debian/0000775000000000000000000000000012301724276007174 5ustar debian/upstream0000664000000000000000000000155312252377600010763 0ustar Bug-Database: https://github.com/PyMVPA/PyMVPA/issues Bug-Submit: https://github.com/PyMVPA/PyMVPA/issues/new Contact: Development and support of PyMVPA FAQ: http://www.pymvpa.org/faq.html Other-References: http://www.pymvpa.org/index.html#peer-reviewed-publications Repository: git://github.com/PyMVPA/PyMVPA.git Repository-Browse: https://github.com/PyMVPA/PyMVPA Reference: Author: Hanke, Michael and Halchenko, Yaroslav O. and Sederberg, Per B. and Hanson, Stephen José and Haxby, James V. and Pollmann, Stefan Title: 'PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data' Journal: Neuroinformatics Year: 2009 Volume: 7 Number: 1 DOI: 10.1007/s12021-008-9041-y PMID: 19184561 URL: http://www.springerlink.com/content/n4jm3533pw2661q3 eprint: http://haxbylab.dartmouth.edu/publications/HHS+09a.pdf debian/patches/0000775000000000000000000000000012301724064010616 5ustar debian/patches/changeset_bab55a4a390c9c4b337ead5877868f7f7debc208.diff0000664000000000000000000000305312252377600021316 0ustar From: Yaroslav Halchenko Subject: BF: tollerate Probabalistic FSL atlases + use warning isntead of undefined printdebug --- a/mvpa2/atlases/warehouse.py +++ b/mvpa2/atlases/warehouse.py @@ -10,6 +10,7 @@ import os +from mvpa2.base import warning from mvpa2.atlases.base import * from mvpa2.atlases.fsl import * @@ -61,7 +62,9 @@ def Atlas(filename=None, name=None, *arg 'PyMVPA': {"Label" : LabelsAtlas, "Reference": ReferencesAtlas}, 'FSL': {"Label" : FSLLabelsAtlas, - "Probabalistic": FSLProbabilisticAtlas} + "Probabalistic": FSLProbabilisticAtlas, + "Probabilistic": FSLProbabilisticAtlas, + } }[atlas_source] atlasType = tempAtlas.header.type.text if atlasTypes.has_key(atlasType): @@ -69,9 +72,9 @@ def Atlas(filename=None, name=None, *arg return atlasTypes[atlasType](filename=filename, *args, **kwargs) #return ReferencesAtlas(filename) else: - printdebug("Unknown %s type '%s' of atlas in %s." " Known are %s" % - (atlas_source, atlasType, filename, - atlasTypes.keys()), 2) + warning("Unknown %s type '%s' of atlas in %s." " Known are %s" % + (atlas_source, atlasType, filename, + atlasTypes.keys()), 2) return tempAtlas except XMLAtlasException, e: print "File %s is not a valid XML based atlas due to %s" \ debian/patches/series0000664000000000000000000000032312301723231012024 0ustar changeset_bab55a4a390c9c4b337ead5877868f7f7debc208.diff changeset_cdba16f73f5aa74cf3002f027a1d38e408b0361b.diff changeset_79bc8ecad13fe43447f8a262ed03147cbe7da326.diff no-pyshared.diff python3_test_support.diff debian/patches/changeset_79bc8ecad13fe43447f8a262ed03147cbe7da326.diff0000664000000000000000000000214612252377600021301 0ustar From: Yaroslav Halchenko Subject: BF+TST: compatibility with numpy 1.7.1 -- use is_the_same_base helper more --- a/mvpa2/tests/test_splitter.py +++ b/mvpa2/tests/test_splitter.py @@ -398,7 +398,7 @@ class SplitterTests(unittest.TestCase): else: assert_true(s[0].samples.base is None) # we get slicing all the time - assert_true(s[1].samples.base.base is self.data.samples) + assert_true(is_the_same_base(s[1].samples)) step_ds = Dataset(np.random.randn(20,2), sa={'chunks': np.tile([0,1], 10)}) oes = OddEvenPartitioner() @@ -411,8 +411,8 @@ class SplitterTests(unittest.TestCase): assert_equal(len(splits), 2) for s in splits: # we get slicing all the time - assert_true(s[0].samples.base.base is step_ds.samples) - assert_true(s[1].samples.base.base is