debian/0000755000000000000000000000000011636165622007176 5ustar debian/source/0000755000000000000000000000000011636165622010476 5ustar debian/source/format0000644000000000000000000000001411636165622011704 0ustar 3.0 (quilt) debian/watch0000644000000000000000000000020711636165622010226 0ustar version=3 opts="filenamemangle=s/.*\/(.*)/dipy-$1\.tar\.gz/" \ http://github.com/Garyfallidis/dipy/downloads .*tarball/([\d\.a-z]+) debian/patches/0000755000000000000000000000000011636174135010624 5ustar debian/patches/deb_no_sources_for_docs0000644000000000000000000000056411636165622015424 0ustar --- a/doc/conf.py +++ b/doc/conf.py @@ -93,6 +93,9 @@ rst_epilog = open('links_names.inc', 'rt # for source files. exclude_trees = ['_build', 'examples'] +# If true, the reST sources are included in the HTML build as _sources/. +html_copy_source = False + # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None debian/patches/series0000644000000000000000000000010711636165761012044 0ustar up_explicit_cdefs_inits deb_no_sources_for_docs debian-changes-0.5.0-3 debian/patches/up_explicit_cdefs_inits0000644000000000000000000000072111636165622015447 0ustar --- a/dipy/tracking/distances.pyx +++ b/dipy/tracking/distances.pyx @@ -488,7 +488,7 @@ def bundles_distances_mam(tracksA, track # preprocess tracks cdef: size_t longest_track_len = 0, track_len - longest_track_lenA, longest_track_lenB + size_t longest_track_lenA = 0, longest_track_lenB = 0 cnp.ndarray[object, ndim=1] tracksA32 cnp.ndarray[object, ndim=1] tracksB32 cnp.ndarray[cnp.double_t, ndim=2] DM debian/patches/debian-changes-0.5.0-30000644000000000000000000000262411636174135014201 0ustar Description: Upstream changes introduced in version 0.5.0-3 This patch has been created by dpkg-source during the package build. Here's the last changelog entry, hopefully it gives details on why those changes were made: . dipy (0.5.0-3) unstable; urgency=low . * Added patch up_explicit_cdefs_inits to prevent FTBFS with cython >= 0.15 . The person named in the Author field signed this changelog entry. Author: Yaroslav Halchenko --- 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: , Bug: Bug-Debian: http://bugs.debian.org/ Bug-Ubuntu: https://launchpad.net/bugs/ Forwarded: Reviewed-By: Last-Update: --- dipy-0.5.0.orig/dipy/COMMIT_INFO.txt +++ dipy-0.5.0/dipy/COMMIT_INFO.txt @@ -1,6 +1,6 @@ # This is an ini file that may contain information about the code state [commit hash] # The line below may contain a valid hash if it has been substituted during 'git archive' -archive_subst_hash=2cbfd62 +archive_subst_hash=05655ba # This line may be modified by the install process install_hash= debian/changelog0000644000000000000000000000156011636165622011052 0ustar dipy (0.5.0-3) unstable; urgency=low * Added patch up_explicit_cdefs_inits to prevent FTBFS with cython >= 0.15 -- Yaroslav Halchenko Tue, 20 Sep 2011 15:37:06 -0400 dipy (0.5.0-2) unstable; urgency=low * Upload to unstable * Fixed binary-arch build -- extensions were not installed. Thanks Jiří Keller for the report * Fixed ${Python:depends} -> ${python:Depends} (thanks Lintian) * Boosted policy to 3.9.2 (no changes are due) -- Yaroslav Halchenko Fri, 01 Jul 2011 13:55:03 -0400 dipy (0.5.0-1) experimental; urgency=low * Initial release (Closes: #610347) -- Yaroslav Halchenko Wed, 09 Feb 2011 17:38:53 -0500 dipy (0.5.0~dev20110117-1~pre1) UNRELEASED; urgency=low * Initial packaging. -- Yaroslav Halchenko Mon, 17 Jan 2011 15:13:17 -0500 debian/python-dipy-doc.links0000644000000000000000000000013311636165622013264 0ustar usr/share/javascript/jquery/jquery.js usr/share/doc/python-dipy-doc/html/_static/jquery.js debian/copyright0000644000000000000000000000400511636165622011130 0ustar Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 Name: dipy Maintainer: Eleftherios Garyfallidis Source: http://github.com/Garyfallidis/dipy Files: * Copyright: 2009-2010, Dipy Developers License: BSD-3 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 dipy developers 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: doc/sphinxext/* Copyright: 2007-2010, Stefan van der Walt and Sphinx team License: BSD-3 Files: dipy/testing/lightunit.py Copyright: 2009, The IPython Development Team License: BSD-3 Files: debian/* Copyright: 2010, Yaroslav Halchenko License: BSD-3 debian/python-dipy-doc.docs0000644000000000000000000000002011636165622013067 0ustar doc/_build/html debian/rules0000755000000000000000000000663311636165622010266 0ustar #!