[med-svn] r13079 - in trunk/packages/cellprofiler: branches trunk/debian trunk/debian/bin trunk/debian/patches

Sun Feb 24 11:41:52 UTC 2013

Author: ivomaintz-guest
Date: 2013-02-24 11:41:52 +0000 (Sun, 24 Feb 2013)
New Revision: 13079

Added:
   trunk/packages/cellprofiler/trunk/debian/bin/
   trunk/packages/cellprofiler/trunk/debian/bin/cellprofiler
   trunk/packages/cellprofiler/trunk/debian/patches/Makefile.patch
Removed:
   trunk/packages/cellprofiler/branches/experimental/
   trunk/packages/cellprofiler/trunk/debian/cellprofiler2.py
   trunk/packages/cellprofiler/trunk/debian/patches/remove_test.patch
Modified:
   trunk/packages/cellprofiler/trunk/debian/cellprofiler.install
   trunk/packages/cellprofiler/trunk/debian/changelog
   trunk/packages/cellprofiler/trunk/debian/compat
   trunk/packages/cellprofiler/trunk/debian/control
   trunk/packages/cellprofiler/trunk/debian/copyright
   trunk/packages/cellprofiler/trunk/debian/get-orig-source
   trunk/packages/cellprofiler/trunk/debian/patches/series
   trunk/packages/cellprofiler/trunk/debian/rules
Log:
deleted the unused experimental branch
added a simple manpage



Added: trunk/packages/cellprofiler/trunk/debian/bin/cellprofiler
===================================================================

--- trunk/packages/cellprofiler/trunk/debian/bin/cellprofiler	                        (rev 0)
+++ trunk/packages/cellprofiler/trunk/debian/bin/cellprofiler	2013-02-24 11:41:52 UTC (rev 13079)
@@ -0,0 +1,8 @@
+#!/bin/sh
+CP_DIR="/usr/share/cellprofiler"
+LOG="$HOME/cellprofiler_err.log"
+export PYTHONPATH="$PYTHONPATH":"$CP_DIR"
+export JAVA_HOME="$(readlink -f /usr/bin/java | cut -d/ -f1-5)"
+export LD_LIBRARY_PATH=`find "$JAVA_HOME" -type d -name server`:"$LD_LIBRARY_PATH"
+cd "$CP_DIR"
+python CellProfiler.py -b --do-not-fetch $@ 2>/"$LOG" | grep -v Gtk-*


Property changes on: trunk/packages/cellprofiler/trunk/debian/bin/cellprofiler
___________________________________________________________________
Added: svn:executable
   + *

Modified: trunk/packages/cellprofiler/trunk/debian/cellprofiler.install
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/cellprofiler.install	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/cellprofiler.install	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1 +1,23 @@
-debian/cellprofiler2.py usr/bin
+debian/bin/cellprofiler /usr/bin/
+debian/cellprofiler.desktop /usr/share/applications/
+bioformats /usr/share/cellprofiler/
+contrib /usr/share/cellprofiler/
+imagej /usr/share/cellprofiler/
+killjavabridge /usr/share/cellprofiler/
+plugins /usr/share/cellprofiler/
+CellProfilerIcon.png /usr/share/cellprofiler/
+CellProfiler.py /usr/share/cellprofiler/
+cpnose.py /usr/share/cellprofiler/
+CPy.py /usr/share/cellprofiler/
+external_dependencies.py /usr/share/cellprofiler/
+cellprofiler/*.py /usr/share/cellprofiler/cellprofiler/
+cellprofiler/cpmath/*.py /usr/share/cellprofiler/cellprofiler/cpmath/
+cellprofiler/gui/*.py /usr/share/cellprofiler/cellprofiler/gui/
+cellprofiler/gui/html /usr/share/cellprofiler/cellprofiler/gui/
+cellprofiler/icons/*.png /usr/share/cellprofiler/cellprofiler/icons/
+cellprofiler/icons/*.py /usr/share/cellprofiler/cellprofiler/icons/
+cellprofiler/matlab/*.py /usr/share/cellprofiler/cellprofiler/matlab/
+cellprofiler/modules/*.py /usr/share/cellprofiler/cellprofiler/modules/
+cellprofiler/modules/plugins /usr/share/cellprofiler/cellprofiler/modules
+cellprofiler/utilities/*.py /usr/share/cellprofiler/cellprofiler/utilities/
+cellprofiler/utilities/*.class /usr/share/cellprofiler/cellprofiler/utilities/