step_ds.samples) + assert_true(is_the_same_base(s[0].samples, step_ds.samples)) + assert_true(is_the_same_base(s[1].samples, step_ds.samples)) def suite(): debian/patches/changeset_cdba16f73f5aa74cf3002f027a1d38e408b0361b.diff0000664000000000000000000000151412252377600021164 0ustar From: Yaroslav Halchenko Subject: BF: do not rely on identical FP results in a test_over_axis since numpy 1.7.0, for performance improvements, order of summation could be different thus affecting precise FP result value. See http://permalink.gmane.org/gmane.comp.python.numeric.general/54061 for more discussion/examples --- a/mvpa2/tests/test_transformers.py +++ b/mvpa2/tests/test_transformers.py @@ -79,7 +79,7 @@ class TransformerTests(unittest.TestCase for axis in [None, 0, 1, 2]: oversum = OverAxis(np.sum, axis=axis)(data) sum_ = np.sum(data, axis=axis) - self.assertTrue(np.all(sum_ == oversum)) + assert_array_almost_equal(sum_, oversum) # Transformer which doesn't modify dimensionality of the data data = data.reshape((6, -1)) debian/patches/changeset_master.diff0000664000000000000000000000214612252377600014774 0ustar From: Yaroslav Halchenko Subject: BF+TST: compatibility with numpy 1.7.1 -- use is_the_same_base helper more --- a/mvpa2/tests/test_splitter.py +++ b/mvpa2/tests/test_splitter.py @@ -398,7 +398,7 @@ class SplitterTests(unittest.TestCase): else: assert_true(s[0].samples.base is None) # we get slicing all the time - assert_true(s[1].samples.base.base is self.data.samples) + assert_true(is_the_same_base(s[1].samples)) step_ds = Dataset(np.random.randn(20,2), sa={'chunks': np.tile([0,1], 10)}) oes = OddEvenPartitioner() @@ -411,8 +411,8 @@ class SplitterTests(unittest.TestCase): assert_equal(len(splits), 2) for s in splits: # we get slicing all the time - assert_true(s[0].samples.base.base is step_ds.samples) - assert_true(s[1].samples.base.base is step_ds.samples) + assert_true(is_the_same_base(s[0].samples, step_ds.samples)) + assert_true(is_the_same_base(s[1].samples, step_ds.samples)) def suite(): debian/patches/no-pyshared.diff0000664000000000000000000000125612276715507013722 0ustar Index: b/doc/Makefile =================================================================== --- a/doc/Makefile +++ b/doc/Makefile @@ -32,7 +32,7 @@ -rm -rf $(BUILDDIR) source/generated source/examples -rm generate-stamp -SPHINXEXT_PATH=$(shell python -c 'import sphinx; from distutils.version import LooseVersion; print LooseVersion(sphinx.__version__) < "1.1.2" and "sphinxext" or "/usr/share/pyshared/sphinx/ext"') +SPHINXEXT_PATH=$(shell python -c 'import sphinx; from distutils.version import LooseVersion; print LooseVersion(sphinx.__version__) < "1.1.2" and "sphinxext" or "/usr/lib/python2.7/dist-packages/sphinx/ext"') #SPHINXEXT_PATH=sphinxext generate: generate-stamp debian/patches/python3_test_support.diff0000664000000000000000000000250412301724027015707 0ustar Description: Change how elements are tested for equality for python3 Origin: http://anonscm.debian.org/gitweb/?p=pkg-exppsy%2Fpymvpa.git;a=blobdiff_plain;f=mvpa2%2Ftests%2Ftest_support.py;h=e8b4c66ab3aab74fd27b8b3a83773ba0f0a482c6;hp=defa1c099ea7235715744a1e559fa164e8902295;hb=3e631dd8cd3c6aba91c0f0cf70cfc76dadcd9292;hpb=6cf43b57082a4ff41f89b298d326b84953f7f81f Index: pymvpa2-2.2.0/mvpa2/tests/test_support.py =================================================================== --- pymvpa2-2.2.0.orig/mvpa2/tests/test_support.py 2012-09-16 12:58:32.000000000 -0700 +++ pymvpa2-2.2.0/mvpa2/tests/test_support.py 2014-02-21 11:19:40.392064093 -0800 @@ -169,7 +169,13 @@ i_con = asobjarray(i) self.assertTrue(i_con.dtype is np.dtype('object')) self.assertEqual(len(i), len(i_con)) - self.assertTrue(np.all(i == i_con)) + + # Note: in Python3 the ['a' , 2, '3'] list is converted to + # an array with elements 'a', '2',' and '3' (i.e. string representation + # for the second element), and thus np.all(i==i_con) fails. + # Instead here each element is tested for equality seperately + # XXX is this an issue? + self.assertTrue(np.all((i[j] == i_con[j]) for j in xrange(len(i)))) @reseed_rng() def test_correlation(self): debian/changelog0000664000000000000000000002617012301724143011045 0ustar pymvpa2 (2.2.0-4ubuntu2) trusty; urgency=medium * debian/patches/python3_test_support.diff: added to update a test for python3 -- Brian Murray Fri, 21 Feb 2014 11:25:51 -0800 pymvpa2 (2.2.0-4ubuntu1) trusty; urgency=medium * Don't lookup sphinx extensions in /usr/share/pyshared. -- Matthias Klose Wed, 12 Feb 2014 17:03:27 +0100 pymvpa2 (2.2.0-4) unstable; urgency=low * debian/control: - specify git branch for debian packaging of pymvpa2. Thanks Julien Cristau for the report - build-depends on python-numpydoc - recommend python-pprocess (removed from the Debian archive since we missed a dependency on it and otherwise was unused, but is present from NeuroDebian ) - policy boosted to 3.9.5 (no changes) * debian/rules: - mkdir target -lib directories before moving .so files. It should resolve FTBFS with debhelper 9.20130507 and robustify build - quote paths with globs to avoid their expansion in find command. Thanks Julien Cristau for the hint -- Yaroslav Halchenko Thu, 12 Dec 2013 08:55:02 -0500 pymvpa2 (2.2.0-3) unstable; urgency=low * debian/patches - changeset_bab55a4a390c9c4b337ead5877868f7f7debc208.diff Tollerate "Probabalistic" (mention the typo) and "fixed" FSL atlases -- Yaroslav Halchenko Mon, 06 May 2013 15:02:58 -0400 pymvpa2 (2.2.0-2) unstable; urgency=low * debian/patches - changeset_79bc8ecad13fe43447f8a262ed03147cbe7da326.diff changeset_cdba16f73f5aa74cf3002f027a1d38e408b0361b.diff Address numpy 1.7.1 compatibility in unittests -- Yaroslav Halchenko Tue, 30 Apr 2013 11:35:24 -0400 pymvpa2 (2.2.0-1) unstable; urgency=low * Fresh upstream release: - provides tutorial (in -doc package) as ipython notebooks. Added ipython-notebook into Suggests - all cmdline tools have disambiguating prefix thus are installed now without conflict with pymvpa (0.4.x) package. * Dropping support of python 2.5 (failing tests) -- added X-Python-Version -- Yaroslav Halchenko Sun, 16 Sep 2012 06:23:51 -0400 pymvpa2 (2.1.0-1) unstable; urgency=low * Fresh upstream release * debian/control - unwrapped Depends/Recommends and sorted - moved python-lxml and python-sklearn into Recommends - added liblapack-dev into Recommends -- provides liblapack.so optionally used by Hyperalignment * debian/upstream -- added with a canonical reference -- Yaroslav Halchenko Thu, 28 Jun 2012 13:28:19 -0400 pymvpa2 (2.0.1-1) unstable; urgency=low * Fresh upstream release - all debian/patches were upstreamed * debian/control - policy boosted to 3.9.3 (no changes) * debian/copyright - updated for DEP5 v1.0 * debian/rules - added a call to dh_numpy where available for proper NumPy dependencies -- Yaroslav Halchenko Tue, 27 Mar 2012 09:47:23 -0400 pymvpa2 (2.0.0-6) unstable; urgency=low * Fixed FTBFS due to sphinx API changes braking old copy of autosummary. System-wide autosummary should be used now for sphinx >= 1.1.2 (Closes: #658593). Thanks to Jakub Wilk and Julian Taylor for help Patch: up_sphinx_1.1.2_autosummary -- Yaroslav Halchenko Tue, 07 Feb 2012 11:16:39 -0500 pymvpa2 (2.0.0-5) unstable; urgency=low * Fixed FTBFS due to test failure in test_niftidataset on big-endians. Patch: 0001-BF-assure-native-endianness-in-test_assumptions_on_n.patch * Fixed oblivious typo of removing system-installed underscore.js leading to stall and thus FTBFS on Debian build hosts * Run unittests with verbose output for easy troubleshooting of FTBFSs -- Yaroslav Halchenko Tue, 27 Dec 2011 16:26:12 -0500 pymvpa2 (2.0.0-4) unstable; urgency=low * debian/rules: export HOME=$(CURDIR)/build to assure rw $HOME for every aspect of package building (finally Closes:#652903) -- Yaroslav Halchenko Thu, 22 Dec 2011 23:03:26 -0500 pymvpa2 (2.0.0-3) unstable; urgency=low * Add up_robust_doc_building to the patch queue series (really Closes: #652903) -- Yaroslav Halchenko Thu, 22 Dec 2011 10:38:37 -0500 pymvpa2 (2.0.0-2) unstable; urgency=low * up_robust_doc_building patch to point HOME to build/ directory (Closes: #652903) -- Yaroslav Halchenko Wed, 21 Dec 2011 18:34:32 -0500 pymvpa2 (2.0.0-1) unstable; urgency=low * Long-awaited upstream release of mvpa2 * Removed conflict with python-mvpa-lib -- both python-mvpa and python-mvpa2 must be co-installable now * Reincrarnated -doc package providing HTML documentation -- Yaroslav Halchenko Thu, 15 Dec 2011 18:32:02 -0500 pymvpa2 (2.0.0~rc5-1) unstable; urgency=low * mvpa module was renamed into mvpa2 to allow co-installability with stable mvpa 0.4.x (hence source package name change) * Command line tools (atlaslabeler, mvpa-prep-fmri) are not provided for this release * Bump Standards-Version to 3.9.2 -- no changes necessary -- Yaroslav Halchenko Wed, 19 Oct 2011 14:18:14 -0400 pymvpa-snapshot (0.6.0~rc4-1) neurodebian; urgency=low * PyMVPA development snapshot. * Pruned unneeded now XS-DM-Upload-Allowed. -- Yaroslav Halchenko Tue, 14 Jun 2011 21:03:07 -0400 pymvpa-snapshot (0.6.0~rc3-1) neurodebian; urgency=low * PyMVPA development snapshot. * Includes upstream changelog now. -- Yaroslav Halchenko Tue, 12 Apr 2011 12:08:15 -0400 pymvpa-snapshot (0.6.0~rc2-1) neurodebian; urgency=low * PyMVPA development snapshot. -- Michael Hanke Thu, 03 Mar 2011 16:06:46 -0500 pymvpa (0.4.3-2) unstable; urgency=low [ Sandro Tosi ] * Drop Python 2.4; thanks to Luca Falavigna for the report and to Jakub Wilk for the patch (Closes: #562482) - debian/control + bump b-d on python-all-dev to '>= 2.5' + drop python-ctypes + drop explicit Depends on python: we use ${python:Depends} - debian/pyversions + bump it to '+2.5-' [ Yaroslav Halchenko ] * debian/control - Thanks Sandro Tosi for NMU attempt to fix #560606. - Build-Conflict on python-epydoc=3.0.1-4: this version works incorrectly with python-docutils 0.6 (thanks to Lucas Nussbaum for the report). Also Build-Depends on python-docutils (<< 0.6) | python-docutils (>= 0.6-3~) which would assure that we still can build on lenny or with fresh docutils which pull in fresh epydoc (thanks to Jakub Wilk for suggestion). Those 2 steps fix the FTBFS (Closes: #560606) - Added python-mvpa-doc to suggests. * Cherry pick 2 commits from maint/0.4 branch to be compatible with recent versions of shogun-python-modular present in sid/squeeze. -- Yaroslav Halchenko Tue, 12 Jan 2010 17:55:55 -0500 pymvpa (0.4.3-1) unstable; urgency=low * New upstream release. * Bump Standards-Version to 3.8.3 -- no changes necessary. * Maintainer field points to ExpPsy Maintainers now. * Recommend python-reportlab. * Added python-nose, python-nifti, python-lxml to