/usr/bin/make -f # -*- makefile -*- PACKAGE_NAME = python-dipy PACKAGE_ROOT_DIR = debian/${PACKAGE_NAME} INSTALL_PATH = $(CURDIR)/debian/tmp # default Python PYTHON=$(shell pyversions -d) PYVER=$(shell pyversions -d -v) srcpkg = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Source:' | cut -d ' ' -f 2,2) debver = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Version:' | cut -d ' ' -f 2,2 ) upver = $(shell echo $(debver) | cut -d '-' -f 1,1 ) %: dh --buildsystem=python_distutils $@ override_dh_auto_test: : # Do not test just after build, lets install and then test override_dh_auto_build: dh_auto_build echo "backend : Agg" >| build/matplotlibrc override_dh_auto_install: dh_auto_install : # Prune duplicate LICENSE file find debian/ -name LICENSE -delete : # Only now lets build docs ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS))) : # Copy pregenerated examples cp -rp doc-examples/doc/examples_built/* doc/examples_built/ export PYTHONPATH=$$(/bin/ls -d $(INSTALL_PATH)/usr/lib/$(PYTHON)/*-packages) \ MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \ cd doc; $(MAKE) html-after-examples -rm doc/_build/html/_static/jquery.js -rm -r doc/_build/html/_sources : # objects inventory is of no use for the package -rm doc/_build/html/objects.inv endif : # Run tests later on : # cd build to prevent use of local/not-built source tree ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) cd build; \ for PYTHON in $(shell pyversions -r); do \ echo "I: Running Dipy unittests using $$PYTHON"; \ PYTHONPATH=$$(/bin/ls -d $(INSTALL_PATH)/usr/lib/$$PYTHON/*-packages) \ MPLCONFIGDIR=/tmp/ \ $$PYTHON /usr/bin/nosetests dipy; \ done endif override_dh_pysupport: : # I: Move libraries into the -lib and -lib-dbg packages find $(PACKAGE_ROOT_DIR)/ -iname *.so -delete || : # remove .so from indep pkg if present find $(INSTALL_PATH)/ -iname *.so | \ while read so; do \ d=$$(dirname $$so); \ if [ $${so%_d.so} = $${so} ]; then suf=""; else suf="-dbg"; fi; \ d=$$(echo $$d | sed -e "s,$(INSTALL_PATH)/,$(PACKAGE_ROOT_DIR)-lib$$suf/,g"); \ mkdir -p $$d; echo "Moving $$so under $$d"; mv $$so $$d; \ done dh_pysupport ## immediately useable documentation ## and exemplar data (they are small excerpts anyway) override_dh_compress: dh_compress -X.py -X.html -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -X.par -X.bin -Xobjects.inv override_dh_clean: : # I: Custom cleaning rm -rf build doc-stamp $(MAKE) -C doc clean dh_clean get-orig-source: -quilt pop -a : # I Testing for uncommited changes @git diff --quiet HEAD : # I Composing main tarball mkdir -p tarballs git archive --format=tar --prefix=$(srcpkg)-$(upver)/ HEAD \ | gzip -9 > ../tarballs/$(srcpkg)_$(upver).orig.tar.gz # : # I Building examples figures and tarball # python setup.py build # export PYTHONPATH=$$(/bin/ls -d $(CURDIR)/build/lib.*$(PYVER)); \ # cd doc; $(MAKE) examples-tgz # mv dist/dipy-*-doc-examples.tar.gz ../tarballs/$(srcpkg)_$(upver).orig-doc-examples.tar.gz wget -O ../tarballs/$(srcpkg)_$(upver).orig-doc-examples.tar.gz \ http://nipy.sourceforge.net/dipy/dipy-$(upver)-doc-examples.tar.gz : # Symlinking back into build-area for git-buildpackage not supporting multi-tarball atm [ -d ../build-area ] && ln -sf ../tarballs/$(srcpkg)_$(upver).orig*.tar.gz ../build-area inject-doc-examples: mkdir -p doc-examples tar -C doc-examples --strip-components 1 \ -xzvf ../tarballs/$(srcpkg)_$(upver).orig-doc-examples.tar.gz debian/python-dipy.install0000644000000000000000000000001711636165622013050 0ustar debian/tmp/usr debian/README.source0000644000000000000000000000060111636165622011352 0ustar DiPy for Debian --------------- Documentation uses snapshots which require rendering on GLX capable X, thus are difficult to render during documentation building. Therefore