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 <[email protected]> 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 <[email protected]> +Uploaders: Mathieu Malaterre <[email protected]> +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 <[email protected]> +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 <[email protected]> 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 <[email protected]> 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 <[email protected]> + +--- +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