Deleted: trunk/packages/cellprofiler/trunk/debian/cellprofiler2.py
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/cellprofiler2.py	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/cellprofiler2.py	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1,9 +0,0 @@
-#!/usr/bin/python
-# TODO: this file should be called cellprofiler, but this breaks debian build
-# this file cannot be called cellprofiler.py as it conflicts with CellProfiler.py
-import sys
-import CellProfiler
-# fix sys.path to allow numpy import
-if '/usr/share/pyshared' in sys.path:
-   sys.path.remove('/usr/share/pyshared')
-CellProfiler.main()

Modified: trunk/packages/cellprofiler/trunk/debian/changelog
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/changelog	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/changelog	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1,5 +1,49 @@
-cellprofiler (2.0~svn10997.dfsg-1) unstable; urgency=low
+cellprofiler (2.0~svn11717-1) unstable; urgency=low
 
+  * update from upstream
+  * split the package into the arch-dependend cellprofiler-libs and
+    arch-independend cellprofiler
+
+ -- Ivo Maintz <ivo at maintz.de>  Sun, 24 Feb 2013 12:38:45 +0100
+
+cellprofiler (2.0~svn11713-3) UNRELEASED; urgency=low
+
+  * removed some hardcoded pathes in cellprofiler/utilities/setup.py and in the
+    startup script/usr/bin/cellprofiler
+
+ -- Ivo Maintz <ivo at maintz.de>  Mon, 02 Apr 2012 11:59:48 +0200
+
+cellprofiler (2.0~svn11713-2) UNRELEASED; urgency=low
+
+  * moved most of the stuff back to /usr/share/cellprofiler
+  * adjusted the startup script /usr/bin/cellprofiler
+  * added the dependency to tifffile
+  * errors are written to $HOME/cellprofiler_err.log
+
+ -- Ivo Maintz <ivo at maintz.de>  Wed, 28 Mar 2012 15:27:58 +0200
+
+cellprofiler (2.0~svn11713-1) UNRELEASED; urgency=low
+
+  * update from upstream
+  * externalized the killjavabridge module (now python-killjavabridge)
+  * moved BatchProfiler directory to /usr/share/doc/cellprofiler/, the files in it
+    are rather examples; same for python-2.6.sh
+  * moved the *.so files to /usr/python2.7/libs-dynload
+  * changed the startup script '/usr/bin/cellprofiler', it now really accepts
+    command line parameters and throws all error messages away; not sure,
+    if this is the best way...
+
+ -- Ivo Maintz <ivo at maintz.de>  Thu, 08 Mar 2012 13:12:55 +0100
+
+cellprofiler (2.0~svn11691-1) unstable; urgency=low
+
+  * merging Mathieus works with mine
+  * update from upstream
+
+ -- Ivo Maintz <ivo at maintz.de>  Wed, 07 Dec 2011 14:59:39 +0100
+
+cellprofiler (2.0~svn10997-1) unstable; urgency=low
+
   * Initial Debian Upload (Closes: #647995)
 
- -- Mathieu Malaterre <mathieu.malaterre at gmail.com>  Tue, 22 Nov 2011 16:37:34 +0100
+ -- Mathieu Malaterre <mathieu.malaterre at gmail.com>  Mon, 12 Sep 2011 09:56:16 +0200

Modified: trunk/packages/cellprofiler/trunk/debian/compat
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/compat	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/compat	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1 +1 @@
-8
+9

Modified: trunk/packages/cellprofiler/trunk/debian/control
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/control	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/control	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1,32 +1,43 @@
 Source: cellprofiler
+Section: python
 Priority: extra
-Section: python
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
-Uploaders: Mathieu Malaterre <mathieu.malaterre at gmail.com>
-Build-Depends: debhelper (>= 8), python-nose (>= 1.0), cython, python-mysqldb, python-numpy,
- python-scipy, python-setuptools, python-matplotlib, python-wxgtk2.8,
- python-decorator, python-dev (>= 2.6.6-3~), python-libtiff, default-jdk
-Standards-Version: 3.9.2
-X-Python-Version: 2.7
-Homepage: http://cellprofiler.org
+Uploaders: Mathieu Malaterre <mathieu.malaterre at gmail.com>,
+ Ivo Maintz <ivo at maintz.de>
+Build-Depends: debhelper (>= 9),
+ python-nose (>= 1.0),
+ cython,
+ python-mysqldb,
+ python-numpy,
+ python-scipy,
+ python-setuptools,
+ python-matplotlib,
+ python-wxgtk2.8,
+ python-decorator,
+ python-dev (>= 2.6.6-3~),
+ default-jdk
+Standards-Version: 3.9.3
+Homepage: http://www.cellprofiler.org
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cellprofiler/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cellprofiler/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/cellprofiler/trunk/
 
