[med-svn] [Git][med-team/wise][master] 14 commits: Let dh_auto_build pass cross tools to make

Andreas Tille gitlab at salsa.debian.org
Fri Apr 17 13:28:34 BST 2020 


Andreas Tille pushed to branch master at Debian Med / wise


Commits:
66f8bb01 by Andreas Tille at 2020-04-17T13:25:59+02:00
Let dh_auto_build pass cross tools to make

- - - - -
0d14c5d5 by Andreas Tille at 2020-04-17T13:26:17+02:00
routine-update: Standards-Version: 4.5.0

- - - - -
6e95a045 by Andreas Tille at 2020-04-17T13:26:17+02:00
routine-update: debhelper-compat 12

- - - - -
e996e52a by Andreas Tille at 2020-04-17T13:35:52+02:00
routine-update: DEB_BUILD_OPTIONS allow override_dh_auto_test

- - - - -
d7aa9785 by Andreas Tille at 2020-04-17T13:35:52+02:00
R-U: Trailing whitespace in debian/changelog

- - - - -
73c9c996 by Andreas Tille at 2020-04-17T13:35:52+02:00
R-U: Trailing whitespace in debian/control

- - - - -
15b048bb by Andreas Tille at 2020-04-17T13:35:52+02:00
R-U: Trailing whitespace in debian/copyright

- - - - -
88f09e29 by Andreas Tille at 2020-04-17T13:35:52+02:00
routine-update: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g

- - - - -
527003f7 by Andreas Tille at 2020-04-17T13:35:52+02:00
routine-update: Add salsa-ci file

- - - - -
0e038032 by Andreas Tille at 2020-04-17T13:35:52+02:00
routine-update: Rules-Requires-Root: no

- - - - -
9d4416a8 by Andreas Tille at 2020-04-17T13:35:54+02:00
Wrap long lines in changelog entries: 2.4.0-1.

Fixes: lintian: debian-changelog-line-too-long
See-also: https://lintian.debian.org/tags/debian-changelog-line-too-long.html

- - - - -
ef6bd07c by Andreas Tille at 2020-04-17T13:35:59+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

- - - - -
37a0f59c by Andreas Tille at 2020-04-17T13:36:00+02:00
Set field Upstream-Name in debian/copyright.
- - - - -
3dbba28b by Andreas Tille at 2020-04-17T13:36:06+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -


8 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/rules
- + debian/salsa-ci.yml
- debian/tests/run-unit-test
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,28 @@
+wise (2.4.1-21.1) UNRELEASED; urgency=medium
+
+  [ Helmut Grohne ]
+  * Improve cross building: Let dh_auto_build pass cross tools to make.
+    (Closes: #956279)
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 12 (routine-update)
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+    update)
+  * Remove trailing whitespace in debian/changelog (routine-update)
+  * Remove trailing whitespace in debian/control (routine-update)
+  * Remove trailing whitespace in debian/copyright (routine-update)
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Wrap long lines in changelog entries: 2.4.0-1.
+  * Use secure URI in Homepage field.
+  * Set field Upstream-Name in debian/copyright.
+  * Remove obsolete field Name from debian/upstream/metadata (already
+    present in machine-readable debian/copyright).
+
+ -- Helmut Grohne <helmut at subdivi.de>  Thu, 09 Apr 2020 11:46:11 +0200
+
 wise (2.4.1-21) unstable; urgency=medium
 
   * debhelper 11
@@ -41,9 +66,9 @@ wise (2.4.1-18) unstable; urgency=medium
 wise (2.4.1-17) unstable; urgency=medium
 
   * debian/tests/control: explicitly depend on wise.  This avoids that
-    ‘sadt’ skips the test when wise-doc is not installed. 
+    ‘sadt’ skips the test when wise-doc is not installed..
   * debian/tests/run-unit-test: skip the first line of testman.pl, that
-    misses a proper shebang and trigger a failure. 
+    misses a proper shebang and trigger a failure.
   * debian/control: shorten synopsis to less than 72 characters.
   * Conforms with Policy 3.9.6.
 
