debian/changelog

-paraclu (9-1) UNRELEASED; urgency=low
+paraclu (9-2) unstable; urgency=medium
+
+  * Team upload.
+  * [692ba80] Sort out metadata between debian/upstream/metadata and d/copyright
+  * [c947345] Fix watch file
+  * [34b03c9] New style gbp config
+  * [7e8085a] cme fix dpkg-control
+               + Point VCS fields to Salsa
+               + Standards-Version: 4.1.4
+  * [2dc507c] debhelper 11
+  * [02c17ec] Lintian override for script-with-language-extension
+  * [2734571] hardening=+all
+  * [c2ed054] Enable debug symbols
+  * [2f4adde] Add manpage if possible
+
+ -- Andreas Tille <tille@debian.org>  Tue, 03 Jul 2018 15:12:25 +0200
+
+paraclu (9-1) unstable; urgency=low
 
   * First upload to the Debian archive, closes: #762412.
 
- -- Charles Plessy <plessy@debian.org>  Mon, 22 Sep 2014 10:59:31 +0900
+ -- Charles Plessy <plessy@debian.org>  Tue, 23 Sep 2014 19:32:34 +0900

debian/compat

-9
+11

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Charles Plessy <plessy@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/paraclu.git
-Vcs-Git: git://anonscm.debian.org/debian-med/paraclu.git
-Homepage: http://www.cbrc.jp/paraclu/
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/paraclu
+Vcs-Git: https://salsa.debian.org/med-team/paraclu.git
+Homepage: http://cbrc3.cbrc.jp/~martin/paraclu/
 
 Package: paraclu
 Architecture: any

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: http://www.cbrc.jp/paraclu/archive/paraclu-5.zip
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: paraclu
+Upstream-Contact: paraclu@cbrc.jp
+Source: http://cbrc3.cbrc.jp/~martin/paraclu/paraclu-9.zip
 License: GPL-3+
 
 Files: *
-Copyright: © 2011–2012 Martin C. Frith
+Copyright: 2011–2012 Martin C. Frith
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2014 Charles Plessy <plessy@debian.org>
 License: GPL-3+
 
 License: GPL-3+
@@ -21,4 +27,3 @@ License: GPL-3+
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 Comment: On Debian systems, a copy of the GNU General Public License
  version 3 is placed in “/usr/share/common-licenses/GPL-3”.
-

debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=paraclu-cut.sh
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+

debian/gbp.conf

@@ -4,6 +4,6 @@
 # use pristine-tar:
 pristine-tar = True
 
-[git-dch]
+[dch]
 # include 7 digits of the commit id in the changelog enty:
 id-length = 7

debian/lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+paraclu: script-with-language-extension usr/bin/paraclu-cut.sh

debian/manpages

+debian/*.1

debian/paraclu-cut.sh.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH PARACLU-CUT.SH "1" "July 2018" "paraclu-cut.sh 9" "User Commands"
+.SH NAME
+paraclu-cut.sh \- Parametric clustering of genomic and transcriptomic features
+.SH SYNOPSIS
+.B paraclu-cut.sh
+[\fI\,options\/\fR] [\fI\,paraclu-output-file(s)\/\fR]
+.SH DESCRIPTION
+Extract a subset of clusters from the output of paraclu.
+.SH OPTIONS
+.TP
+\fB\-h\fR
+show this help message and exit
+.TP
+\fB\-l\fR
+maximum cluster length (default 200)
+.TP
+\fB\-d\fR
+minimum density increase (default 2)
+.TP
+\fB\-s\fR
+density increase applies to single clusters, not cumulatively
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/patches/enable_debug.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 03 Jul 2018 14:54:48 +0200
+Description: Enable debug symbols
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+ CXX = g++
+-CXXFLAGS = -Wall -W -O3
++CXXFLAGS += -Wall -W -O3 -g
+ 
+ all: paraclu
+ 

debian/patches/series

+enable_debug.patch

debian/rules

@@ -2,5 +2,11 @@
 
 export DH_VERBOSE=1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@
+
+override_dh_installman:
+	# dh_installman is messing up .sh extension as language extension
+	dh_install debian/*.1	usr/share/man/man1

debian/source/lintian-overrides

+# upstream seems to be dead so we can not do much about this
+paraclu source: debian-watch-uses-insecure-uri http://cbrc3.cbrc.jp/~martin/paraclu/
\ No newline at end of file

debian/upstream/metadata

-Contact: paraclu (ATmark) cbrc (dot) jp
-Name: paraclu
 Reference:
  - author: Frith, Martin C. and Valen, Eivind and Krogh, Anders and Hayashizaki, Yoshihide and Carninci, Piero and Sandelin, Albin
    title: A code for transcription initiation in mammalian genomes

debian/watch

-version=3
-http://www.cbrc.jp/paraclu/paraclu-(.*).zip
+version=4
+
+http://cbrc3.cbrc.jp/~martin/paraclu/ paraclu-(.*).zip