[med-svn] r7987 - in trunk/packages: . cain cain/trunk cain/trunk/debian cain/trunk/debian/patches cain/trunk/debian/source
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Thu Sep 29 20:37:25 UTC 2011
Author: ivomaintz-guest
Date: 2011-09-29 20:37:25 +0000 (Thu, 29 Sep 2011)
New Revision: 7987
Added:
trunk/packages/cain/
trunk/packages/cain/trunk/
trunk/packages/cain/trunk/debian/
trunk/packages/cain/trunk/debian/README.Debian-source
trunk/packages/cain/trunk/debian/cain.desktop
trunk/packages/cain/trunk/debian/cain.install
trunk/packages/cain/trunk/debian/cain.links
trunk/packages/cain/trunk/debian/cain.sh
trunk/packages/cain/trunk/debian/changelog
trunk/packages/cain/trunk/debian/compat
trunk/packages/cain/trunk/debian/control
trunk/packages/cain/trunk/debian/copyright
trunk/packages/cain/trunk/debian/dirs
trunk/packages/cain/trunk/debian/docs
trunk/packages/cain/trunk/debian/menu
trunk/packages/cain/trunk/debian/patches/
trunk/packages/cain/trunk/debian/patches/cain.patch
trunk/packages/cain/trunk/debian/patches/series
trunk/packages/cain/trunk/debian/rules
trunk/packages/cain/trunk/debian/source/
trunk/packages/cain/trunk/debian/source/format
trunk/packages/cain/trunk/debian/watch
Log:
first commit for cain
Property changes on: trunk/packages/cain
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Property changes on: trunk/packages/cain/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/cain/trunk/debian/README.Debian-source
===================================================================
--- trunk/packages/cain/trunk/debian/README.Debian-source (rev 0)
+++ trunk/packages/cain/trunk/debian/README.Debian-source 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,11 @@
+the source package have only .zip file format and a invalid version number
+
+unzip Cain-1_9.zip
+cd Cain
+rm -rf ../__MACOSX
+find . -iname .DS_Store -exec rm -f {} +
+find . -iname .scons* -exec rm -f {} +
+rm -f solvers/*
+tar cvzf ../cain_1.8.orig.tar.gz .
+cd ..
+rm -rf Cain/
Added: trunk/packages/cain/trunk/debian/cain.desktop
===================================================================
--- trunk/packages/cain/trunk/debian/cain.desktop (rev 0)
+++ trunk/packages/cain/trunk/debian/cain.desktop 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,9 @@
+[Desktop Entry]
+Name=Cain
+Comment=simulations of chemical reactions
+Exec=/usr/bin/cain
+Icon=/usr/share/cain/gui/icons/cain.png
+Terminal=false
+Type=Application
+Categories=Development;Science;Biology;
+StartupNotify=true
Added: trunk/packages/cain/trunk/debian/cain.install
===================================================================
--- trunk/packages/cain/trunk/debian/cain.install (rev 0)
+++ trunk/packages/cain/trunk/debian/cain.install 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1 @@
+usr/
Added: trunk/packages/cain/trunk/debian/cain.links
===================================================================
--- trunk/packages/cain/trunk/debian/cain.links (rev 0)
+++ trunk/packages/cain/trunk/debian/cain.links 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,3 @@
+/usr/lib/solvers /usr/share/cain/solvers
+/usr/share/cain/examples /usr/share/doc/cain/examples
+/usr/share/cain/help /usr/share/doc/cain/help
\ No newline at end of file
Added: trunk/packages/cain/trunk/debian/cain.sh
===================================================================
--- trunk/packages/cain/trunk/debian/cain.sh (rev 0)
+++ trunk/packages/cain/trunk/debian/cain.sh 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,3 @@
+#!/bin/sh
+mkdir -p ~/.cain
+python /usr/share/cain/Cain.py
Added: trunk/packages/cain/trunk/debian/changelog
===================================================================
--- trunk/packages/cain/trunk/debian/changelog (rev 0)
+++ trunk/packages/cain/trunk/debian/changelog 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,35 @@
+cain (1.9-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Ivo Maintz <ivo at maintz.de> Wed, 28 Sep 2011 12:02:11 +0200
+
+cain (1.8-1) natty; urgency=low
+
+ * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Fri, 23 Sep 2011 14:18:03 +0200
+
+cain (1.6-3) natty; urgency=low
+
+ * now the solvers are build, too
+
+ -- Ivo Maintz <ivo at maintz.de> Wed, 22 Jun 2011 13:01:39 +0200