Build-depends. -- Yaroslav Halchenko Fri, 04 Sep 2009 16:18:54 -0400 pymvpa (0.4.2-1) unstable; urgency=low [ Michael Hanke ] * New upstream release. * Removing the circular dependency between python-mvpa and python-mvpa-lib (Closes: #519129). * Improve long description of python-mvpa-lib and turn it into complete sentences, as recommended by the developers reference 6.2.3 (Closes: #521332). * Bump Standards-Version to 3.8.1 -- no changes necessary. * Added dependency on python to the python-mvpa package to satisfy lintian. * Added rsync as build-dependency, which is required for building the docs. * The package now honors 'nodoc' in DEB_BUILD_OPTIONS. This is intended to help backporting to releases with insufficient python-sphinx versions. * Added 'graphviz' as a build-dependency (necessary for Sphinx' inheritance graphs). [ Yaroslav Halchenko ] * Compatible with cdbs >= 0.4.54 (use of DEB_PYTHON_MODULE_PACKAGES) and recent pysupport (>=0.9). * Run unittests for each supported python version during build. -- Michael Hanke Mon, 25 May 2009 11:21:39 +0200 pymvpa (0.4.1-1) unstable; urgency=low [ Michael Hanke ] * New upstream release. * Added missing ${misc:Depends} to debian/control. * The package now honors 'nocheck' in DEB_BUILD_OPTIONS. * Speed-up of package build process by preventing the docs from being built twice. * Added 'DM-Upload-Allowed: yes' to enable DM upload. * Install new manpages and add build-dep. to help2man. * Updated debian/copyright. * Imported various bugfixes from the upstream VCS that were pushed into the 0.4 maintenance branch since the release of 0.4.1. [ Yaroslav Halchenko ] * Adjusted long descriptions. * Split libraries (low-level SMLR implementation and LIBSVM custom Python bindings) into a separate python-mvpa-lib package. That allows python-mvpa package to become architecture independent. -- Michael Hanke Sat, 21 Feb 2009 14:07:55 +0100 pymvpa (0.4.0-1) unstable; urgency=low * New upstream release. * Running a subset of the unittests during package build (only tests not requiring a huge amount of cpu-time or memory. -- Michael Hanke Wed, 19 Nov 2008 03:30:53 +0100 pymvpa (0.3.1-1) unstable; urgency=low * New upstream release. * Added dependency to ctypes for python 2.4. -- Michael Hanke Sun, 14 Sep 2008 13:53:31 +0200 pymvpa (0.3.0-1) unstable; urgency=low * New upstream release. * Added python-pywt as recommended package. * Using jquery.js from corresponding Debian package. -- Michael Hanke Sun, 17 Aug 2008 20:56:26 +0200 pymvpa (0.2.2-1) unstable; urgency=low * New upstream maintenance release (missed 0.2.1). This release contains a minimal copy of LIBSVM. The Debian package does not build it, but makes use of the corresponding Debian package. * Shrink Debian diff and move the enabling of LIBSVM into debian/rules. * Convert debian/copyright into machine readable format. * Bump Standards-Version to 3.8.0 -- no changes necessary. * Adjusted list of recommended and suggested packages to the new capabilities of PyMVPA, i.e. add SciPy, MDP, Shogun and Matplotlib. -- Michael Hanke Thu, 03 Jul 2008 10:04:40 +0200 pymvpa (0.2.0-1) unstable; urgency=low * New upstream release. * Added build-dependency to python-ctypes for a new classifier extension. * Added watch file. * Move from python-docutils to python-sphinx for building the package docs. * Disable libsvm setting check and add setup.cfg to permanently enable building the libsvm wrapper for Debian. -- Michael Hanke Thu, 29 May 2008 08:13:14 +0200 pymvpa (0.1.0-1) unstable; urgency=low * Initial