@@ -177,7 +202,7 @@ wise (2.4.1-4) unstable; urgency=low
 
   * Changed the doc-base section according to the new policy
     [Charles Plessy].
-    
+
  -- Philipp Benner <pbenner at uni-osnabrueck.de>  Mon, 31 Mar 2008 10:07:35 +0200
 
 wise (2.4.1-3) unstable; urgency=low
@@ -222,7 +247,8 @@ wise (2.4.0-2) unstable; urgency=low
 wise (2.4.0-1) unstable; urgency=low
 
   * New upstream release (Closes: #431392)
-  * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
+  * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by
+    isdigit()
   * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
 
  -- Philipp Benner <mail at philipp-benner.de>  Tue, 24 Jul 2007 11:58:36 +0200


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -5,16 +5,17 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                texlive-latex-base,
                texlive-extra-utils,
                hevea,
                docbook-to-man,
                libglib2.0-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
 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/
+Homepage: https://www.ebi.ac.uk/~birney/wise2/
+Rules-Requires-Root: no
 
 Package: wise
 Architecture: any
@@ -25,7 +26,7 @@ Suggests: wise-doc (= ${source:Version})
 Description: comparison of biopolymers, like DNA and protein sequences
  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 
+ 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.
@@ -38,10 +39,10 @@ Description: comparison of biopolymers, like DNA and protein sequences
  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. 
+ 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 
+ 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.
@@ -55,7 +56,7 @@ Recommends: wise (= ${source:Version}),
 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 
+ 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.
@@ -68,10 +69,10 @@ Description: documentation for the wise package
  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. 
+ 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 
+ 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.
@@ -87,7 +88,7 @@ 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 
+ 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.
@@ -100,10 +101,10 @@ Description: data files for the wise package
  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. 
+ 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 
+ 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.


=====================================
debian/copyright
=====================================
@@ -1,5 +1,6 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Source: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz
+Upstream-Name: Wise2
 
 Files: *
 Copyright: © 1996-2001 Genome Research Limited (GRL) and
@@ -51,7 +52,7 @@ License: GPL-2
  GNU General Public License. See the files COPYING and
  GNULICENSE for details.
 
-Files: 
+Files:
  src/dynlibsrc/histogram.dy src/dynlibsrc/histogram.pod
  src/dynlibsrc/histogram.tex
 Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy
@@ -85,4 +86,3 @@ Comment: On Debian GNU/Linux systems, the complete text of the GNU General Publi
  License version 2 can be found in `/usr/share/common-licenses/GPL-2' and the
  complete text of the GNU Lesser General Public License can be found in
  `/usr/share/common-licenses/LGPL-3'.
-


=====================================
debian/rules
=====================================
@@ -18,7 +18,7 @@ include /usr/share/dpkg/buildflags.mk
 	dh $@
 
 override_dh_auto_build:
-	$(MAKE) -C src all
+	dh_auto_build --sourcedirectory=src
 	$(MAKE) -C debian/manpages.d
 #	build documentation manually (docs/makefile is not useable)
 	find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex
@@ -88,6 +88,8 @@ override_dh_installexamples-indep:
 	sed -i -e 's?"../bin/$$do"?"$$do"?' -e 's?#!/usr/local/bin/perl?/usr/bin/perl?' debian/$(pkg-data)/usr/share/doc/wise-data/examples/testman.pl
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more."
 	echo "A autopkgtest was added as compensation."
 	# make -C src test
+endif


=====================================
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/run-unit-test
=====================================
@@ -1,11 +1,11 @@
 #!/bin/bash -e
 
 pkg=wise
-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
-cp /usr/share/doc/wise-data/examples/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp /usr/share/doc/wise-data/examples/* $AUTOPKGTEST_TMP
 gunzip *.gz
 perl <(sed 1d testman.pl) < short.test
-# rm -f $ADTTMP/*
+# rm -f $AUTOPKGTEST_TMP/*


=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,3 @@
-Name: Wise2
 Webservice: http://www.ebi.ac.uk/Tools/Wise2/
 Reference:
  - Author: Ewan Birney and Michele Clamp and Richard Durbin



View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/e7d7fac26c5ae3c725671d459c8db231a66ada38...3dbba28bba1aad91a06d77a88325378e1c8fe7dd

-- 
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/e7d7fac26c5ae3c725671d459c8db231a66ada38...3dbba28bba1aad91a06d77a88325378e1c8fe7dd
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