[med-svn] r12807 - in trunk/packages: . oiffile oiffile/trunk oiffile/trunk/debian oiffile/trunk/debian/patches oiffile/trunk/debian/source

Mathieu Malaterre malat at alioth.debian.org
Sun Jan 20 16:41:56 UTC 2013 

Author: malat
Date: 2013-01-20 16:41:56 +0000 (Sun, 20 Jan 2013)
New Revision: 12807

Added:
   trunk/packages/oiffile/
   trunk/packages/oiffile/trunk/
   trunk/packages/oiffile/trunk/debian/
   trunk/packages/oiffile/trunk/debian/changelog
   trunk/packages/oiffile/trunk/debian/compat
   trunk/packages/oiffile/trunk/debian/control
   trunk/packages/oiffile/trunk/debian/copyright
   trunk/packages/oiffile/trunk/debian/get-orig-source
   trunk/packages/oiffile/trunk/debian/oiffile.1
   trunk/packages/oiffile/trunk/debian/oiffile.1.in
   trunk/packages/oiffile/trunk/debian/oiffile.sh
   trunk/packages/oiffile/trunk/debian/patches/
   trunk/packages/oiffile/trunk/debian/patches/new
   trunk/packages/oiffile/trunk/debian/patches/series
   trunk/packages/oiffile/trunk/debian/patches/setuppy.patch
   trunk/packages/oiffile/trunk/debian/rules
   trunk/packages/oiffile/trunk/debian/source/
   trunk/packages/oiffile/trunk/debian/source/format
   trunk/packages/oiffile/trunk/debian/watch
Log:
Work on oiffile

Added: trunk/packages/oiffile/trunk/debian/changelog
===================================================================
--- trunk/packages/oiffile/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/changelog	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,5 @@
+oiffile (20130118-1) unstable; urgency=low
+
+  * Initial Debian Upload (Closes: #)
+
+ -- Mathieu Malaterre <mathieu.malaterre at gmail.com>  Sun, 13 Nov 2011 19:41:37 +0100

Added: trunk/packages/oiffile/trunk/debian/compat
===================================================================
--- trunk/packages/oiffile/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/compat	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1 @@
+8

Added: trunk/packages/oiffile/trunk/debian/control
===================================================================
--- trunk/packages/oiffile/trunk/debian/control	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/control	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,27 @@
+Source: oiffile
+Priority: optional
+Section: python
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Mathieu Malaterre <malat at debian.org>
+Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6.6-3~)
+X-Python-Version: >= 2.6
+Standards-Version: 3.9.4
+Homepage: http://www.lfd.uci.edu/~gohlke/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/oiffile/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/oiffile/trunk/
+
+Package: oiffile
+Architecture: any
+Depends: ${python:Depends}, ${misc:Depends}, ${shlibs:Depends}
+Provides: ${python:Provides}
+Description: read image and metadata from TIFF, STK, LSM, OME-TIFF and FluoView files
+ Only a subset of the TIFF specification is supported, mainly uncompressed and
+ losslessly compressed 1-32 bit integer as well as 32 and 64-bit float images,
+ which are commonly used in scientific imaging.
+ .
+ This tool is implemented to support TIFF with custom extensions, namely:
+  * STK (MetaMorph)
+  * LSM (Carl Zeiss MicroImaging)
+ .
+ Currently only primary info records are read for STK, FluoView, and NIH image
+ formats.

Added: trunk/packages/oiffile/trunk/debian/copyright
===================================================================
--- trunk/packages/oiffile/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/copyright	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,37 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: tifffile
+Source: http://www.lfd.uci.edu/~gohlke/
+
+Files: *
+Copyright: © 2008-2011, Christoph Gohlke,
+ © 2008-2011, The Regents of the University of California
+ Produced by the Laboratory for Fluorescence Dynamics.
+License: BSD
+ 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 copyright holders nor the names of any
+   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: debian/*
+Copyright: © 2011 Mathieu Malaterre <malat at debian.org>
+License: BSD
+ Same as above