we ship upstream-provided dipy_*.orig-doc-examples.tar.gz with renderings of the images. See get-orig-upstream of debian/rules. -- Yaroslav Halchenko , Sun, 13 Feb 2011 09:14:08 -0500 debian/docs0000644000000000000000000000001311636165622010043 0ustar README.txt debian/gbp.conf0000644000000000000000000000066411636165622010623 0ustar [DEFAULT] upstream-branch = master debian-branch = debian upstream-tag = %(version)s debian-tag = debian/%(version)s # Options only affecting git-buildpackage [git-buildpackage] # ignore some any non-gitted files ignore-new = True #upstream-branch = dfsgclean # uncomment this to automatically GPG sign tags sign-tags = True # use this for more svn-buildpackage like bahaviour: export-dir = ../build-area/ tarball-dir = ../tarballs/ debian/blends0000644000000000000000000000106311636165622010370 0ustar Format: extended Tasks: debian-med/imaging-dev Depends: python-dipy Language: Python Author: Dipy Developers License: BSD Version: 0.5.0.dev Published-Title: Identification of corresponding tracks in diffusion MRI tractographies Published-Authors: Garyfallidis E, Brett M, Tsiaras V, Vogiatzis G, Nimmo-Smith I Published-In: Proc. Intl. Soc. Mag. Reson. Med. 18 Published-Year: 2010 Tasks: debian-med/imaging Recommends: python-dipy Why: Although listed in -dev task, it also has a strong focus on interactive data analysis. debian/python-dipy-doc.doc-base0000644000000000000000000000041311636165622013622 0ustar Document: dipy Title: Dipy Manual Author: Dipy Developers Abstract: This manual provides Dipy user guide and examples Section: Science/Data Analysis Format: HTML Index: /usr/share/doc/python-dipy-doc/html/index.html Files: /usr/share/doc/python-dipy-doc/html/*.html debian/control0000644000000000000000000000457711636165622010616 0ustar Source: dipy Section: python Priority: extra Maintainer: NeuroDebian Team Uploaders: Yaroslav Halchenko , Michael Hanke Build-Depends: debhelper (>= 7.0.50~), python-all-dev, python-support, python-numpy, python-scipy, cython (>= 0.13), python-matplotlib, python-sphinx (>= 1.0), python-nose, python-nibabel Standards-Version: 3.9.2 Homepage: http://nipy.org/dipy Vcs-Git: git://github.com/neurodebian/dipy.git Vcs-Browser: http://github.com/neurodebian/dipy Package: python-dipy Architecture: all Depends: ${python:Depends}, ${shlibs:Depends}, ${misc:Depends}, python-numpy, python-scipy, python-dipy-lib (>= ${source:Version}) Recommends: python-matplotlib, python-vtk, python-nose, python-nibabel, python-tables Suggests: ipython Provides: ${python:Provides} XB-Python-Version: ${python:Versions} Description: toolbox for analysis of MR diffusion imaging data Dipy is a toolbox for the analysis of diffusion magnetic resonance imaging data. It features: - Reconstruction algorithms, e.g. GQI, DTI - Tractography generation algorithms, e.g. EuDX - Intelligent downsampling of tracks - Ultra fast tractography clustering - Resampling datasets with anisotropic voxels to isotropic - Visualizing multiple brains simultaneously - Finding track correspondence between different brains - Warping tractographies into another space, e.g. MNI space - Reading many different file formats, e.g. Trackvis or NIfTI - Dealing with huge tractographies without memory restrictions - Playing with datasets interactively without storing Package: python-dipy-lib Architecture: any Depends: ${python:Depends}, ${shlibs:Depends}, ${misc:Depends} Provides: ${python:Provides} XB-Python-Version: ${python:Versions} Description: toolbox for analysis of MR diffusion imaging data -- extensions Dipy is a toolbox for the analysis of diffusion magnetic resonance imaging data. . This package provides architecture-dependent builds of the extensions. Package: python-dipy-doc Architecture: all Section: doc Depends: ${misc:Depends}, libjs-jquery Suggests: python-dipy Description: toolbox for analysis of MR diffusion imaging data -- documentation Dipy is a toolbox for the analysis of diffusion magnetic resonance imaging data. . This package provides the documentation in HTML format. debian/compat0000644000000000000000000000000211636165622010374 0ustar 7