-
 Package: cellprofiler
-Architecture: any
-Depends: ${python:Depends}, ${misc:Depends}, ${shlibs:Depends},
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
+ cellprofiler-libs,
  default-jre | openjdk-6-jre | gcj-jre,
+ jarwrapper | java-wrappers,
+ python-decorator,
  python-h5py,
  python-libtiff,
+ python-matplotlib,
+ python-mysqldb,
+ python-nose,
  python-numpy,
  python-scipy,
- python-matplotlib,
  python-wxgtk2.8,
- python-decorator,
- python-mysqldb,
- python-nose
+ tifffile | python-tifffile
 Recommends: tifffile
 Provides: ${python:Provides}
 Description: quantitatively measure phenotypes from images automatically
@@ -34,3 +45,14 @@
  biologists without training in computer vision or programming to
  quantitatively measure phenotypes from thousands of images
  automatically.
+
+Package: cellprofiler-libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: libraries for cellprofiler
+ CellProfiler is cell image analysis software designed to enable
+ biologists without training in computer vision or programming to
+ quantitatively measure phenotypes from thousands of images
+ automatically.
+ .
+ This package ships the libraries for cellprofiler

Modified: trunk/packages/cellprofiler/trunk/debian/copyright
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/copyright	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/copyright	2013-02-24 11:41:52 UTC (rev 13079)
@@ -3,17 +3,83 @@
 Source: http://cellprofiler.org
 
 Files: *
-Copyright: © 2003-2009 Massachusetts Institute of Technology
+Copyright: (c) 2003-2012 Massachusetts Institute of Technology
 License: GPL-2
- CellProfiler is licensed under the GNU General Public License version
- 2.  See the file COPYING for the terms of the GNU GPL license.
-Comment: On Debian systems, the complete text of the GNU General Public
-License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License version 2 as published
+ by the Free Software Foundation.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
 
-Files: CellProfiler/cpmath, CellProfiler/utilities, bioformats
+Files: contrib/asizeof.py
+Copyright: (c) 2002-2009 -- ProphICy Semiconductor, Inc.
+License: BSD-alike
+ 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 ProphICy Semiconductor, Inc. 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.
+
+Files: contrib/objgraph.py
+Copyright: (c) 2008 Marius Gedminas <marius at pov.lt>
+License: MIT
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated
+ documentation files (the "Software"), to deal in the Software
+ without restriction, including without limitation the rights to
+ use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to
+ whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright n<otice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT  WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERSBE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Files: CellProfiler/cpmath CellProfiler/utilities bioformats/*
 Copyright: © 2003-2009 Massachusetts Institute of Technology
            © 2009-2010 Broad Institute
-Licence: BSD
+License: BSD
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are met:
  .
@@ -44,6 +110,7 @@
  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 Files: debian/*
-Copyright: © 2011 Mathieu Malaterre <mathieu.malaterre at gmail.com>
+Copyright: (c) 2011 Mathieu Malaterre <mathieu.malaterre at gmail.com>
 License: BSD
   Same as above
+

Modified: trunk/packages/cellprofiler/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/get-orig-source	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/get-orig-source	2013-02-24 11:41:52 UTC (rev 13079)
@@ -28,11 +28,11 @@
 git clone git://github.com/thouis/CellProfiler.git ${FOLDER}
 cd ${FOLDER}
 git checkout wrap-cppy-in-main
-rm -rf .git
+rm -rf .git*
 cd ..
 
 # 
-find ${FOLDER} -name *.exe -delete -o -name *.pdf -delete
+find ${FOLDER} -name *.exe -delete
 # remove left over java stuff
 find ${FOLDER} -name *.jar -delete -o -name *.class -delete
 # remove Matlab v5 mat-file (little endian) version 0x0100

