[med-svn] r8876 - in trunk/packages/cellprofiler: . branches branches/experimental branches/experimental/debian branches/experimental/debian/patches branches/experimental/debian/source
Mathieu Malaterre
malat-guest at alioth.debian.org
Fri Dec 9 13:03:18 UTC 2011
Author: malat-guest
Date: 2011-12-09 13:03:17 +0000 (Fri, 09 Dec 2011)
New Revision: 8876
Added:
trunk/packages/cellprofiler/branches/
trunk/packages/cellprofiler/branches/experimental/
trunk/packages/cellprofiler/branches/experimental/debian/
trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.desktop
trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.install
trunk/packages/cellprofiler/branches/experimental/debian/changelog
trunk/packages/cellprofiler/branches/experimental/debian/compat
trunk/packages/cellprofiler/branches/experimental/debian/control
trunk/packages/cellprofiler/branches/experimental/debian/copyright
trunk/packages/cellprofiler/branches/experimental/debian/docs
trunk/packages/cellprofiler/branches/experimental/debian/files
trunk/packages/cellprofiler/branches/experimental/debian/get-orig-source
trunk/packages/cellprofiler/branches/experimental/debian/patches/
trunk/packages/cellprofiler/branches/experimental/debian/patches/Makefile.patch
trunk/packages/cellprofiler/branches/experimental/debian/patches/series
trunk/packages/cellprofiler/branches/experimental/debian/postinst
trunk/packages/cellprofiler/branches/experimental/debian/prerm
trunk/packages/cellprofiler/branches/experimental/debian/rules
trunk/packages/cellprofiler/branches/experimental/debian/source/
trunk/packages/cellprofiler/branches/experimental/debian/source/format
Log:
Adding experimental branch
Added: trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.desktop
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.desktop (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.desktop 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,8 @@
+[Desktop Entry]
+Name=CellProfiler
+Comment=quantitative analysis of biological images
+Exec=/usr/bin/cellprofiler
+Icon=/usr/share/cellprofiler/CellProfilerIcon.png
+Terminal=false
+Type=Application
+Categories=Development;Science;Biology;
Added: trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.install
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.install (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/cellprofiler.install 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,22 @@
+debian/bin/cellprofiler /usr/bin/
+debian/cellprofiler.desktop /usr/share/applications/
+BatchProfiler /usr/share/cellprofiler/
+bioformats /usr/share/cellprofiler/
+cellprofiler /usr/share/cellprofiler/
+contrib /usr/share/cellprofiler/
+imagej /usr/share/cellprofiler/
+killjavabridge /usr/share/cellprofiler/
+plugins /usr/share/cellprofiler/
+CellProfiler64.iss /usr/share/cellprofiler/
+CellProfilerIcon.icns /usr/share/cellprofiler/
+CellProfilerIcon.ico /usr/share/cellprofiler/
+CellProfilerIcon_old.png /usr/share/cellprofiler/
+CellProfilerIcon.png /usr/share/cellprofiler/
+CellProfiler.iss /usr/share/cellprofiler/
+CellProfiler.py /usr/share/cellprofiler/
+TestNewBatch.py /usr/share/cellprofiler/
+cp_logo_small.png /usr/share/cellprofiler/
+cpnose.py /usr/share/cellprofiler/
+CPy.py /usr/share/cellprofiler/
+decorator.py /usr/share/cellprofiler/
+external_dependencies.py /usr/share/cellprofiler/
Added: trunk/packages/cellprofiler/branches/experimental/debian/changelog
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/changelog (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/changelog 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,12 @@
+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> Mon, 12 Sep 2011 09:56:16 +0200
Added: trunk/packages/cellprofiler/branches/experimental/debian/compat
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/compat (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/compat 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1 @@
+8
Added: trunk/packages/cellprofiler/branches/experimental/debian/control
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/control (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/control 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,36 @@
+Source: cellprofiler
+Section: science
+Priority: extra
+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>,
+ Ivo Maintz <ivo at maintz.de>
+Build-Depends: debhelper (>= 8)
+Build-Depends-Indep: 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
+Standards-Version: 3.9.2
+Homepage: http://www.cellprofiler.org
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cellprofiler/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/cellprofiler/trunk/
+
+Package: cellprofiler
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends},
+ cython,
+ default-jre | openjdk-6-jre | gcj-jre,
+ python-h5py,
+ python-libtiff,
+ python-numpy,
+ python-scipy,
+ python-matplotlib,
+ python-wxgtk2.8,
+ python-decorator,
+ python-mysqldb,
+ python-nose
+Description: quantitatively measure phenotypes from images automatically
+ 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.
