[med-svn] r8070 - in trunk/packages/cain/trunk/debian: . patches
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Tue Oct 4 14:54:07 UTC 2011
Author: ivomaintz-guest
Date: 2011-10-04 14:54:07 +0000 (Tue, 04 Oct 2011)
New Revision: 8070
Added:
trunk/packages/cain/trunk/debian/cain-common.install
trunk/packages/cain/trunk/debian/cain-common.links
trunk/packages/cain/trunk/debian/patches/eigen.patch
trunk/packages/cain/trunk/debian/python-cain.install
Removed:
trunk/packages/cain/trunk/debian/cain.install
trunk/packages/cain/trunk/debian/cain.links
Modified:
trunk/packages/cain/trunk/debian/README.Debian-source
trunk/packages/cain/trunk/debian/control
trunk/packages/cain/trunk/debian/dirs
trunk/packages/cain/trunk/debian/menu
trunk/packages/cain/trunk/debian/patches/series
trunk/packages/cain/trunk/debian/rules
Log:
I splitted cain into cain-common and python-cain
Modified: trunk/packages/cain/trunk/debian/README.Debian-source
===================================================================
--- trunk/packages/cain/trunk/debian/README.Debian-source 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/README.Debian-source 2011-10-04 14:54:07 UTC (rev 8070)
@@ -2,10 +2,14 @@
unzip Cain-1_9.zip
cd Cain
+# remove superfluous files and directories
rm -rf ../__MACOSX
find . -iname .DS_Store -exec rm -f {} +
find . -iname .scons* -exec rm -f {} +
+# clean the solvers directory
rm -f solvers/*
-tar cvzf ../cain_1.8.orig.tar.gz .
+# remove third-party files
+rm -rf src/third-party/*
+tar cvzf ../cain_1.9.orig.tar.gz .
cd ..
rm -rf Cain/
Copied: trunk/packages/cain/trunk/debian/cain-common.install (from rev 7987, trunk/packages/cain/trunk/debian/cain.install)
===================================================================
--- trunk/packages/cain/trunk/debian/cain-common.install (rev 0)
+++ trunk/packages/cain/trunk/debian/cain-common.install 2011-10-04 14:54:07 UTC (rev 8070)
@@ -0,0 +1,6 @@
+usr/lib
+usr/bin
+usr/share/applications
+usr/share/cain/examples
+usr/share/cain/help
+usr/include/cain
Copied: trunk/packages/cain/trunk/debian/cain-common.links (from rev 7987, trunk/packages/cain/trunk/debian/cain.links)
===================================================================
--- trunk/packages/cain/trunk/debian/cain-common.links (rev 0)
+++ trunk/packages/cain/trunk/debian/cain-common.links 2011-10-04 14:54:07 UTC (rev 8070)
@@ -0,0 +1,4 @@
+/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
+usr/include/cain /usr/share/cain/src
Deleted: trunk/packages/cain/trunk/debian/cain.install
===================================================================
--- trunk/packages/cain/trunk/debian/cain.install 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/cain.install 2011-10-04 14:54:07 UTC (rev 8070)
@@ -1 +0,0 @@
-usr/
Deleted: trunk/packages/cain/trunk/debian/cain.links
===================================================================
--- trunk/packages/cain/trunk/debian/cain.links 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/cain.links 2011-10-04 14:54:07 UTC (rev 8070)
@@ -1,3 +0,0 @@
-/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
Modified: trunk/packages/cain/trunk/debian/control
===================================================================
--- trunk/packages/cain/trunk/debian/control 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/control 2011-10-04 14:54:07 UTC (rev 8070)
@@ -10,10 +10,57 @@
Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/cain/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cain/trunk/
-Package: cain
+Package: python-cain
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, python-wxgtk2.8, python-matplotlib, python-numpy, python-scipy, python-sympy
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
+ python-wxgtk2.8,
+ python-matplotlib,
+ python-numpy,
+ python-scipy,
+ python-sympy,
+ cain-common
+Provides: cain
+Replaces: cain
Description: simulations of chemical reactions
- <some intro here>
- Cain performs stochastic and deterministic simulations of chemical reactions
- <and some words on the context it is used here>
+ Cain performs stochastic and deterministic simulations of chemical reactions.
+ It can spawn multiple simulation processes to utilize multi-core computers.
+ It stores models, methods, and simulation output (populations and reaction counts)
+ in an XML format. In addition, SBML models can be imported and exported. The
+ models and methods can be read from input files or edited within the program.
+ .
+ The GUI (Graphical User Interface) is written in Python and uses the wxPython
+ toolkit. Most of the solvers are implemented as command line executables, written
+ in C++, which are driven by Cain. This makes it easy to launch batch jobs. It also
+ simplifies the process of adding new solvers. Cain offers a variety of solvers:
+ * Gillespie's direct method.
+ * Gillespie's first reaction method.
+ * Gibson and Bruck's next reaction method.
+ * Tau-leaping.
+ * Hybrid direct/tau-leaping.
+ * ODE integration.
