debian/0000755000000000000000000000000011772653246007203 5ustar debian/source/0000755000000000000000000000000011772653246010503 5ustar debian/source/format0000644000000000000000000000001411772653246011711 0ustar 3.0 (quilt) debian/source/options0000644000000000000000000000026611772653246012125 0ustar # ignore changes to the commit info file, since it will always have the # shasum of the release tag and the repository version does not. extend-diff-ignore = nibabel/COMMIT_INFO.txt debian/watch0000644000000000000000000000025511772653246010236 0ustar # Compulsory line, this is a version 3 file version=3 opts="filenamemangle=s/.*\/(.*)/nibabel-$1\.tar\.gz/" \ http://github.com/nipy/nibabel/tags .*tarball/(\d[\d\.a-z]+) debian/patches/0000755000000000000000000000000011772653246010632 5ustar debian/patches/series0000644000000000000000000000001711772653246012045 0ustar no_doc_sources debian/patches/lenny-dsc-patch_numpy_testing0000644000000000000000000000526611772653246016544 0ustar Description: Disable the unit tests on Debian lenny, because they need NumPy 1.2 which is not available. Forwarded: not-needed Author: Michael Hanke diff --git a/nibabel/info.py b/nibabel/info.py index d05485f..081d6fb 100644 --- a/nibabel/info.py +++ b/nibabel/info.py @@ -88,7 +88,7 @@ nibabel distribution. """ # versions for dependencies -NUMPY_MIN_VERSION='1.2' +NUMPY_MIN_VERSION='1.0' PYDICOM_MIN_VERSION='0.9.5' # Main setup parameters diff --git a/debian/python-nibabel-doc.docs b/debian/python-nibabel-doc.docs index 6d28621..e69de29 100644 --- a/debian/python-nibabel-doc.docs +++ b/debian/python-nibabel-doc.docs @@ -1 +0,0 @@ -build/html diff --git a/debian/rules b/debian/rules index e930b26..f75e5ba 100755 --- a/debian/rules +++ b/debian/rules @@ -8,21 +8,14 @@ override_dh_auto_build: dh_auto_build - # and docs - $(MAKE) htmldoc - # but remove jquery copy (later on link to Debian's version) - -rm build/html/_static/jquery.js - # objects inventory is of no use for the package - -rm build/html/objects.inv - # also doc source files only consume space - -rm -r build/html/_sources + # and docs -- nope on lenny since it needs numpy 1.2 # enable when we believe that the tests should pass override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) for buildver in $(shell pyversions -vr); do \ - echo "I: Running NiBabel unittests using python$$buildver"; \ - $(MAKE) unittest PYTHON=python$$buildver || exit 1 ;\ + echo "I: Disabled NiBabel unittests using python$$buildver"; \ + #$(MAKE) unittest PYTHON=python$$buildver || exit 1 ;\ done endif @@ -31,11 +24,6 @@ endif override_dh_compress: dh_compress -X.py -X.html -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -X.par -X.bin -override_dh_installman: - PYTHONPATH=build/lib:$(PYTHONPATH) help2man -N \ - -n 'convert PARREC image to NIfTI' bin/parrec2nii > build/parrec2nii.1 - dh_installman build/parrec2nii.1 - override_dh_clean: $(MAKE) clean dh_clean diff --git a/debian/control b/debian/control index e43d240..6921705 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Section: python Priority: extra Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko -Build-Depends: debhelper (>= 7.2.18), python-all (>= 2.5), python-support (>= 0.6), python-numpy (>= 1.2), python-nose, python-scipy, help2man, python-sphinx +Build-Depends: debhelper (>= 7.2.18), python-all (>= 2.5), python-support (>= 0.6), python-numpy (>= 1), python-nose, python-scipy Standards-Version: 3.9.2 Homepage: http://nipy.sourceforge.net/nibabel Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/pynifti.git debian/patches/no_doc_sources0000644000000000000000000000124511772653246013563 0ustar Description: Do not put links to source documention source in HTML files Documentation source files are not shipped in the binary package, because the are not very useful and occupy space, hence these links would be broken. Forwarded: not-needed Author: Michael Hanke --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -201,7 +201,7 @@ #html_split_index = False # If true, links to the reST sources are added to the pages. -html_show_sourcelink = True +html_show_sourcelink = False # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the debian/changelog0000644000000000000000000000354711772653246011066 0ustar nibabel (1.2.2-1) unstable; urgency=low * New upstream bugfix release - addresses import and test failures on power7 (powerpc) causing FTBFS of nipy. -- Yaroslav Halchenko Wed, 27 Jun 2012 14:52:08 -0400 nibabel (1.2.1-1) unstable; urgency=low * New upstream bugfix release - new tools (nib-dicomfs, nib-nifti-dx) -- Yaroslav Halchenko Thu, 14 Jun 2012 00:15:09 -0400 nibabel (1.2.0-1) unstable; urgency=low * New upstream release: bugfixes, support for new formats (Freesurfer, ECAT, etc), nib-ls tool. * debian/copyright - corrected reference to the format specs - points to github's repository as the origin of sources - removed lightunit license/copyright -- removed upstream - added netcdf module license/copyright terms * debian/control - added python-fuse to Recommends and Build-Depends for dicomfs - boosted policy compliance to 3.9.3 (no further changes) * debian/watch - adjusted to download numbered tag -- Yaroslav Halchenko Sun, 06 May 2012 12:58:22 -0400 nibabel (1.1.0-1) unstable; urgency=low * New upstream release: better gifti and trackvis support, bugfixes. -- Yaroslav Halchenko Wed, 04 May 2011 16:44:55 -0400 nibabel (1.0.2-1) unstable; urgency=low * Fresh bugfix upstream release * debian/copyright: - changes to confirm to DEP5 rev 174 - added myself - updated years * debian/control: - boosted policy compliance to 3.9.2 (no