[med-svn] [Git][med-team/vienna-rna][master] 9 commits: routine-update: debhelper-compat 13
Andreas Tille
gitlab at salsa.debian.org
Thu Jul 16 13:45:28 BST 2020
Andreas Tille pushed to branch master at Debian Med / vienna-rna
Commits:
82baa287 by Andreas Tille at 2020-07-16T14:17:03+02:00
routine-update: debhelper-compat 13
- - - - -
1a9f02db by Andreas Tille at 2020-07-16T14:28:20+02:00
routine-update: Remove trailing whitespace in debian/control
- - - - -
58fa9452 by Andreas Tille at 2020-07-16T14:28:20+02:00
routine-update: Remove trailing whitespace in debian/rules
- - - - -
29042b58 by Andreas Tille at 2020-07-16T14:28:20+02:00
routine-update: Add salsa-ci file
- - - - -
bdd5863e by Andreas Tille at 2020-07-16T14:28:22+02:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
c043a264 by Andreas Tille at 2020-07-16T14:28:24+02:00
debian/copyright: use spaces rather than tabs to start continuation lines..
Changes-By: lintian-brush
Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html
- - - - -
63a681b2 by Andreas Tille at 2020-07-16T14:28:26+02:00
Update renamed lintian tag names in lintian overrides.
Changes-By: lintian-brush
Fixes: lintian: renamed-tag
See-also: https://lintian.debian.org/tags/renamed-tag.html
- - - - -
af4b0f30 by Andreas Tille at 2020-07-16T14:28:30+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
- - - - -
7f9dce1e by Andreas Tille at 2020-07-16T14:28:33+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
8 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/rules
- + debian/salsa-ci.yml
- debian/source/lintian-overrides
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+vienna-rna (2.4.14+dfsg-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * debhelper-compat 13 (routine-update)
+ * Remove trailing whitespace in debian/control (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Trim trailing whitespace.
+ * debian/copyright: use spaces rather than tabs to start continuation lines.
+ * Update renamed lintian tag names in lintian overrides.
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+ * Remove obsolete field Name from debian/upstream/metadata (already present in
+ machine-readable debian/copyright).
+
+ -- Andreas Tille <tille at debian.org> Thu, 16 Jul 2020 14:17:03 +0200
+
vienna-rna (2.4.14+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -5,13 +5,12 @@ Uploaders: Olivier Sallou <osallou at debian.org>,
Section: non-free/science
XS-Autobuild: yes
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all-dev,
swig,
perl-doc,
perl,
- libtool,
graphviz,
libgsl-dev,
xxd,
@@ -52,7 +51,7 @@ Description: RNA sequence analysis
most used function in the package. It provides three kinds of dynamic
programming algorithms for structure prediction:
* the minimum free energy algorithm of (Zuker & Stiegler 1981) which
- yields a single optimal structure,
+ yields a single optimal structure,
* the partition function algorithm of (McCaskill 1990) which calculates
base pair probabilities in the thermodynamic ensemble, and the
suboptimal folding algorithm of (Wuchty et.al 1999) which generates
=====================================
debian/copyright
=====================================
@@ -3,12 +3,12 @@ Upstream-Name: ViennaRNA
Source: https://www.tbi.univie.ac.at/RNA/
https://github.com/ViennaRNA/ViennaRNA/releases
Files-Excluded:
- src/json
- src/libsvm-3.23.tar.gz
+ src/json
+ src/libsvm-3.23.tar.gz
src/libsvm-3.23
- src/cthreadpool
- doc/latex
- doc/html
+ src/cthreadpool
+ doc/latex
+ doc/html
doc/RNAlib-*.pdf
RNA-Tutorial/Data/programs/alifoldz_adopted.tar.gz
