[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


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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)

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