[med-svn] r8136 - trunk/packages/cain/trunk/debian
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Thu Oct 13 11:48:10 UTC 2011
Author: ivomaintz-guest
Date: 2011-10-13 11:48:10 +0000 (Thu, 13 Oct 2011)
New Revision: 8136
Added:
trunk/packages/cain/trunk/debian/cain-examples.install
trunk/packages/cain/trunk/debian/cain-examples.links
trunk/packages/cain/trunk/debian/cain-solvers.install
trunk/packages/cain/trunk/debian/cain-solvers.links
trunk/packages/cain/trunk/debian/cain.install
trunk/packages/cain/trunk/debian/cain.links
Removed:
trunk/packages/cain/trunk/debian/cain-common.install
trunk/packages/cain/trunk/debian/cain-common.links
trunk/packages/cain/trunk/debian/cain-common.manpages
trunk/packages/cain/trunk/debian/lintian/
trunk/packages/cain/trunk/debian/python-cain.install
trunk/packages/cain/trunk/debian/python-cain.postinst
trunk/packages/cain/trunk/debian/python-cain.prerm
Modified:
trunk/packages/cain/trunk/debian/changelog
trunk/packages/cain/trunk/debian/control
trunk/packages/cain/trunk/debian/rules
Log:
changed the partitioning of cain
Deleted: trunk/packages/cain/trunk/debian/cain-common.install
===================================================================
--- trunk/packages/cain/trunk/debian/cain-common.install 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/cain-common.install 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1,6 +0,0 @@
-usr/lib
-usr/bin
-usr/share/applications
-usr/share/cain/examples
-usr/share/cain/help
-usr/include/cain
Deleted: trunk/packages/cain/trunk/debian/cain-common.links
===================================================================
--- trunk/packages/cain/trunk/debian/cain-common.links 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/cain-common.links 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1,4 +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
-/usr/include/cain /usr/share/cain/src
Deleted: trunk/packages/cain/trunk/debian/cain-common.manpages
===================================================================
--- trunk/packages/cain/trunk/debian/cain-common.manpages 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/cain-common.manpages 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1 +0,0 @@
-debian/*1
Added: trunk/packages/cain/trunk/debian/cain-examples.install
===================================================================
--- trunk/packages/cain/trunk/debian/cain-examples.install (rev 0)
+++ trunk/packages/cain/trunk/debian/cain-examples.install 2011-10-13 11:48:10 UTC (rev 8136)
@@ -0,0 +1 @@
+usr/share/cain/examples
Added: trunk/packages/cain/trunk/debian/cain-examples.links
===================================================================
--- trunk/packages/cain/trunk/debian/cain-examples.links (rev 0)
+++ trunk/packages/cain/trunk/debian/cain-examples.links 2011-10-13 11:48:10 UTC (rev 8136)
@@ -0,0 +1 @@
+/usr/share/cain/examples /usr/share/doc/cain-examples/examples
Added: trunk/packages/cain/trunk/debian/cain-solvers.install
===================================================================
--- trunk/packages/cain/trunk/debian/cain-solvers.install (rev 0)
+++ trunk/packages/cain/trunk/debian/cain-solvers.install 2011-10-13 11:48:10 UTC (rev 8136)
@@ -0,0 +1 @@
+usr/lib
Added: trunk/packages/cain/trunk/debian/cain-solvers.links
===================================================================
--- trunk/packages/cain/trunk/debian/cain-solvers.links (rev 0)
+++ trunk/packages/cain/trunk/debian/cain-solvers.links 2011-10-13 11:48:10 UTC (rev 8136)
@@ -0,0 +1 @@
+/usr/lib/solvers /usr/share/cain/solvers
Added: trunk/packages/cain/trunk/debian/cain.install
===================================================================
--- trunk/packages/cain/trunk/debian/cain.install (rev 0)
+++ trunk/packages/cain/trunk/debian/cain.install 2011-10-13 11:48:10 UTC (rev 8136)
@@ -0,0 +1,9 @@
+usr/bin
+usr/include/cain
+usr/share/applications
+usr/share/cain/fio
+usr/share/cain/gui
+usr/share/cain/help
+usr/share/cain/simulation
+usr/share/cain/state
+usr/share/cain/*.py
Added: trunk/packages/cain/trunk/debian/cain.links
===================================================================
--- trunk/packages/cain/trunk/debian/cain.links (rev 0)
+++ trunk/packages/cain/trunk/debian/cain.links 2011-10-13 11:48:10 UTC (rev 8136)
@@ -0,0 +1,2 @@
+/usr/share/cain/help /usr/share/doc/cain/help
+/usr/include/cain /usr/share/cain/src
Modified: trunk/packages/cain/trunk/debian/changelog
===================================================================
--- trunk/packages/cain/trunk/debian/changelog 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/changelog 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1,3 +1,9 @@
+cain (1.9-2) unstable; urgency=low
+
+ * changed the partitioning of the package
+
+ -- Ivo Maintz <ivo at maintz.de> Thu, 13 Oct 2011 13:12:12 +0200
+
cain (1.9-1) unstable; urgency=low
* New upstream release
Modified: trunk/packages/cain/trunk/debian/control
===================================================================
--- trunk/packages/cain/trunk/debian/control 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/control 2011-10-13 11:48:10 UTC (rev 8136)
@@ -14,8 +14,8 @@
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: python-cain
-Architecture: any
+Package: cain
+Architecture: all
Depends: ${python:Depends}, ${shlibs:Depends}, ${misc:Depends},
python (<< 3.0),
python-wxgtk2.8,
@@ -23,7 +23,8 @@
python-numpy,
python-scipy,
python-sympy,
- cain-common
+ cain-solvers
+Recommends: cain-examples
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.