RNA-Tutorial/Data/programs/qrna-2.0.3d.tar.gz
@@ -18,8 +18,8 @@ Files-Excluded:
RNA-Tutorial/RNA-tutorial-*.pdf
*/*eps-converted-to.pdf
*/aclocal.m4
- src/*_cmdl.h
- src/*_cmdl.c
+ src/*_cmdl.h
+ src/*_cmdl.c
compile
config/ar-lib
config/compile
@@ -91,25 +91,25 @@ Files-Excluded:
src/RNAlocmin/RNAlocmin_cmdline.c
src/RNAlocmin/RNAlocmin_cmdline.h
src/RNAlocmin/config.h.in
- */autom4te.cache
- doc/refman-html
- install-sh
- interfaces/Perl/RNA.pm
- interfaces/Perl/RNA_wrap.cpp
- interfaces/Perl/version.i
- interfaces/Python3/RNA.py
- interfaces/Python3/RNA_wrap.cpp
- interfaces/Python3/version.i
- packaging/macosx/resources/welcome.txt
- src/Kinfold/INSTALL
- src/Kinfold/configure
- src/Kinwalker/configure
- src/RNAforester/INSTALL
- src/RNAforester/configure
- src/RNAforester/g2-0.72/configure
- src/RNAlocmin/configure
- src/ViennaRNA/static/energy_parameter_sets.h
- src/ViennaRNA/static/templates_postscript.h
+ */autom4te.cache
+ doc/refman-html
+ install-sh
+ interfaces/Perl/RNA.pm
+ interfaces/Perl/RNA_wrap.cpp
+ interfaces/Perl/version.i
+ interfaces/Python3/RNA.py
+ interfaces/Python3/RNA_wrap.cpp
+ interfaces/Python3/version.i
+ packaging/macosx/resources/welcome.txt
+ src/Kinfold/INSTALL
+ src/Kinfold/configure
+ src/Kinwalker/configure
+ src/RNAforester/INSTALL
+ src/RNAforester/configure
+ src/RNAforester/g2-0.72/configure
+ src/RNAlocmin/configure
+ src/ViennaRNA/static/energy_parameter_sets.h
+ src/ViennaRNA/static/templates_postscript.h
Files: *
Copyright: 2009 Ivo Hofacker <ivo at tbi.univie.ac.at>
=====================================
debian/rules
=====================================
@@ -52,7 +52,7 @@ override_dh_auto_clean:
find . -name "*eps-converted-to.pdf" -delete
rm -f src/bin/RNAfold_cmdl.[ch]
rm -f aclocal.m4 src/Kinfold/aclocal.m4
- grep -rl "DO NOT MODIFY THIS FILE! It was generated by help2man" man | xargs -r rm -f
+ grep -rl "DO NOT MODIFY THIS FILE! It was generated by help2man" man | xargs -r rm -f
grep -lri "DO NOT EDIT THIS FILE." src | grep -v debian | xargs -r rm
grep -lri "File autogenerated by gengetopt" src | grep -v debian | xargs -r rm
grep -lri "Generated from configure.ac" . | grep -v debian | xargs -r rm
@@ -81,4 +81,3 @@ override_dh_auto_clean:
override_dh_compress:
dh_compress --exclude=.pdf
-
=====================================
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/source/lintian-overrides
=====================================
@@ -1,3 +1,3 @@
# These links are to a build-dependency of ViennaRNA
-vienna-rna source: source-contains-unsafe-symlink thpool.c
-vienna-rna source: source-contains-unsafe-symlink thpool.h
+vienna-rna source: wayward-symbolic-link-target-in-source thpool.c
+vienna-rna source: wayward-symbolic-link-target-in-source thpool.h
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,5 @@
-Name: ViennaRNA
+Bug-Database: https://github.com/ViennaRNA/ViennaRNA/issues
+Bug-Submit: https://github.com/ViennaRNA/ViennaRNA/issues/new
Reference:
- Author: >
Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen,
@@ -22,3 +23,5 @@ Registry:
Entry: vienna_rna_package
- Name: SciCrunch
Entry: SCR_008550
+Repository: https://github.com/ViennaRNA/ViennaRNA.git
+Repository-Browse: https://github.com/ViennaRNA/ViennaRNA
View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/8941153d6e3ee30df0dc645cd7defa70e7503ce0...7f9dce1eb149c5cbd06d19f755a2365c6d845dc3
--
View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/8941153d6e3ee30df0dc645cd7defa70e7503ce0...7f9dce1eb149c5cbd06d19f755a2365c6d845dc3
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