[med-svn] [Git][med-team/wise][master] 8 commits: debhelper 11

Andreas Tille gitlab at salsa.debian.org
Thu Oct 4 14:04:34 BST 2018 

Andreas Tille pushed to branch master at Debian Med / wise


Commits:
092d2289 by Andreas Tille at 2018-10-04T12:38:22Z
debhelper 11

- - - - -
d514cba8 by Andreas Tille at 2018-10-04T12:38:35Z
Point Vcs fields to salsa.debian.org

- - - - -
8468b11e by Andreas Tille at 2018-10-04T12:38:35Z
Standards-Version: 4.2.1

- - - - -
139d181b by Andreas Tille at 2018-10-04T12:46:54Z
Adapt doc-base control files to doc location by debhelper 11

- - - - -
d0642c55 by Andreas Tille at 2018-10-04T12:47:51Z
Typo

- - - - -
bd1f5861 by Andreas Tille at 2018-10-04T12:49:01Z
Long description for all packages

- - - - -
8a296ca9 by Andreas Tille at 2018-10-04T12:49:47Z
Drop unneeded Testsuite: autopkgtest

- - - - -
be215cf8 by Andreas Tille at 2018-10-04T12:54:46Z
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/patches/09_dnal-add-return-statement.patch
- debian/wise-doc.doc-base.api
- debian/wise-doc.doc-base.dynamite
- debian/wise-doc.doc-base.wise


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+wise (2.4.1-21) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Long description for all packages
+  * Drop unneeded Testsuite: autopkgtest
+
+ -- Andreas Tille <tille at debian.org>  Thu, 04 Oct 2018 14:49:55 +0200
+
 wise (2.4.1-20) unstable; urgency=medium
 
   * Moved packaging from SVN to Git


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
@@ -5,16 +5,15 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Testsuite: autopkgtest
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                texlive-latex-base,
                texlive-extra-utils,
                hevea,
                docbook-to-man,
                libglib2.0-dev
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/wise.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/wise.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/wise
+Vcs-Git: https://salsa.debian.org/med-team/wise.git
 Homepage: http://www.ebi.ac.uk/~birney/wise2/
 
 Package: wise
@@ -54,6 +53,29 @@ Depends: ${misc:Depends}
 Recommends: wise (= ${source:Version}),
             xpdf-reader | pdf-viewer
 Description: documentation for the wise package
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the 
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the environment used by Wise2. 
+ .
+ Wise2 has also been written with an eye for reuse and maintainability. 
+ Although it is a pure C package you can access its functionality 
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+ .
  This package contains the documentation for Wise2, a package focused on
  comparisons of biopolymers, commonly DNA and protein sequences.
 
@@ -63,5 +85,28 @@ Section: doc
 Depends: ${misc:Depends}
 Recommends: wise (= ${source:Version})
 Description: data files for the wise package
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the 
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the environment used by Wise2. 
+ .
+ Wise2 has also been written with an eye for reuse and maintainability. 
+ Although it is a pure C package you can access its functionality 
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+ .
  This package contains data files for Wise2, a package focused on
  comparisons of biopolymers, commonly DNA and protein sequences.


=====================================
debian/patches/09_dnal-add-return-statement.patch
=====================================
@@ -1,7 +1,7 @@
 Author: Dejan Latinovic <Dejan.Latinovic at imgtec.com>
 Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
 Bug-Debian: http://bugs.debian.org/751277
-Desription: Make sure dnal has a valid return value
+Description: Make sure dnal has a valid return value
  This affects a bug reported against python-biopython.
 
 --- wise-2.4.1.orig/src/models/dnal.c


=====================================
debian/wise-doc.doc-base.api
=====================================
@@ -5,8 +5,8 @@ Abstract: This manual describes the wise API.
 Section: Science/Biology
 
 Format: PDF
-Files: /usr/share/doc/wise-doc/api.pdf.gz
+Files: /usr/share/doc/wise/api.pdf.gz
 
 Format: HTML
-Index: /usr/share/doc/wise-doc/api/api.html
-Files: /usr/share/doc/wise-doc/api/*
+Index: /usr/share/doc/wise/api/api.html
+Files: /usr/share/doc/wise/api/*


=====================================
debian/wise-doc.doc-base.dynamite
=====================================
@@ -6,8 +6,8 @@ Abstract: This manual describes the dynamite code generating
 Section: Science/Biology
 
 Format: PDF
-Files: /usr/share/doc/wise-doc/dynamite.pdf.gz
+Files: /usr/share/doc/wise/dynamite.pdf.gz
 
 Format: HTML
-Index: /usr/share/doc/wise-doc/dynamite/dynamite.html
-Files: /usr/share/doc/wise-doc/dynamite/*
+Index: /usr/share/doc/wise/dynamite/dynamite.html
+Files: /usr/share/doc/wise/dynamite/*


=====================================
debian/wise-doc.doc-base.wise
=====================================
@@ -5,8 +5,8 @@ Abstract: This manual describes wise program usages.
 Section: Science/Biology
 
 Format: PDF
-Files: /usr/share/doc/wise-doc/wise2.pdf.gz
+Files: /usr/share/doc/wise/wise2.pdf.gz
 
 Format: HTML
-Index: /usr/share/doc/wise-doc/wise2/wise2.html
-Files: /usr/share/doc/wise-doc/wise2/*
+Index: /usr/share/doc/wise/wise2/wise2.html
+Files: /usr/share/doc/wise/wise2/*



View it on GitLab: https://salsa.debian.org/med-team/wise/compare/9c695b59c100962c224cef22eac43fe0e951acd6...be215cf805754f75a5bcc045d42a62955bf3c79b

-- 
View it on GitLab: https://salsa.debian.org/med-team/wise/compare/9c695b59c100962c224cef22eac43fe0e951acd6...be215cf805754f75a5bcc045d42a62955bf3c79b
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20181004/b44d8c3f/attachment-0001.html>

More information about the debian-med-commit mailing list