Added: trunk/packages/cellprofiler/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/patches/Makefile.patch	                        (rev 0)
+++ trunk/packages/cellprofiler/trunk/debian/patches/Makefile.patch	2013-02-24 11:41:52 UTC (rev 13079)
@@ -0,0 +1,44 @@
+Description: remove tests and added other options
+ .
+ cellprofiler (2.0~svn11717-1precise1) unstable; urgency=low
+ .
+   * update from upstream
+   * split the package into the arch-dependend cellprofiler-libs and
+     arch-independend cellprofiler
+Author: Ivo Maintz <ivo at maintz.de>
+
+---
+Last-Update: <2012-09-13>
+
+Index: cellprofiler-2.0~svn11717/Makefile
+===================================================================
+--- cellprofiler-2.0~svn11717.orig/Makefile	2012-09-13 22:57:25.158958736 +0200
++++ cellprofiler-2.0~svn11717/Makefile	2012-09-13 23:01:36.162957875 +0200
+@@ -8,7 +8,9 @@
+ 	PYTHON_COMPILER=unix
+ endif
+ 
+-all: exts tests
++all: exts tests last
++	python CellProfiler.py --build-and-exit
++	javac cellprofiler/utilities/findlibjvm.java
+ 
+ build:
+ 	mkdir build
+@@ -31,4 +33,15 @@
+ 	python cellprofiler/cpmath/setup.py build_ext -i --compiler=$(PYTHON_COMPILER)
+ 
+ tests:
+-	python -m nose.core --exe --with-nosexunit --core-target=target/xml-report $(TEST_MODULES)
++#	python -m nose.core --exe --with-nosexunit --core-target=target/xml-report $(TEST_MODULES)
++
++last:
++	python CellProfiler.py --build-and-exit
++
++clean:
++	find -name "*.so" -exec rm {} +
++	find -name "_*.c" -exec rm {} +
++	find -name "*.pyc" -exec rm {} +
++	find -type d -name build -exec rm -rf {} +
++	rm -f cellprofiler/utilities/javabridge.c
++	rm -f cellprofiler/utilities/findlibjvm.class

Deleted: trunk/packages/cellprofiler/trunk/debian/patches/remove_test.patch
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/patches/remove_test.patch	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/patches/remove_test.patch	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1,19 +0,0 @@
-Description: Disabling test for now until nosexunit is packaged
-Author: Mathieu Malaterre <mathieu.malaterre at gmail.com>
-Bug-Debian: http://bugs.debian.org/647998
-Forwarded: not-needed
-Last-Update: 2011-11-22
-
-Index: cellprofiler-2.0~svn10997/Makefile
-===================================================================
---- cellprofiler-2.0~svn10997.orig/Makefile	2011-11-08 09:45:53.000000000 +0100
-+++ cellprofiler-2.0~svn10997/Makefile	2011-11-08 09:45:59.000000000 +0100
-@@ -8,7 +8,7 @@
- 	PYTHON_COMPILER=unix
- endif
- 
--all: exts tests
-+all: exts
- 
- build:
- 	mkdir build

Modified: trunk/packages/cellprofiler/trunk/debian/patches/series
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/patches/series	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/patches/series	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1 +1,4 @@
-remove_test.patch
+hardening.patch
+java_path.patch
+version.patch
+Makefile.patch

Modified: trunk/packages/cellprofiler/trunk/debian/rules
===================================================================
--- trunk/packages/cellprofiler/trunk/debian/rules	2013-02-23 21:01:51 UTC (rev 13078)
+++ trunk/packages/cellprofiler/trunk/debian/rules	2013-02-24 11:41:52 UTC (rev 13079)
@@ -1,25 +1,17 @@
 #!/usr/bin/make -f
+# -*- makefile -*-
 
+export JAVA_HOME=$(shell readlink -f /usr/bin/javac | cut -d/ -f1-5)
+
+DEB_COMPRESS_EXCLUDE = .pdf .py .sh
+
 %:
 	dh $@ --with python2
 
-override_dh_auto_configure:
-	python CellProfiler.py --build-and-exit
+override_dh_fixperms:
+	dh_fixperms
+	find debian/ -name "*.jar" -exec chmod 644 {} + || true
+	find debian/ -name "*.png" -exec chmod 644 {} + || true
 
-override_dh_auto_clean:
-	dh_auto_clean
-	find . -name *.pyc -delete
-	find . -name *.jar -delete
-	find . -name *.o -delete
-	find . -name *.so -delete
-	# cython generated:
-	rm -f cellprofiler/cpmath/_cpmorphology2.c
-	rm -f cellprofiler/cpmath/_filter.c
-	rm -f cellprofiler/cpmath/_lapjv.c
-	rm -f cellprofiler/cpmath/_propagate.c
-	rm -f cellprofiler/cpmath/_watershed.c
-	rm -f cellprofiler/utilities/javabridge.c
-
 get-orig-source:
-	#uscan --force-download --rename
 	./debian/get-orig-source