+ .
+ This package provides the python modules of cain
+
+Package: cain-common
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libeigen3-dev
+Description: simulations of chemical reactions
+ Cain performs stochastic and deterministic simulations of chemical reactions.
+ It can spawn multiple simulation processes to utilize multi-core computers.
+ It stores models, methods, and simulation output (populations and reaction counts)
+ in an XML format. In addition, SBML models can be imported and exported. The
+ models and methods can be read from input files or edited within the program.
+ .
+ The GUI (Graphical User Interface) is written in Python and uses the wxPython
+ toolkit. Most of the solvers are implemented as command line executables, written
+ in C++, which are driven by Cain. This makes it easy to launch batch jobs. It also
+ simplifies the process of adding new solvers. Cain offers a variety of solvers:
+ * Gillespie's direct method.
+ * Gillespie's first reaction method.
+ * Gibson and Bruck's next reaction method.
+ * Tau-leaping.
+ * Hybrid direct/tau-leaping.
+ * ODE integration.
+ .
+ This package provides the basic cain files and solvers
Modified: trunk/packages/cain/trunk/debian/dirs
===================================================================
--- trunk/packages/cain/trunk/debian/dirs 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/dirs 2011-10-04 14:54:07 UTC (rev 8070)
@@ -1,7 +0,0 @@
-usr
-usr/bin
-usr/lib
-usr/lib/solvers
-usr/share
-usr/share/cain
-usr/share/applications
Modified: trunk/packages/cain/trunk/debian/menu
===================================================================
--- trunk/packages/cain/trunk/debian/menu 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/menu 2011-10-04 14:54:07 UTC (rev 8070)
@@ -1,2 +1,2 @@
-?package(cain):needs="X11" section="Applications/Systems Biology"\
+?package(cain):needs="X11" section="Applications/Development/Science"\
title="cain" command="/usr/bin/cain"
Added: trunk/packages/cain/trunk/debian/patches/eigen.patch
===================================================================
--- trunk/packages/cain/trunk/debian/patches/eigen.patch (rev 0)
+++ trunk/packages/cain/trunk/debian/patches/eigen.patch 2011-10-04 14:54:07 UTC (rev 8070)
@@ -0,0 +1,38 @@
+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/src/stochastic/TauLeapingImplicit.h
++++ cain-1.9/src/stochastic/TauLeapingImplicit.h
+@@ -13,8 +13,8 @@
+
+ #include "../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h"
+
+-#include "../third-party/Eigen/LU"
+-#include "../third-party/Eigen/Array"
++#include "/usr/include/eigen2/Eigen/LU"
++#include "/usr/include/eigen2/Eigen/Array"
+
+ namespace stochastic {
+
Modified: trunk/packages/cain/trunk/debian/patches/series
===================================================================
--- trunk/packages/cain/trunk/debian/patches/series 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/patches/series 2011-10-04 14:54:07 UTC (rev 8070)
@@ -1 +1,2 @@
cain.patch
+eigen.patch
Added: trunk/packages/cain/trunk/debian/python-cain.install
===================================================================
--- trunk/packages/cain/trunk/debian/python-cain.install (rev 0)
+++ trunk/packages/cain/trunk/debian/python-cain.install 2011-10-04 14:54:07 UTC (rev 8070)
@@ -0,0 +1,5 @@
+usr/share/cain/fio
+usr/share/cain/gui
+usr/share/cain/simulation
+usr/share/cain/state
+usr/share/cain/*.py
Modified: trunk/packages/cain/trunk/debian/rules
===================================================================
--- trunk/packages/cain/trunk/debian/rules 2011-10-04 09:24:56 UTC (rev 8069)
+++ trunk/packages/cain/trunk/debian/rules 2011-10-04 14:54:07 UTC (rev 8070)
@@ -8,8 +8,25 @@
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
+
+SRC_TMP=$(CURDIR)/SRC_TMP
debtmp := $(CURDIR)/debian/tmp
+get-orig-source:
+ rm -rf $(SRC_TMP) && mkdir $(SRC_TMP)
+ cd $(SRC_TMP)
+ wget http://sf.net/cain/Cain-1_9.zip
+ 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/*
+ rm -rf src/third-party/*
+ tar cvzf ../../cain_1.9.orig.tar.gz .
+ cd $(CURDIR)
+ rm -rf $(SRC_TMP)
+
config.status: configure
dh_testdir
@@ -25,7 +42,7 @@
touch $@
-clean:
+clean:
dh_testdir
dh_testroot
rm -f build-stamp
@@ -47,12 +64,13 @@
mkdir -p $(debtmp)/usr/bin
mkdir -p $(debtmp)/usr/share/cain
mkdir -p $(debtmp)/usr/lib
+ mkdir -p $(debtmp)/usr/include/cain
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 src/* $(debtmp)/usr/include/cain
cp -a simulation $(debtmp)/usr/share/cain
cp -a solvers $(debtmp)/usr/lib/
cp -a state $(debtmp)/usr/share/cain
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