[med-svn] r15249 - in trunk/packages/tifffile/trunk/debian: . patches

Fri Nov 22 18:46:40 UTC 2013

Author: malat
Date: 2013-11-22 18:46:40 +0000 (Fri, 22 Nov 2013)
New Revision: 15249

Added:
   trunk/packages/tifffile/trunk/debian/patches/bug730166.patch
Modified:
   trunk/packages/tifffile/trunk/debian/changelog
   trunk/packages/tifffile/trunk/debian/control
   trunk/packages/tifffile/trunk/debian/patches/series
   trunk/packages/tifffile/trunk/debian/patches/setuppy.patch
   trunk/packages/tifffile/trunk/debian/tifffile.1
   trunk/packages/tifffile/trunk/debian/watch
Log:
prepare next upload

Modified: trunk/packages/tifffile/trunk/debian/changelog
===================================================================

--- trunk/packages/tifffile/trunk/debian/changelog	2013-11-22 15:29:31 UTC (rev 15248)
+++ trunk/packages/tifffile/trunk/debian/changelog	2013-11-22 18:46:40 UTC (rev 15249)
@@ -1,3 +1,18 @@
+tifffile (20131103-1) unstable; urgency=low
+
+  * New upstream
+  * Add support for MicroManager files
+  * Fix tifffile when no option is passed. Closes: #730166
+
+ -- Mathieu Malaterre <malat at debian.org>  Thu, 21 Nov 2013 18:05:24 +0100
+
+tifffile (20130502-1) unstable; urgency=low
+
+  * New upstream
+  * Upload to sid
+
+ -- Mathieu Malaterre <malat at debian.org>  Tue, 21 May 2013 11:01:48 +0200
+
 tifffile (20130118-1) experimental; urgency=low
 
   * New upstream

Modified: trunk/packages/tifffile/trunk/debian/control
===================================================================
--- trunk/packages/tifffile/trunk/debian/control	2013-11-22 15:29:31 UTC (rev 15248)
+++ trunk/packages/tifffile/trunk/debian/control	2013-11-22 18:46:40 UTC (rev 15249)
@@ -3,7 +3,7 @@
 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~), python-numpy (>= 1.6.2)
+Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6.6-3~), python-numpy (>= 1:1.7.1)
 X-Python-Version: >= 2.6
 Standards-Version: 3.9.4
 Homepage: http://www.lfd.uci.edu/~gohlke/
@@ -13,18 +13,23 @@
 Package: python-tifffile
 Architecture: any
 Depends: ${python:Depends}, ${misc:Depends}, ${shlibs:Depends}, python-importlib
-Recommends: python-matplotlib (>= 1.2)
+Recommends: python-matplotlib (>= 1.3)
 Provides: ${python:Provides}
 Replaces: tifffile
 Conflicts: tifffile
-Description: read image and metadata from TIFF, STK, LSM, OME-TIFF and FluoView files
+Description: Read and write image data from and to TIFF files
+ Image and meta-data can be read from TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH,
+ ImageJ, MicroManager, FluoView, SEQ and GEL 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.
+ losslessly compressed 2**(0 to 6) bit integer, 16, 32 and 64-bit float,
+ grayscale and RGB(A) images, which are commonly used in bio-scientific imaging.
+ Specifically, reading JPEG/CCITT compressed image data or EXIF/IPTC/GPS/XMP
+ meta-data is not implemented. Only primary info records are read for STK,
+ FluoView, MicroManager, and NIH image formats.
  .
- 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.
+ TIFF, the Tagged Image File Format, is under the control of Adobe Systems.
+ BigTIFF allows for files greater than 4 GB. STK, LSM, FluoView, SEQ, GEL, and
+ OME-TIFF, are custom extensions defined by MetaMorph, Carl Zeiss MicroImaging,
+ Olympus, Media Cybernetics, Molecular Dynamics, and the Open Microscopy
+ Environment consortium respectively.

