[med-svn] [oiffile] 01/07: Work on oiffile
Andreas Tille
tille at debian.org
Tue Dec 26 19:38:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository oiffile.
commit e6cc9e77e00128fd7bfd0a5609bf4838185c2c5f
Author: Mathieu Malaterre <malat at debian.org>
Date: Sun Jan 20 16:41:56 2013 +0000
Work on oiffile
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 27 ++++++++++++++++++++++++
debian/copyright | 37 +++++++++++++++++++++++++++++++++
debian/get-orig-source | 40 ++++++++++++++++++++++++++++++++++++
debian/oiffile.1 | 27 ++++++++++++++++++++++++
debian/oiffile.1.in | 27 ++++++++++++++++++++++++
debian/oiffile.sh | 9 ++++++++
debian/patches/new | 49 ++++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 2 ++
debian/patches/setuppy.patch | 28 +++++++++++++++++++++++++
debian/rules | 16 +++++++++++++++
debian/source/format | 1 +
debian/watch | 3 +++
14 files changed, 272 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..b5e52f1
--- /dev/null
+++ b/debian/changelog
@@ -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
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..45a4fb7
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+8
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b4a6227
--- /dev/null
+++ b/debian/control
@@ -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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..c477209
--- /dev/null
+++ b/debian/copyright
@@ -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
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..506dbee
--- /dev/null
+++ b/debian/get-orig-source
@@ -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}
diff --git a/debian/oiffile.1 b/debian/oiffile.1
new file mode 100644
index 0000000..ecd409e
--- /dev/null
+++ b/debian/oiffile.1
@@ -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).
diff --git a/debian/oiffile.1.in b/debian/oiffile.1.in
new file mode 100644
index 0000000..ecd409e
--- /dev/null
+++ b/debian/oiffile.1.in
@@ -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).
diff --git a/debian/oiffile.sh b/debian/oiffile.sh
new file mode 100755
index 0000000..0ff412c
--- /dev/null
+++ b/debian/oiffile.sh
@@ -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()
diff --git a/debian/patches/new b/debian/patches/new
new file mode 100644
index 0000000..52dce95
--- /dev/null
+++ b/debian/patches/new
@@ -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'],
+ )
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..be65756
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+setuppy.patch
+new
diff --git a/debian/patches/setuppy.patch b/debian/patches/setuppy.patch
new file mode 100644
index 0000000..0d2e053
--- /dev/null
+++ b/debian/patches/setuppy.patch
@@ -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()]
++ )],
++)
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c8964aa
--- /dev/null
+++ b/debian/rules
@@ -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
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..3af098f
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=uversionmangle=s/\.//g \
+http://githubredir.debian.net/github/malaterre/tifffile/(.*).tar.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/oiffile.git
More information about the debian-med-commit
mailing list