+
+cain (1.6-2) natty; urgency=low
+
+ * recompiled for natty
+
+ -- Ivo Maintz <ivo at maintz.de> Thu, 05 May 2011 10:09:41 +0200
+
+cain (1.6-1) unstable; urgency=low
+
+ * Update from Upstream
+
+ -- Ivo Maintz <ivo at maintz.de> Mon, 07 Feb 2011 12:18:23 +0100
+
+cain (1.5-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Ivo Maintz <ivo at maintz.de> Tue, 05 Oct 2010 14:31:33 +0200
Added: trunk/packages/cain/trunk/debian/compat
===================================================================
--- trunk/packages/cain/trunk/debian/compat (rev 0)
+++ trunk/packages/cain/trunk/debian/compat 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1 @@
+7
Added: trunk/packages/cain/trunk/debian/control
===================================================================
--- trunk/packages/cain/trunk/debian/control (rev 0)
+++ trunk/packages/cain/trunk/debian/control 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,14 @@
+Source: cain
+Section: science
+Priority: extra
+Maintainer: Ivo Maintz <ivo at maintz.de>
+Build-Depends: debhelper (>= 7),
+ python
+Standards-Version: 3.9.2
+Homepage: http://cain.sourceforge.net
+
+Package: cain
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, python-wxgtk2.8, python-matplotlib, python-numpy, python-scipy, python-sympy
+Description: simulations of chemical reactions
+ Cain performs stochastic and deterministic simulations of chemical reactions
Added: trunk/packages/cain/trunk/debian/copyright
===================================================================
--- trunk/packages/cain/trunk/debian/copyright (rev 0)
+++ trunk/packages/cain/trunk/debian/copyright 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,52 @@
+This work was packaged for Debian by:
+
+ Ivo Maintz <ivo at maintz.de> on Tue, 05 Oct 2010 14:31:33 +0200
+
+It was downloaded from:
+
+ http://cain.sourceforge.net
+
+Upstream Author(s):
+
+ Sean Mauch <sean at caltech.edu>
+
+Copyright:
+
+ <Copyright (c) 1999-2011, California Institute of Technology>
+
+License:
+
+
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ Neither the name of the California Institute of Technology nor the names
+ of its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
+ OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+ OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The Debian packaging is:
+
+ Copyright (C) 2010 Ivo Maintz <ivo at maintz.de>
+
+and is licensed under the GPL version 3,
+see `/usr/share/common-licenses/GPL-3'.
Added: trunk/packages/cain/trunk/debian/dirs
===================================================================
--- trunk/packages/cain/trunk/debian/dirs (rev 0)
+++ trunk/packages/cain/trunk/debian/dirs 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,7 @@
+usr
+usr/bin
+usr/lib
+usr/lib/solvers
+usr/share
+usr/share/cain
+usr/share/applications
Added: trunk/packages/cain/trunk/debian/docs
===================================================================
Added: trunk/packages/cain/trunk/debian/menu
===================================================================
--- trunk/packages/cain/trunk/debian/menu (rev 0)
+++ trunk/packages/cain/trunk/debian/menu 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,2 @@
+?package(cain):needs="X11" section="Applications/Systems Biology"\
+ title="cain" command="/usr/bin/cain"
Added: trunk/packages/cain/trunk/debian/patches/cain.patch
===================================================================
--- trunk/packages/cain/trunk/debian/patches/cain.patch (rev 0)
+++ trunk/packages/cain/trunk/debian/patches/cain.patch 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,85 @@
+Description: <short summary of the patch>
+ TODO: Put a short summary on the line above and replace this paragraph
+ with a longer explanation of this change. Complete the meta-information
+ with other relevant fields (see below for details). To make it easier, the
+ information below has been extracted from the changelog. Adjust it or drop
+ it.
+ .
+ cain (1.9-1) unstable; urgency=low
+ .
+ * New upstream release
+Author: Ivo Maintz <ivo at maintz.de>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- cain-1.9.orig/Makefile
++++ cain-1.9/Makefile
+@@ -2,7 +2,7 @@
+
+ # By default make the solvers.
