debian/0000755000000000000000000000000012265554177007204 5ustar debian/changelog0000644000000000000000000000243712265552471011057 0ustar python-fabio (0.1.3-3) unstable; urgency=medium * fix the FTBFS when sphinxdoc is not installed -- Picca Frédéric-Emmanuel Wed, 15 Jan 2014 19:32:16 +0100 python-fabio (0.1.3-2) unstable; urgency=medium [kieffer] * Fix Lintian remarks * Correct compatibility with Python 2.5 [picca] * debian/control - Bump Standard-Versions to 3.9.5 (no change) - Add the python-fabio-dbg package - Add the python-fabio-doc package - Team maintained under debian-science - Build-Depends: add cython * debian/patch + 0001-forwarded-upstream-cythonize-during-the-build.patch (new) -- Picca Frédéric-Emmanuel Fri, 27 Dec 2013 09:46:21 +0100 python-fabio (0.1.3-1) unstable; urgency=low [kieffer] * New upstream version (v0.1.3) [picca] * debian/control - use the right python-all-dev version dependencies for dh_python2. - remove had coded numpy dependencies which are generated by dh_numpy. - add myself as Uploaders. - update the homepage add the VCS informations. -- Picca Frédéric-Emmanuel Sat, 02 Nov 2013 21:40:48 +0100 python-fabio (0.0.8-1) unstable; urgency=low * Initial release (Closes: #649008) -- Jerome Kieffer Fri, 18 Nov 2011 16:19:20 +0100 debian/copyright0000644000000000000000000001421712257350605011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: fabio Source: http://sourceforge.net/projects/fable/files/fabio/0.1.3/ Files: * Copyright: 2007-2009 Henning O. Sorensen & Erik Knudsen Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk 2009-2012 Jonathan P. Wright, Jerome Kieffer and Gael Goret European Synchrotron Radiation Facility 6 rue Jules Horowitz 38000 Grenoble, France License: GPL-2.0+ Files: fabio/cbfimage.py fabio/tifimage.py fabio/xsdimage.py src/byte_offset.* Copyright: 2011 Jerome Kieffer European Synchrotron Radiation Facility License: GPL-3.0+ Files: src/ccp4_pack Copyright: 1995 Jan Pieter Abrahams MRC Cambridge (UK) 2007-2009 Henning O. Sorensen & Erik Knudsen Risoe National Laboratory (DK) 2012 Jerome Kieffer and Gael Goret European Synchrotron Radiation Facility (FR) License: LGPL-3.0+ Files: src/mar345_IO.* Copyright: 2012 Jerome Kieffer and Gael Goret European Synchrotron Radiation Facility License: LGPL-3.0+ Files: fabio/TiffIO.py Copyright: 2011 V. Armando Sole European Synchrotron Radiation Facility License: LGPL-2.0+ Files: test/utilstest.py Copyright: 2011 European Synchrotron Radiation Facility License: LGPL-3.0+ Files: src/stdint.h Copyright: 2006-2008 Alexander Chemeris License: BSD Files: debian/* Copyright: 2011 Jerome Kieffer License: GPL-2.0+ 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 . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". License: GPL-3.0+ 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 3 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 . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". License: LGPL-2.0+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser 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 Lesser General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU Lesser General Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2". License: LGPL-3.0+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 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 Lesser General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU Lesser General Public License version 3 can be found in "/usr/share/common-licenses/LGPL-3". License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . 2. 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. . 3. The name of the author may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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. debian/compat0000644000000000000000000000000212235240725010366 0ustar 8 debian/python-fabio.NEWS0000644000000000000000000000400512257350605012267 0ustar Changelog ========= From FabIO-0.1.2 to FabIO-0.1.3: ................................ - Fixed a memory-leak in mar345 module - Improved support for bruker format (writer & reader) - Fixed a bug in EDF headers (very long headers) - Provide template for new file-formats - Fix a bug related to PIL in new MacOSX - Allow binary-images to be read from end From FabIO-0.1.1 to FabIO-0.1.2: ................................ - Fixed a bug in fabioimage.write (impacted all writers) - added Sphinx documentation "python setup.py build_doc" - PyLint compliance of some classes (rename, ...) - tests from installer with "python setup.py build test" From FabIO-0.1.0 to FabIO-0.1.1: ................................ - Merged Mar345 image reader and writer with cython bindings (towards python3 compliance) - Improve CBF image writing under windows - Bz2, Gzip and Flat files are managed through a common way ... classes are more (python v2.5) or less (python v2.7) overloaded - Fast EDF reading if one assumes offsets are the same between files, same for ROIs From FabIO-0.0.8 to FabIO-0.1.0: ................................ - OXD reader improved and writer implemented - Mar345 reader improved and writer implemented - CBF writer implemented - Clean-up of the code & bug fixes - Move towards python3 - Make PIL optional dependency Python3 is not yet tested but some blocking points have been identified and some fixed. From FabIO-0.0.7 to FabIO-0.0.8: ................................ - Support for Tiff using TiffIO module from V.A.Solé - Clean-up of the code & bug fixes From FabIO-0.0.6 to FabIO-0.0.7: ................................ - Support for multi-frames EDF files - Support for XML images/2D arrays used in EDNA - new method: fabio.open(filename) that is an alias for fabio.openimage.openimage(filename) From FabIO-0.0.4 to FabIO-0.0.6: ................................ - Support for CBF files from Pilatus detectors - Support for KCD files from Nonius Kappa CCD images - write EDF with their native data type (instead of uint16 by default) debian/patches/0000755000000000000000000000000012257355023010621 5ustar debian/patches/series0000644000000000000000000000011712257355023012035 0ustar 0001-forwarded-upstream-cythonize-during-the-build.patch 0002-compat_2.5.patch debian/patches/0002-compat_2.5.patch0000644000000000000000000000206712257355023014075 0ustar From: Debian Science Maintainers Date: Fri, 27 Dec 2013 20:50:24 +0100 Subject: compat_2.5 --- fabio-src/binaryimage.py | 2 +- fabio-src/templateimage.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/fabio-src/binaryimage.py b/fabio-src/binaryimage.py index fdee49b..83b41b4 100644 --- a/fabio-src/binaryimage.py +++ b/fabio-src/binaryimage.py @@ -2,7 +2,7 @@ # coding: utf8 # Get ready for python3: -from __future__ import with_statement, print_function +from __future__ import with_statement __doc__ = """ Authors: Gael Goret, Jerome Kieffer, ESRF, France Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr diff --git a/fabio-src/templateimage.py b/fabio-src/templateimage.py index c6dda06..627e26b 100644 --- a/fabio-src/templateimage.py +++ b/fabio-src/templateimage.py @@ -34,7 +34,7 @@ # their data into another format # Get ready for python3: -from __future__ import with_statement, print_function +from __future__ import with_statement __doc__ = """ Template for FabIO debian/patches/0001-forwarded-upstream-cythonize-during-the-build.patch0000644000000000000000000000414212257355023023207 0ustar From: =?utf-8?q?Picca_Fr=C3=A9d=C3=A9ric-Emmanuel?= Date: Fri, 27 Dec 2013 19:45:08 +0100 Subject: forwarded upstream cythonize during the build --- setup.py | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index ebae18c..221123f 100644 --- a/setup.py +++ b/setup.py @@ -13,21 +13,33 @@ except ImportError: from distutils.core import Extension, Command from numpy.distutils.misc_util import get_numpy_include_dirs +# Check for Cython and use it if it is available +USE_CYTHON = False +try: + from Cython.Build import cythonize + USE_CYTHON = True +except ImportError: + pass +ext = ".pyx" if USE_CYTHON else ".c" cf_backend = Extension('cf_io', include_dirs=get_numpy_include_dirs(), sources=['src/cf_iomodule.c', 'src/columnfile.c']) byteOffset_backend = Extension("byte_offset", include_dirs=get_numpy_include_dirs(), - sources=['src/byte_offset.c']) + sources=['src/byte_offset' + ext]) mar345_backend = Extension('mar345_IO', include_dirs=get_numpy_include_dirs(), - sources=['src/mar345_IO.c', + sources=['src/mar345_IO' + ext, 'src/ccp4_pack.c', ]) +extensions = [cf_backend, byteOffset_backend, mar345_backend] +if USE_CYTHON: + extensions = cythonize(extensions) + version = [eval(l.split("=")[1]) for l in open(op.join(op.dirname(op.abspath(__file__)), "fabio-src", "__init__.py")) if l.strip().startswith("version")][0] @@ -87,7 +99,7 @@ setup(name='fabio', url="http://fable.wiki.sourceforge.net/fabio", download_url="http://sourceforge.net/projects/fable/files/fabio/0.1.2", ext_package="fabio", - ext_modules=[mar345_backend, cf_backend, byteOffset_backend], + ext_modules=extensions, packages=["fabio"], package_dir={"fabio": "fabio-src" }, test_suite="test", debian/watch0000644000000000000000000000016512257350605010226 0ustar https://sourceforge.net/projects/fable/files/fabio/(\d\S*)/fabio-(\d\S*)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) debian/control0000644000000000000000000000613312257350602010576 0ustar Source: python-fabio Maintainer: Debian Science Maintainers Uploaders: Jerome Kieffer , Picca Frédéric-Emmanuel Section: science Priority: extra Build-Depends: cython, cython-dbg, debhelper (>= 9), python-all-dev, python-all-dbg, python-numpy, python-numpy-dbg, python-setuptools Build-Depends-Indep: python-imaging, python-lxml, python-sphinx (>= 1.0.7+dfsg-1~) Standards-Version: 3.9.5 Vcs-Browser: http://git.epn-campus.eu/projects/fabio/repository Vcs-Git: git://git@git.epn-campus.eu:python-fabio Homepage: http://git.epn-campus.eu/projects/fabio X-Python-Version: >= 2.5 Package: python-fabio Architecture: any Section: python Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends} Recommends: python-imaging, python-lxml, python-matplotlib Suggests: pyfai, pymca, python-fabio-doc Description: I/O library for images produced by 2D X-ray detector FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats) . This is the Python 2 version of the package. Package: python-fabio-doc Architecture: all Section: doc Depends: ${misc:Depends}, ${sphinxdoc:Depends} Description: I/O library for images produced by 2D X-ray detector (common documentation) FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats) . This is the common documentation package. Package: python-fabio-dbg Architecture: any Section: debug Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends}, python-fabio (= ${binary:Version}) Recommends: python-dbg, python-imaging-dbg, python-lxml-dbg, python-matplotlib-dbg Description: I/O library for images produced by 2D X-ray detector (debug ext) FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats) . This package contains the extension built for the Python 2 debug interpreter. debian/rules0000755000000000000000000000203712265551732010260 0ustar #!/usr/bin/make -f PY2VERS = $(shell pyversions -r -v) # to build without sphinxdoc WITH_SPHINXDOC = $(shell if [ -x /usr/bin/dh_sphinxdoc ]; then echo "--with sphinxdoc"; fi) %: dh $@ --with python2 $(WITH_SPHINXDOC) override_dh_clean: # remove the cython generated files distributed by upstream rm -f $(patsubst %.pyx,%.c,$(wildcard src/*.pyx)) rm -rf build/sphinx rm -rf *.egg-info dh_clean override_dh_auto_build-indep: dh_auto_build # build the documentation set -e -x;\ for py in $(PY2VERS); do \ env http_proxy='localhost' python$$py setup.py build_doc ;\ done override_dh_install: dh_numpy # Install everything excluding the *_d.so debug extensions to python-foo dh_install -X"*_d.so" "debian/tmp/*" -p python-fabio # Install the debug extensions to python-foo-dbg dh_install "debian/tmp/usr/lib/python*/*-packages/fabio/*_d.so" -p python-fabio-dbg # Continue with regular dh_install dh_install override_dh_installdocs-indep: # install the documentation dh_installdocs "build/sphinx/html" -p python-fabio-doc debian/source/0000755000000000000000000000000012234276440010472 5ustar debian/source/format0000644000000000000000000000001412234276440011700 0ustar 3.0 (quilt)