release (Closes: #466556). -- Michael Hanke Tue, 19 Feb 2008 16:10:05 +0100 debian/TODO0000664000000000000000000000037312252377600007667 0ustar * Reincarnate the tools -- removed meanwhile to avoid conflicts but allowing coinstallation with python-mvpa package * RF (unify) to use libjs-sphinxdoc and dh_sphinxdoc (introduced in 1.0.7+dfsg-1 of sphinx, so would require a backport for ND) debian/pycompat0000664000000000000000000000000212252377600010743 0ustar 2 debian/python-mvpa-snapshot.install0000777000000000000000000000000012252377600020632 2python-mvpa2.installustar debian/watch0000664000000000000000000000012412252377600010222 0ustar version=3 http://alioth.debian.org/frs/?group_id=30954 .*/pymvpa_([\d\.]+)\.tar\.gz debian/compat0000664000000000000000000000000212252377600010372 0ustar 5 debian/copyright0000664000000000000000000000770412252377600011137 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: PyMVPA Upstream-Contact: pkg-exppsy-pymvpa@lists.alioth.debian.org Source: https://github.com/PyMVPA/PyMVPA Files: * Copyright: 2006-2012, Michael Hanke 2007-2012, Yaroslav Halchenko 2007-2009, Per B. Sederberg 2008, Emanuele Olivetti License: Expat Files: debian/* Copyright: 2006-2013, Michael Hanke 2006-2013, Yaroslav Halchenko License: Expat Files: 3rd/libsvm/* Copyright: 2000-2007, Chih-Chung Chang and Chih-Jen Lin License: BSD-3 The source tarball contains a partial copy of the LIBSVM package. However, the corresponding library is available from the libsvm source package (or rather the binary packages it builds). Therefore this code is not used and the respective packages are used as dependencies. This copy of the libsvm code is, however, left in place, as it does not hurt and does not justify repackaging of the upstream sources. . 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. Neither the name of the University 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 REGENTS 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. Files: tools/pdfbook.c Copyright: Tigran Aivazian Jaap Eldering Roman Buchert Pierre Francois License: GPL-2 On Debian GNU/Linux systems, the complete text of the GPL-2 License can be found in `/usr/share/common-licenses/GPL-2'. 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/gbp.conf0000664000000000000000000000072612252377600010620 0ustar [DEFAULT] # the default branch for upstream sources: upstream-branch = master # the default branch for the debian patch: debian-branch = dist2/proper/debian/sid # the default tag formats used: upstream-tag = upstream/%(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 debian/control0000664000000000000000000000645312301724272010603 0ustar Source: pymvpa2 Section: python Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: NeuroDebian team Uploaders: Michael Hanke , Yaroslav Halchenko Build-Depends: debhelper (>= 7.0.50~), python-all-dev (>= 2.4), python-support (>= 0.6), swig, python-numpy, python-scipy, python-nibabel, python-nose, python-h5py, python-lxml, libsvm-dev (>= 2.84.0), help2man, python-sphinx, python-numpydoc, graphviz, inkscape, imagemagick, bc, Standards-Version: 3.9.5 Homepage: http://www.pymvpa.org Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/pymvpa.git Vcs-Git: git://git.debian.org/git/pkg-exppsy/pymvpa.git -b dist2/debian/proper/sid X-Python-Version: >= 2.6 Package: python-mvpa2 Architecture: all Depends: ${misc:Depends}, ${python:Depends}, python-mvpa2-lib(>= ${source:Version}), python-numpy, Recommends: python-h5py, python-lxml, python-matplotlib, python-mdp, python-nibabel, python-psutil, python-psyco, python-pywt, python-reportlab, python-scipy, python-sklearn, shogun-python-modular, liblapack-dev, python-pprocess, Suggests: fslview, fsl, python-mvpa2-doc, python-nose, python-openopt, python-rpy2, Provides: ${python:Provides} XB-Python-Version: ${python:Versions} Description: multivariate pattern analysis with Python v. 2 PyMVPA eases pattern classification analyses of large datasets, with an accent on neuroimaging. It provides high-level abstraction of typical processing steps (e.g. data preparation, classification, feature selection, generalization testing), a number of implementations of some popular algorithms (e.g. kNN, Ridge Regressions, Sparse Multinomial Logistic Regression), and bindings to external machine learning libraries (libsvm, shogun). . While it is not limited to neuroimaging data (e.g. fMRI, or EEG) it is eminently suited for such datasets. . This is a package of PyMVPA v.2. Previously released stable version is provided by the python-mvpa package. Package: python-mvpa2-lib Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends}, python-numpy Provides: ${python:Provides} XB-Python-Version: ${python:Versions} Description: low-level implementations and bindings for PyMVPA v. 2 This is an add-on package for the PyMVPA framework. It provides a low-level implementation of an SMLR classifier and custom Python bindings for the LIBSVM library. . This is a package of a development snapshot. The latest released version is provided by the python-mvpa-lib package. Package: python-mvpa2-doc Architecture: all Section: doc Depends: ${misc:Depends}, libjs-jquery, libjs-underscore Suggests: python-mvpa2, python-mvpa2-tutorialdata, ipython-notebook Description: documentation and examples for PyMVPA v. 2 This is an add-on package for the PyMVPA framework. It provides a HTML documentation (tutorial, FAQ etc.), and example scripts. In addition the PyMVPA tutorial is also provided as IPython notebooks. debian/source/0000775000000000000000000000000012252377600010474 5ustar debian/source/options0000664000000000000000000000026012252377600012110 0ustar # ignore changes to the commit hash file, since it will always have the # shasum of the release tag and the repository version does not. extend-diff-ignore = mvpa2/COMMIT_HASH debian/source/format0000664000000000000000000000001412252377600011702 0ustar 3.0 (quilt) debian/python-mvpa2.manpages0000664000000000000000000000001412252377600013250 0ustar build/man/* debian/rules0000775000000000000000000000746512252377600010270 0ustar #!/usr/bin/make -f # -*- mode: makefile; coding: utf-8 -*- 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 ) upstreamver = $(shell echo $(debver) | sed -e 's/-[^-]*$$//' ) # this figures out the last merge point from 'master' into the 'dist' branch and # then described this commit relative to the last release tag (upstream/...) # If this should make any sense the local master branch must track remote # master. gitver = $(shell [ -x /usr/bin/git ] && git describe --tags --match 'upstream/*' $$(git merge-base -a HEAD master) | sed -e 's,^upstream/,,' -e 's/\.dev/~dev/' -e 's/\.rc/~rc/') export HOME=$(CURDIR)/build # 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_configure: dh_auto_configure mkdir -p $(CURDIR)/build override_dh_auto_build: dh_auto_build -- --with-libsvm $(MAKE) manpages ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS))) $(MAKE) htmldoc -rm build/html/_static/jquery.js build/html/_static/underscore.js $(MAKE) tutorial2notebooks endif # we run