Added: trunk/packages/tifffile/trunk/debian/patches/bug730166.patch
===================================================================
--- trunk/packages/tifffile/trunk/debian/patches/bug730166.patch	                        (rev 0)
+++ trunk/packages/tifffile/trunk/debian/patches/bug730166.patch	2013-11-22 18:46:40 UTC (rev 15249)
@@ -0,0 +1,17 @@
+Description: AttributeError: 'NoneType' object has no attribute 'group'
+Author: Philipp Kern <pkern at debian.org>
+Bug-Debian: http://bugs.debian.org/730166
+Forwarded: http://bugs.debian.org/730166#19
+Reviewed-By: Mathieu Malaterre <malat at debian.org>
+
+--- tifffile-20131103.orig/tifffile.py
++++ tifffile-20131103/tifffile.py
+@@ -3124,7 +3124,7 @@ def main(argv=None):
+     search_doc = lambda r, d: re.search(r, __doc__).group(1) if __doc__ else d
+     parser = optparse.OptionParser(
+         usage="usage: %prog [options] path",
+-        description=search_doc("\n\n([^|]*?)\n\n", ''),
++        description=search_doc("^([^\n]+)", ""),
+         version="%%prog %s" % search_doc(":Version: (.*)", "Unknown"))
+     opt = parser.add_option
+     opt('-p', '--page', dest='page', type='int', default=-1,

Modified: trunk/packages/tifffile/trunk/debian/patches/series
===================================================================
--- trunk/packages/tifffile/trunk/debian/patches/series	2013-11-22 15:29:31 UTC (rev 15248)
+++ trunk/packages/tifffile/trunk/debian/patches/series	2013-11-22 18:46:40 UTC (rev 15249)
@@ -1 +1,2 @@
 setuppy.patch
+bug730166.patch

Modified: trunk/packages/tifffile/trunk/debian/patches/setuppy.patch
===================================================================
--- trunk/packages/tifffile/trunk/debian/patches/setuppy.patch	2013-11-22 15:29:31 UTC (rev 15248)
+++ trunk/packages/tifffile/trunk/debian/patches/setuppy.patch	2013-11-22 18:46:40 UTC (rev 15249)
@@ -13,7 +13,7 @@
 +import numpy
 +
 +setup(name='_tifffile',
-+    version="2013.01.18",
++    version="2013.11.03",
 +    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",

Modified: trunk/packages/tifffile/trunk/debian/tifffile.1
===================================================================
--- trunk/packages/tifffile/trunk/debian/tifffile.1	2013-11-22 15:29:31 UTC (rev 15248)
+++ trunk/packages/tifffile/trunk/debian/tifffile.1	2013-11-22 18:46:40 UTC (rev 15249)
@@ -1,5 +1,5 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
-.TH TIFFFILE "1" "January 2013" "tifffile 2013.01.18" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
+.TH TIFFFILE "1" "November 2013" "tifffile 2013.11.03" "User Commands"
 .SH NAME
 tifffile \- Read image and meta-data from TIFF, STK, LSM, OME-TIFF, and FluoView files.
 .SH SYNOPSIS
@@ -15,13 +15,7 @@
 Carl Zeiss MicroImaging. Currently only primary info records are read for
 STK, FluoView, and NIH image formats.
 .PP
-Image and meta\-data can be read from TIFF, BigTIFF, OME\-TIFF, STK, LSM, NIH,
-ImageJ, FluoView, SEQ and GEL files. Only a subset of the TIFF specification
-is supported, mainly uncompressed and losslessly compressed 2**(0 to 6) bit
-integer, 16, 32 and 64\-bit float, grayscale and RGB(A) images, which are
-commonly used in bio\-scientific imaging. Specifically, reading JPEG/CCITT
-compressed image data or EXIF/IPTC/GPS/XMP meta\-data is not implemented. Only
-primary info records are read for STK, FluoView, and NIH image formats.
+Read and write image data from and to TIFF files.
 .SH OPTIONS
 .TP
 \fB\-\-version\fR

Modified: trunk/packages/tifffile/trunk/debian/watch
===================================================================
--- trunk/packages/tifffile/trunk/debian/watch	2013-11-22 15:29:31 UTC (rev 15248)
+++ trunk/packages/tifffile/trunk/debian/watch	2013-11-22 18:46:40 UTC (rev 15249)
@@ -1,6 +1,4 @@
 version=3
-#http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html ^:Version:(.*)$
-#opts="uversionmangle=s/^/tifffile_/,dversionmangle=s/\./tifffile_/" \
-#opts=uversionmangle=s/^/tifffile_/,dversionmangle=s/\.//g \
-opts=uversionmangle=s/\.//g \
-http://githubredir.debian.net/github/malaterre/tifffile/(.*).tar.gz
+opts=uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha|b|a)\d*)$/$1~$2/,\
+dversionmangle=s/\+(debian|dfsg|ds|deb)\d*$//;s/^(\d{4})(\d\d)(\d\d)$/$1.$2.$3/ \
+https://github.com/malaterre/tifffile/tags .*/(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))


