[med-svn] [khmer] 04/04: update citations & upstream location
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Sep 8 17:21:26 UTC 2015
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 <michael.crusoe at gmail.com>
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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>, Kevin Murray <spam at kdmurray.id.au>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>,
+ Kevin Murray <spam at kdmurray.id.au>
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: 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 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
More information about the debian-med-commit
mailing list