the test suite on the install override_dh_auto_test: : # Tests will be ran later on against installed version override_dh_auto_install: dh_auto_install -- --with-libsvm # run unit tests here to actually check the deployed package # whenever we don't have to build for python 2.5 anymore call # python with -B and remove the find for pyc files ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) for buildver in $(shell pyversions -vr); do \ echo "I: Running PyMVPA unittests using python$$buildver"; \ cd $(CURDIR)/debian/tmp/usr/lib/python$$buildver/*-packages && \ PYTHONPATH=. MVPA_TESTS_LABILE=no MVPA_TESTS_LOWMEM=yes \ MVPA_TESTS_QUICK=yes MVPA_TESTS_VERBOSITY=3 \ python$$buildver mvpa2/tests/__init__.py \ || exit 1 ; find . -type f -name '*.pyc' -delete ; \ done endif # and now move libraries into -lib package (account for snapshot name # as well) mkdir -p $(CURDIR)/debian/python-mvpa2-lib cd $(CURDIR)/debian/python-mvpa2-lib && \ for so in $$(find ../tmp -name '*.so'); do \ install -D $$so $${so#../tmp/*} ; \ rm $$so ; \ done : # Do not install some existing scripts yet for now find debian -wholename '*/bin/*' -o -wholename '*/man/*' \ | grep -e 'pymvpa2-\(analysis\)' \ | xargs -r rm -rf override_dh_pysupport: dh_pysupport if [ -x /usr/bin/dh_numpy ]; then dh_numpy; fi override_dh_installchangelogs: dh_installchangelogs Changelog override_dh_auto_clean: $(MAKE) clean dh_auto_clean -rm -rf $(CURDIR)/build # make orig tarball from repository content get-orig-source: # orig tarball, turn directory into something nicer git archive --format=tar --prefix=$(srcpkg)-$(gitver)/ HEAD | \ tar --delete $(srcpkg)-$(gitver)/debian | \ gzip -9 > $(srcpkg)_$(gitver).orig.tar.gz # same for dev snapshots, but here it produces a dev changelog entry first # that converts the source package name to -snapshot dev-source: dev-changelog get-orig-source mv $(srcpkg)_$(gitver).orig.tar.gz .. # helper to create a new changelog entry for a development snapshot package # go with default changelog item for each new snapshot, but fire up editor # if there already was a changelog for this upstream version, as there is # probably something to say about this new Debian snapshot package release dev-changelog: @if [ "$(gitver)" = "$(upstreamver)" ]; then \ dch -i --package pymvpa-snapshot ; \ else \ dch --newversion $(gitver)-1 --package pymvpa-snapshot \ --allow-lower-version "PyMVPA development snapshot." ; \ fi ## immediately useable documentation and exemplar scripts/data override_dh_compress: dh_compress -X.py -X.html -X.pdf -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -Xobjects.inv -X.ipynb debian/python-mvpa2.docs0000664000000000000000000000002012252377600012402 0ustar debian/upstream debian/python-mvpa2-doc.docs0000664000000000000000000000004212252377600013151 0ustar build/html/ build/html/notebooks/ debian/python-mvpa2-doc.examples0000664000000000000000000000001712252377600014041 0ustar doc/examples/* debian/python-mvpa2.install0000664000000000000000000000001712252377600013126 0ustar debian/tmp/usr debian/python-mvpa2-doc.links0000664000000000000000000000067712252377600013357 0ustar usr/share/javascript/jquery/jquery.js usr/share/doc/python-mvpa2-doc/html/_static/jquery.js usr/share/javascript/underscore/underscore.js usr/share/doc/python-mvpa2-doc/html/_static/underscore.js usr/share/doc/python-mvpa2-doc/html usr/share/doc/python-mvpa2/html usr/share/doc/python-mvpa2-doc/examples usr/share/doc/python-mvpa2/examples usr/share/doc/python-mvpa2-doc/notebooks usr/share/doc/python-mvpa2/notebooks