@@ -44,15 +45,12 @@
* Hybrid direct/tau-leaping.
* ODE integration.
.
- This package provides the python modules of cain.
+ This package provides the architecture independent files for cain
-Package: cain-common
+Package: cain-solvers
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends},
libeigen2-dev
-Provides: cain
-Replaces: cain
-Conflicts: cain
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.
@@ -73,14 +71,30 @@
* Hybrid direct/tau-leaping.
* ODE integration.
.
- This package provides the basic cain files and solvers.
+ This package provides the solver libraries
-Package: cain-dbg
-Architecture: any
-Depends: ${misc:Depends},cain (= ${binary:Version})
-Description: debug symbols for cain
- The binaries are all stripped from information that is not needed
- for their execution. But when there is a problem with a particular
- potion of the code, you want to know what function was coding for
- it. This package provides this extra information. You may be asked
- to install it for the deeper investigation of a particular problem.
+Package: cain-examples
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ cain
+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 cain examples
Deleted: trunk/packages/cain/trunk/debian/python-cain.install
===================================================================
--- trunk/packages/cain/trunk/debian/python-cain.install 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/python-cain.install 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1,6 +0,0 @@
-usr/share/cain/fio
-usr/share/cain/gui
-usr/share/cain/simulation
-usr/share/cain/state
-usr/share/cain/*.py
-../lintian/python-cain usr/share/lintian/overrides
Deleted: trunk/packages/cain/trunk/debian/python-cain.postinst
===================================================================
--- trunk/packages/cain/trunk/debian/python-cain.postinst 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/python-cain.postinst 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1,6 +0,0 @@
-#!/bin/sh
-set -e
-
-if which pycompile >/dev/null 2>&1; then
- pycompile -p python-cain /usr/share/cain
-fi
Deleted: trunk/packages/cain/trunk/debian/python-cain.prerm
===================================================================
--- trunk/packages/cain/trunk/debian/python-cain.prerm 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/python-cain.prerm 2011-10-13 11:48:10 UTC (rev 8136)
@@ -1,11 +0,0 @@
-#!/bin/sh
-set -e
-
-if which pyclean >/dev/null 2>&1; then
- pyclean -p python-cain
-else
- dpkg -L python-cain | grep \.py$ | while read file
- do
- rm -f "${file}"[co] >/dev/null
- done
-fi
Modified: trunk/packages/cain/trunk/debian/rules
===================================================================
--- trunk/packages/cain/trunk/debian/rules 2011-10-13 11:00:56 UTC (rev 8135)
+++ trunk/packages/cain/trunk/debian/rules 2011-10-13 11:48:10 UTC (rev 8136)
@@ -15,17 +15,17 @@
UVESRION=1_9
VERSION=1.9
get-orig-source:
- rm -rf $(SRC_TMP) && mkdir $(SRC_TMP)
- #[ -f ../cain_$(VERSION).zip ] || wget -O ../cain_$(VERSION).zip http://sf.net/cain/Cain-$(UVERSION).zip # URL did not work
- [ -f ../cain_$(VERSION).zip ] || wget -O ../cain_$(VERSION).zip http://qa.debian.org/watch/sf.php/cain/Cain-$(UVERSION).zip
- cd $(SRC_TMP) && unzip ../../cain_$(VERSION).zip
- mv $(SRC_TMP)/Cain $(SRC_TMP)/cain-$(VERSION)
- find $(SRC_TMP) -name __MACOSX -type d | xargs -r rm -rf
- find $(SRC_TMP) -iname .DS_Store -exec rm -f {} +
- find $(SRC_TMP) -iname .scons* -exec rm -f {} +
- rm -f $(SRC_TMP)/cain-$(VERSION)/solvers/*
- rm -rf $(SRC_TMP)/cain-$(VERSION)/src/third-party/*
- cd $(SRC_TMP) && tar cvzf ../../cain_$(VERSION).orig.tar.gz cain-$(VERSION)
+ rm -rf $(SRC_TMP) && mkdir $(SRC_TMP) \
+ #[ -f ../cain_$(VERSION).zip ] || wget -O ../cain_$(VERSION).zip http://sf.net/cain/Cain-$(UVERSION).zip # URL did not work \
+ [ -f ../cain_$(VERSION).zip ] || wget -O ../cain_$(VERSION).zip http://qa.debian.org/watch/sf.php/cain/Cain-$(UVERSION).zip \
+ cd $(SRC_TMP) && unzip ../../cain_$(VERSION).zip \
+ mv $(SRC_TMP)/Cain $(SRC_TMP)/cain-$(VERSION) \
+ find $(SRC_TMP) -name __MACOSX -type d | xargs -r rm -rf \
+ find $(SRC_TMP) -iname .DS_Store -exec rm -f {} + \
+ find $(SRC_TMP) -iname .scons* -exec rm -f {} + \
+ rm -f $(SRC_TMP)/cain-$(VERSION)/solvers/* \
+ rm -rf $(SRC_TMP)/cain-$(VERSION)/src/third-party/* \
+ cd $(SRC_TMP) && tar cvzf ../../cain_$(VERSION).orig.tar.gz cain-$(VERSION) \
rm -rf $(SRC_TMP)
config.status: configure
@@ -96,7 +96,7 @@
dh_install
dh_installman
dh_link
- dh_strip --dbg-package=cain-dbg
+ dh_strip
dh_compress
dh_fixperms
dh_makeshlibs
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