[med-svn] [libsbml-odesolver] 02/03: Initial Debian packaging
Andreas Tille
tille at debian.org
Fri Jan 27 16:01:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libsbml-odesolver.
commit fbf3ef8d1329530073daf0caa442dfd38002a832
Author: Andreas Tille <tille at debian.org>
Date: Fri Jan 27 16:52:46 2017 +0100
Initial Debian packaging
---
debian/changelog | 8 ++++++++
debian/compat | 1 +
debian/control | 32 ++++++++++++++++++++++++++++++++
debian/copyright | 11 +++++++++++
debian/doc-base | 20 ++++++++++++++++++++
debian/get-orig-source | 28 ++++++++++++++++++++++++++++
debian/rules | 26 ++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 8 ++++++++
10 files changed, 147 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..c6579e5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,8 @@
+libsbml-odesolver (1.6.0+20161004-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+ TODO: configure:
+ Can not link to GRACE Library!
+ odeSolver will be installed without XMGrace functionality
+
+ -- Andreas Tille <tille at debian.org> Fri, 27 Jan 2017 13:51:25 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..fb7fba8
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,32 @@
+Source: libsbml-odesolver
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ check,
+ pkg-config,
+ libsbml5-dev,
+ libxml2-dev,
+ libsundials-serial-dev,
+ graphviz,
+ libgraphviz-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libsbml-odesolver.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libsbml-odesolver.git
+Homepage: http://www.tbi.univie.ac.at/~raim/odeSolver/
+
+Package: libsbml-odesolver
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: SBML ODE Solver Library
+ SOSlib (SBML ODE Solver Library) is both a programming library and a
+ commandline application for symbolic and numerical analysis of a system
+ of ordinary differential equations (ODEs) derived from a chemical
+ reaction network encoded in the Systems Biology Markup Language (SBML).
+ It is written in ANSI/ISO C. The package employs libSBML's AST (Abstract
+ Syntax Tree) for formula representation to construct ODE systems, their
+ Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled
+ ODE solver in the SUNDIALS package is used for numerical integration and
+ sensitivity analysis of stiff and non-stiff ODE systems.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..3416315
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5e7e1d4
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+Document: <pkg>
+Title: <title for this doc>
+Author: <author of this doc>
+Abstract: <if you have no better clue the short and
+ long description from debian/control might fit here as well>
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+# pick one of the below options
+Format: Text
+Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
+
+Format: html
+Index: /usr/share/doc/<pkg>/html/index.html
+Files: /usr/share/doc/<pkg>/html/*
+
+Format: pdf
+Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
+
+Format: postscript
+Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..ef1fca6
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,28 @@
+#!/bin/sh -e
+
+COMPRESS=xz
+
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+ONAME=`echo $NAME | sed 's/lib\(.*\)-java/\1/'`
+MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
+
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+git clone --quiet https://github.com/raim/SBML_odeSolver ${NAME}
+cd $NAME
+VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d`
+# for esthetical reasons set file timestamps (if git-restore-mtime is installed)
+git restore-mtime || true
+cd ..
+TARDIR=${NAME}-${VERSION}
+mv ${NAME} ${TARDIR}
+rm -rf ${TARDIR}/.git
+rm -rf ${TARDIR}/jars/batik*
+rm -rf ${TARDIR}/jars/Jama-*
+find ${TARDIR} -name .DS_Store -delete
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1ef14d9
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..dfe9181
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,8 @@
+version=4
+
+# Upstream issue opened: https://github.com/raim/SBML_odeSolver/issues/2
+
+# https://github.com/raim/SBML_odeSolver/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz
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