+
Added: trunk/packages/cellprofiler/branches/experimental/debian/copyright
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/copyright (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/copyright 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,28 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: cellprofiler
+Source: http://www.cellprofiler.org/download.shtml
+
+Files: *
+Copyright: (c) 2003-2009 Massachusetts Institute of Technology
+ (c) 2009-2011 Broad Institute
+License: GPL-2.0+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ 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: debian/*
+Copyright: 2011 Mathieu Malaterre <mathieu.malaterre at gmail.com>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
\ No newline at end of file
Added: trunk/packages/cellprofiler/branches/experimental/debian/docs
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/docs (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/docs 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1 @@
+CellProfiler_Manual.pdf
Added: trunk/packages/cellprofiler/branches/experimental/debian/files
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/files (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/files 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1 @@
+cellprofiler_2.0~svn11691-1_amd64.deb science extra
Added: trunk/packages/cellprofiler/branches/experimental/debian/get-orig-source
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/get-orig-source (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/get-orig-source 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,29 @@
+#!/bin/sh
+set -ex
+
+PACKAGE=cellprofiler
+
+VERSION=${VERSION:-$2}
+TARFILE=${TARFILE:-$3}
+
+if [ -z ${VERSION}]; then
+VERSION=`dpkg-parsechangelog | sed -n -e 's/^Version: \(.*\)-[^-]*$/\1/p'`
+fi
+
+REVISION=`echo $VERSION | sed -e 's/^.*svn//g'`
+
+
+if [ -z ${TARFILE}]; then
+TARFILE=${PACKAGE}_${VERSION}.orig.tar.gz
+fi
+
+FOLDER=${PACKAGE}-${VERSION}
+
+svn export -r ${REVISION} https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler ${FOLDER}
+#
+find ${FOLDER} -name *.exe -delete
+
+cd ${FOLDER}
+GZIP="--best --no-name" tar czf ../../${TARFILE} .
+cd ..
+rm -rf ${FOLDER}
Added: trunk/packages/cellprofiler/branches/experimental/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/patches/Makefile.patch (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/patches/Makefile.patch 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,48 @@
+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.
+ .
+ cellprofiler (2.0-1) unstable; urgency=low
+ .
+ * Initial 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>
+
+Index: cellprofiler-2.0~svn11691/Makefile
+===================================================================
+--- cellprofiler-2.0~svn11691.orig/Makefile 2011-12-08 15:16:12.000000000 +0100
++++ cellprofiler-2.0~svn11691/Makefile 2011-12-09 09:59:58.240001727 +0100
+@@ -8,7 +8,7 @@
+ PYTHON_COMPILER=unix
+ endif
+
+-all: exts tests
++all: exts
+
+ build:
+ mkdir build
+@@ -32,3 +32,9 @@
+
+ tests:
+ python -m nose.core --exe --with-nosexunit --core-target=target/xml-report $(TEST_MODULES)
++
++clean:
++ rm -rf cellprofiler/utilities
++ rm -rf cellprofiler/cpmath
++ find . -name "*.pyc" -exec rm -f {} +
++ tar xzf ../cellprofiler_2.0.orig.tar.gz --exclude=Makefile
Added: trunk/packages/cellprofiler/branches/experimental/debian/patches/series
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/patches/series (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/patches/series 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1 @@
+Makefile.patch
Added: trunk/packages/cellprofiler/branches/experimental/debian/postinst
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/postinst (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/postinst 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,3 @@
+#!/bin/sh
+set -e
+/usr/bin/cellprofiler --build-and-exit
Added: trunk/packages/cellprofiler/branches/experimental/debian/prerm
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/prerm (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/prerm 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,5 @@
+#!/bin/sh
+set -e
+INSTALL_DIR="/usr/share/cellprofiler"
+UTILITIES="$INSTALL_DIR/cellprofiler/utilities"
+rm -f $UTILITIES/|| true
Added: trunk/packages/cellprofiler/branches/experimental/debian/rules
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/rules (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/rules 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1,22 @@
+#!/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
+
+DEB_COMPRESS_EXCLUDE := .pdf
+
+%:
+ dh $@ --with python2
+
+### this should be run after the installation, it's now in postinst ###
+#override_dh_auto_configure:
+# python CellProfiler.py --build-and-exit
+
+get-orig-source:
+ ./debian/get-orig-source
Added: trunk/packages/cellprofiler/branches/experimental/debian/source/format
===================================================================
--- trunk/packages/cellprofiler/branches/experimental/debian/source/format (rev 0)
+++ trunk/packages/cellprofiler/branches/experimental/debian/source/format 2011-12-09 13:03:17 UTC (rev 8876)
@@ -0,0 +1 @@
+3.0 (quilt)
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