+ default:
+- $(MAKE) -C src/solvers $(MAKEFLAGS) $(MAKECMDGOALS)
++ $(MAKE) -C src/solvers
+
+ again:
+
+@@ -17,6 +17,8 @@ distclean: clean
+ rm -rf Cain.app/Contents/Resources/simulation
+ rm -rf Cain.app/Contents/Resources/solvers
+ rm -rf Cain.app/Contents/Resources/state
++ rm -f solvers/*
++ rm -f src/solvers/*.d
+
+ test:
+ nosetests --with-doctest -v simulation state
+--- cain-1.9.orig/gui/Application.py
++++ cain-1.9/gui/Application.py
+@@ -7,6 +7,7 @@ import os.path
+ import wx
+ from MainFrame import MainFrame
+ from resourcePath import resourcePath
++from os.path import expanduser, join
+
+ class Application(wx.App):
+ """The application class for Cain."""
+@@ -14,7 +15,7 @@ class Application(wx.App):
+ def __init__(self):
+ """Construct the base class and redirect the output."""
+ if not sys.platform in ('win32', 'win64'):
+- wx.App.__init__(self, redirect=True, filename="ErrorLog.txt")
++ wx.App.__init__(self, redirect=True, filename=join(expanduser('~'),".cain","ErrorLog.txt"))
+ else:
+ # On windows we might not have write permission for the log file.
+ wx.App.__init__(self)
+--- cain-1.9.orig/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
++++ cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
+@@ -9,7 +9,7 @@
+ #define __ads_indexedPriorityQueue_IndexedPriorityQueueBinaryHeap_h__
+
+ #include "IndexedPriorityQueueBase.h"
+-
++#include <stddef.h>
+ #include <iostream>
+
+ namespace ads {
+--- cain-1.9.orig/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
++++ cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
+@@ -9,6 +9,7 @@
+ #define __ads_indexedPriorityQueue_IndexedPriorityQueueBinaryHeapPair_h__
+
+ #include "IndexedPriorityQueueBase.h"
++#include <stddef.h>
+
+ namespace ads {
+
Added: trunk/packages/cain/trunk/debian/patches/series
===================================================================
--- trunk/packages/cain/trunk/debian/patches/series (rev 0)
+++ trunk/packages/cain/trunk/debian/patches/series 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1 @@
+cain.patch
Added: trunk/packages/cain/trunk/debian/rules
===================================================================
--- trunk/packages/cain/trunk/debian/rules (rev 0)
+++ trunk/packages/cain/trunk/debian/rules 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,92 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+debtmp := $(CURDIR)/debian/tmp
+
+config.status: configure
+ dh_testdir
+
+#build: build-stamp
+build: build-arch build-indep
+build-arch: build-stamp
+build-indep: build-stamp
+build-stamp:
+build-stamp:
+
+ # Add here commands to compile the package.
+ $(MAKE)
+
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ [ ! -f Makefile ] || $(MAKE) distclean
+ rm -f config.sub config.guess
+ rm -rf $(debtmp)
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_prep
+ dh_installdirs
+
+ # Add here commands to install the package into debian/cain
+ mkdir -p $(debtmp)/usr/share/applications
+ mkdir -p $(debtmp)/usr/bin
+ mkdir -p $(debtmp)/usr/share/cain
+ mkdir -p $(debtmp)/usr/lib
+ cp -a examples $(debtmp)/usr/share/cain/
+ cp -a gui $(debtmp)/usr/share/cain
+ cp -a help $(debtmp)/usr/share/cain/
+ rm -f $(debtmp)/usr/share/cain/help/Licen*
+ cp -a fio $(debtmp)/usr/share/cain
+ cp -a src $(debtmp)/usr/share/cain
+ cp -a simulation $(debtmp)/usr/share/cain
+ cp -a solvers $(debtmp)/usr/lib/
+ cp -a state $(debtmp)/usr/share/cain
+ cp -a Cain.py $(debtmp)/usr/share/cain/
+ cp -a resourcePath.py $(debtmp)/usr/share/cain/
+ find $(debtmp)/usr/share/cain/ -type f -executable -exec chmod 644 {} +
+ rm -f $(debtmp)/usr/share/cain/help/License.*
+ cp -a debian/cain.desktop $(debtmp)/usr/share/applications
+ cp -a debian/cain.sh $(debtmp)/usr/bin/cain
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_install
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_makeshlibs
+ dh_python2 --no-guessing-versions
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/cain/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/cain/trunk/debian/source/format
===================================================================
--- trunk/packages/cain/trunk/debian/source/format (rev 0)
+++ trunk/packages/cain/trunk/debian/source/format 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/cain/trunk/debian/watch
===================================================================
--- trunk/packages/cain/trunk/debian/watch (rev 0)
+++ trunk/packages/cain/trunk/debian/watch 2011-09-29 20:37:25 UTC (rev 7987)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/cain/[cC]ain-(\d_\d).zip
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