmer/tests/test_read_parsers.py @@ -114,7 +114,10 @@ diff --git a/debian/patches/get_version b/debian/patches/get_version index f66ff13..eec7811 100644 --- a/debian/patches/get_version +++ b/debian/patches/get_version @@ -1,4 +1,4 @@ -Use debian package version instead of git version +Description: Use debian package version instead of git version --- a/doc/conf.py +++ b/doc/conf.py @@ -13,6 +13,7 @@ diff --git a/debian/patches/install-prefix b/debian/patches/install-prefix index 5372e73..bbb5e77 100644 --- a/debian/patches/install-prefix +++ b/debian/patches/install-prefix @@ -1,4 +1,4 @@ -Use correct library version etc. (fixed by upstream #1240, remove for 2.0) +Description: Use correct library version etc. (fixed by upstream #1240, remove for 2.0) --- khmer.orig/lib/Makefile +++ khmer/lib/Makefile @@ -63,7 +63,7 @@ diff --git a/debian/patches/setup-py-py3 b/debian/patches/setup-py-py3 index 05823cd..cdec813 100644 --- a/debian/patches/setup-py-py3 +++ b/debian/patches/setup-py-py3 @@ -1,4 +1,4 @@ -Use /usr/bin/env python3 as the crunchbang interpreter in setup.py +Description: Use /usr/bin/env python3 as the crunchbang interpreter in setup.py --- khmer.orig/setup.py +++ khmer/setup.py @@ -1,4 +1,4 @@ diff --git a/debian/upstream/metadata b/debian/upstream/metadata index dc157cd..1ad12de 100644 --- a/debian/upstream/metadata +++ b/debian/upstream/metadata @@ -6,16 +6,28 @@ 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 and Edvenson, Greg and Fish, Jordan and Howe, - Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and - Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille - and Srinivasan, Ramakrishnan Rajaram and Zhang, Qingpeng and Brown, C. Titus +- Author: Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine + and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau, + Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton, + Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and + Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah + and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and + Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David + and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric + and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy, + Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory, + Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and + Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and + Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan, + Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and + Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather + L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and + Brown, C. Titus Title: "The khmer software package: enabling efficient sequence analysis" - Publisher: Figshare - Year: 2014 - DOI: 10.6084/m9.figshare.979190 - URL: http://dx.doi.org/10.6084/m9.figshare.979190 - eprint: http://files.figshare.com/1441148/khmer_software.pdf + Publisher: F1000Research + Year: 2015 + DOI: 10.12688/f1000research.6924.1 + URL: http://dx.doi.org/10.12688/f1000research.6924.1 Type: article - Author: Pell, Jason and Hintze, Arend and Canino-Koning, Rosangela and Howe, Adina and Tiedje, James M. and Brown, C. Titus @@ -49,8 +61,7 @@ Reference: Number: 7 Type: article Eprint: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0101271&representation=PDF -- Author: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, - Knut +- Author: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut Title: SeqAn An efficient, generic C++ library for sequence analysis Journal: BMC Bioinformatics Volume: 9 @@ -61,7 +72,11 @@ Reference: DOI: 10.1186/1471-2105-9-11 PMID: 18184432 ISSN: 1471-2105 +- Author: Qingpeng Zhang and Sherine Awad and C. Titus Brown + Title: Crossing the streams: a framework for streaming analysis of short DNA + sequencing reads + Year: 2015 + eprint: PeerJ Preprints 3:e1100 + url: https://dx.doi.org/10.7287/peerj.preprints.890v1 Repository-Browse: https://github.com/dib-lab/khmer Repository: https://github.com/dib-lab/khmer.git - - diff --git a/debian/watch b/debian/watch index ba6d13b..2226f4f 100644 --- a/debian/watch +++ b/debian/watch @@ -1,4 +1,4 @@ version=3 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/khmer-$1.tar.gz/" \ - https://github.com/ged-lab/khmer/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) + https://github.com/dib-lab/khmer/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) -- 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