Added: trunk/packages/oiffile/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/oiffile/trunk/debian/get-orig-source	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/get-orig-source	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,40 @@
+#!/bin/sh
+set -e
+
+PACKAGE=oiffile
+
+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}
+
+mkdir ${FOLDER}
+cd ${FOLDER}
+# http://bugs.debian.org/692752
+#wget -c http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html
+curl -s -o oiffile.py.html "http://www.lfd.uci.edu/~gohlke/code/oiffile.py.html"
+links -dump oiffile.py.html > oiffile.py
+sed -i -e 's/^ //g' oiffile.py
+rm *.html
+
+# compute version:
+PYVERSION=`grep "^:Version:" oiffile.py | cut -d' ' -f2 | sed -e 's/\.//g'`
+if [ "$PYVERSION" != "$VERSION" ]; then
+  echo "$PYVERSION and $VERSION are not compatible"
+  exit 1
+fi
+cd ..
+
+GZIP="--best --no-name" tar czf ${TARFILE} ${FOLDER}
+rm -rf ${FOLDER}


Property changes on: trunk/packages/oiffile/trunk/debian/get-orig-source
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/oiffile/trunk/debian/oiffile.1
===================================================================
--- trunk/packages/oiffile/trunk/debian/oiffile.1	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/oiffile.1	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,27 @@
+[NAME]
+tifffile \- Read image and meta-data from TIFF, STK, LSM, OME-TIFF, and FluoView files.
+
+[SYNOPSIS]
+.B tifffile
+.RI [ options ] " files" ...
+
+[DESCRIPTION]
+Only a subset of the TIFF specification is supported, mainly uncompressed and
+losslessly compressed 1-32 bit integer as well as 32 and 64-bit float
+images, which are commonly used in scientific imaging.
+
+TIFF, the Tagged Image File Format, is under the control of Adobe Systems.
+STK and LSM are TIFF with custom extensions used by MetaMorph respectively
+Carl Zeiss MicroImaging. Currently only primary info records are read for
+STK, FluoView, and NIH image formats.
+
+[AUTHOR]
+Christoph Gohlke <http://www.lfd.uci.edu/~gohlke
+Laboratory for Fluorescence Dynamics, University of California, Irvine
+
+This  manual  page was written by Mathieu Malaterre <malat at debian.org> for
+the Debian GNU/Linux system, but may be used by others.
+
+[SEE ALSO]
+.BR tiffdump (1),
+.BR tiffinfo (1).

Added: trunk/packages/oiffile/trunk/debian/oiffile.1.in
===================================================================
--- trunk/packages/oiffile/trunk/debian/oiffile.1.in	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/oiffile.1.in	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,27 @@
+[NAME]
+tifffile \- Read image and meta-data from TIFF, STK, LSM, OME-TIFF, and FluoView files.
+
+[SYNOPSIS]
+.B tifffile
+.RI [ options ] " files" ...
+
+[DESCRIPTION]
+Only a subset of the TIFF specification is supported, mainly uncompressed and
+losslessly compressed 1-32 bit integer as well as 32 and 64-bit float
+images, which are commonly used in scientific imaging.
+
+TIFF, the Tagged Image File Format, is under the control of Adobe Systems.
+STK and LSM are TIFF with custom extensions used by MetaMorph respectively
+Carl Zeiss MicroImaging. Currently only primary info records are read for
+STK, FluoView, and NIH image formats.
+
+[AUTHOR]
+Christoph Gohlke <http://www.lfd.uci.edu/~gohlke
+Laboratory for Fluorescence Dynamics, University of California, Irvine
+
+This  manual  page was written by Mathieu Malaterre <malat at debian.org> for
+the Debian GNU/Linux system, but may be used by others.
+
+[SEE ALSO]
+.BR tiffdump (1),
+.BR tiffinfo (1).