changes) - purged DM-Upload-Allowed (no need any more) - slight tune up of the long description -- Yaroslav Halchenko Thu, 28 Apr 2011 10:27:22 -0400 nibabel (1.0.0-1) unstable; urgency=low * Initial release (Closes: #600275). -- Michael Hanke Fri, 15 Oct 2010 08:20:14 -0400 debian/copyright0000644000000000000000000000674711772653246011154 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: nibabel Upstream-Contact: nipy-devel@neuroimaging.scipy.org Source: https://github.com/nipy/nibabel Files: * Copyright: 2006-2011, Michael Hanke 2009-2012, Matthew Brett 2010-2011, Stephan Gerhard 2011, Christian Haselgrove 2010-2011, Jarrod Millman 2011-2012, Yaroslav Halchenko License: Expat Files: doc/sphinxext/autosummary/* Copyright: 2007-2009, Stefan van der Walt and Sphinx team License: BSD-3 Files: nibabel/externals/*netcdf* Copyright: 1999-2010, SciPy Developers License: BSD-3 Files: debian/* Copyright: 2006-2010, Michael Hanke 2011, Yaroslav Halchenko License: Expat License: BSD-3 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . a. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. b. 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. c. Neither the name of the Enthought nor the names of its 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 REGENTS 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. License: Expat Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. debian/python-nibabel-doc.links0000644000000000000000000000013611772653246013723 0ustar usr/share/javascript/jquery/jquery.js usr/share/doc/python-nibabel-doc/html/_static/jquery.js debian/rules0000755000000000000000000000313211772653246010262 0ustar #!/usr/bin/make -f # -*- mode: makefile; coding: utf-8 -*- # one ring to rule them all ... %: # need to enforce distutils, since we also have a makefile dh $@ --buildsystem=python_distutils --builddirectory=build override_dh_auto_build: dh_auto_build # and docs $(MAKE) htmldoc # but remove jquery copy (later on link to Debian's version) -rm build/html/_static/jquery.js # objects inventory is of no use for the package -rm build/html/objects.inv # also doc source files only consume space -rm -r build/html/_sources # enable when we believe that the tests should pass override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) for buildver in $(shell pyversions -vr); do \ echo "I: Running NiBabel unittests using python$$buildver"; \ $(MAKE) unittest PYTHON=python$$buildver || exit 1 ;\ done endif ## immediately useable documentation ## and exemplar data (they are small excerpts anyway) override_dh_compress: dh_compress -X.py -X.html -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -X.par -X.bin override_dh_installman: PYTHONPATH=build/lib:$(PYTHONPATH) help2man -N \ -n 'convert PARREC image to NIfTI' bin/parrec2nii > build/parrec2nii.1 PYTHONPATH=build/lib:$(PYTHONPATH) help2man -N \ -n 'FUSE filesystem on top of a directory with DICOMs' bin/nib-dicomfs > build/nib-dicomfs.1 PYTHONPATH=build/lib:$(PYTHONPATH) help2man -N \ -n "'ls' for neuroimaging files" bin/nib-ls > build/nib-ls.1 PYTHONPATH=build/lib:$(PYTHONPATH) help2man -N \ -n "header diagnostic tool" bin/nib-nifti-dx > build/nib-nifti-dx.1 dh_installman build/*.1 override_dh_clean: $(MAKE) clean dh_clean debian/python-nibabel-doc.docs0000644000000000000000000000001311772653246013525 0ustar build/html debian/gbp.conf0000644000000000000000000000036711772653246010630 0ustar [DEFAULT] # the default branch for upstream sources: upstream-branch = master # the default branch for the debian patch: debian-branch = dist/debian/proper # the default tag formats used: upstream-tag = %(version)s debian-tag = debian/%(version)s debian/pycompat0000644000000000000000000000000211772653246010752 0ustar 2 debian/python-nibabel.install0000644000000000000000000000002611772653246013504 0ustar debian/tmp/usr/* usr/ debian/control0000644000000000000000000000402111772653246010603 0ustar Source: nibabel Section: python Priority: extra Maintainer: NeuroDebian Team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.2.18), python-all (>= 2.5), python-support (>= 0.6), python-numpy (>= 1.2), python-nose, python-scipy, help2man, python-sphinx, python-fuse Standards-Version: 3.9.3 Homepage: http://nipy.sourceforge.net/nibabel Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/pynifti.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/pynifti.git XS-Python-Version: >= 2.5 Package: python-nibabel Architecture: all Depends: ${misc:Depends}, ${python:Depends}, python-numpy, python-scipy Recommends: python-dicom, python-fuse Suggests: python-nibabel-doc Provides: ${python:Provides} XB-Python-Version: ${python:Versions} Description: Python bindings to various neuroimaging data formats NiBabel provides read and write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, as well as PAR/REC. The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays. NiBabel is the successor of PyNIfTI. . This package also provides a commandline tools: . - dicomfs - FUSE filesystem on top of a directory with DICOMs - nib-ls - 'ls' for neuroimaging files - parrec2nii - for conversion of PAR/REC to NIfTI images Package: python-nibabel-doc Section: doc Architecture: all Depends: ${misc:Depends}, libjs-jquery Description: documentation for NiBabel NiBabel provides read and write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, as well as PAR/REC. The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays. NiBabel is the successor of PyNIfTI. . This package provides the documentation in HTML format. debian/compat0000644000000000000000000000000211772653246010401 0ustar 7