Added: trunk/packages/oiffile/trunk/debian/oiffile.sh
===================================================================
--- trunk/packages/oiffile/trunk/debian/oiffile.sh	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/oiffile.sh	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,9 @@
+#!/usr/bin/env python
+
+import oiffile
+import numpy
+
+if __name__ == "__main__":
+    import doctest
+    numpy.set_printoptions(suppress=True, precision=5)
+    doctest.testmod()


Property changes on: trunk/packages/oiffile/trunk/debian/oiffile.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/oiffile/trunk/debian/patches/new
===================================================================
--- trunk/packages/oiffile/trunk/debian/patches/new	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/patches/new	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,49 @@
+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.
+ .
+ oiffile (20130118-1) unstable; urgency=low
+ .
+   * Initial Debian Upload (Closes: #)
+Author: Mathieu Malaterre <mathieu.malaterre at gmail.com>
+
+---
+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>
+
+--- oiffile-20130118.orig/setup.py
++++ oiffile-20130118/setup.py
+@@ -7,17 +7,12 @@ Usage:: ``python setup.py build_ext --in
+ from distutils.core import setup, Extension
+ import numpy
+ 
+-setup(name='_tifffile',
++setup(name='oiffile',
+     version="2013.01.18",
+-    description="Reads image and meta-data from many bio-scientific formats such as plain TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, GEL, and FluoView files",
+-    keywords="tiff,stk,lsm",
++    description="Reads image and meta-data from Olympus(r) OIF and OIB microscopy files, and also converts from OIB to OIF.",
++    keywords="oif,oib",
+     author="Christoph Gohlke",
+     url="http://www.lfd.uci.edu/~gohlke/",
+     license="BSD",
+-    py_modules=['tifffile'],
+-    ext_modules=[
+-      Extension(
+-        '_tifffile', ['tifffile.c'],
+-        include_dirs=[numpy.get_include()]
+-        )],
++    py_modules=['oiffile'],
+ )

Added: trunk/packages/oiffile/trunk/debian/patches/series
===================================================================
--- trunk/packages/oiffile/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/patches/series	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,2 @@
+setuppy.patch
+new

Added: trunk/packages/oiffile/trunk/debian/patches/setuppy.patch
===================================================================
--- trunk/packages/oiffile/trunk/debian/patches/setuppy.patch	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/patches/setuppy.patch	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,28 @@
+Index: tifffile-20130118/setup.py
+===================================================================
+--- /dev/null	1970-01-01 00:00:00.000000000 +0000
++++ tifffile-20130118/setup.py	2013-01-20 16:54:05.050851246 +0100
+@@ -0,0 +1,23 @@
++"""A Python script to build the _tifffile extension module.
++
++Usage:: ``python setup.py build_ext --inplace``
++
++"""
++
++from distutils.core import setup, Extension
++import numpy
++
++setup(name='_tifffile',
++    version="2013.01.18",
++    description="Reads image and meta-data from many bio-scientific formats such as plain TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, ImageJ, GEL, and FluoView files",
++    keywords="tiff,stk,lsm",
++    author="Christoph Gohlke",
++    url="http://www.lfd.uci.edu/~gohlke/",
++    license="BSD",
++    py_modules=['tifffile'],
++    ext_modules=[
++      Extension(
++        '_tifffile', ['tifffile.c'],
++        include_dirs=[numpy.get_include()]
++        )],
++)

Added: trunk/packages/oiffile/trunk/debian/rules
===================================================================
--- trunk/packages/oiffile/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/rules	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+%:
+	dh $@ --with python2
+
+override_dh_install:
+	install -D -m0755 $(CURDIR)/debian/oiffile.sh $(CURDIR)/debian/oiffile/usr/bin/oiffile
+
+override_dh_installman:
+	dh_installman debian/oiffile.1
+
+debian/oiffile.1: debian/oiffile.1.in
+	help2man --include=debian/oiffile.1.in --output=debian/oiffile.1 --no-info oiffile
+
+get-orig-source:
+	./debian/get-orig-source


Property changes on: trunk/packages/oiffile/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/oiffile/trunk/debian/source/format
===================================================================
--- trunk/packages/oiffile/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/source/format	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/oiffile/trunk/debian/watch
===================================================================
--- trunk/packages/oiffile/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/oiffile/trunk/debian/watch	2013-01-20 16:41:56 UTC (rev 12807)
@@ -0,0 +1,3 @@
+version=3
+opts=uversionmangle=s/\.//g \
+http://githubredir.debian.net/github/malaterre/tifffile/(.*).tar.gz

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