From: Peter Michael Green Date: Sat, 4 Nov 2017 03:07:42 +0000 (+0000) Subject: nipy (0.4.0+git26-gf8d3149-2+rpi1) buster-staging; urgency=medium X-Git-Tag: archive/raspbian/0.4.1-1+rpi1~5 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=40401accb31d313d16338a6186a22ff1fc2d8958;p=nipy.git nipy (0.4.0+git26-gf8d3149-2+rpi1) buster-staging; urgency=medium * Disable testsuite. [dgit import unpatched nipy 0.4.0+git26-gf8d3149-2+rpi1] --- 40401accb31d313d16338a6186a22ff1fc2d8958 diff --cc debian/changelog index 0000000,0000000..2190ffa new file mode 100644 --- /dev/null +++ b/debian/changelog @@@ -1,0 -1,0 +1,270 @@@ ++nipy (0.4.0+git26-gf8d3149-2+rpi1) buster-staging; urgency=medium ++ ++ * Disable testsuite. ++ ++ -- Peter Michael Green Sat, 04 Nov 2017 03:07:42 +0000 ++ ++nipy (0.4.0+git26-gf8d3149-2) unstable; urgency=medium ++ ++ * debian/pathes picked up few fixes from upstream adjusting ++ some tests for compatibility ++ - 78ced182c4b4583c9a2ed3c1fc01764941560c72 ++ TST: relax test precision a little for 32-bit ++ (replaces "custom" up_relax_assumption patch) ++ - 32cb61eab2e92525c2497294d3be40e361507c4e (fixed failing doctest) ++ - 751531a2894e69383f75e6a9b97586e74759ab1b ++ BF: allow for generic IOError-based exception to be thrown when ++ loading non existing file (Closes: #836538) ++ * .gitignore, debian/source/options ++ - to not ignore .diff files since interfers with helper to CP ++ them from upstream ++ ++ -- Yaroslav Halchenko Sun, 04 Sep 2016 10:18:55 -0400 ++ ++nipy (0.4.0+git26-gf8d3149-1) unstable; urgency=medium ++ ++ * New upstream snapshot from 0.4.0-26-gf8d3149 ++ - various compatibility fixes (Closes: #816983) ++ * debian/rules ++ - fixed up PATH/invocation of scripts so that manpages generate and ++ tests pass ++ ++ -- Yaroslav Halchenko Wed, 03 Aug 2016 22:54:08 -0400 ++ ++nipy (0.3.0+git262-gbb838d7-1) unstable; urgency=medium ++ ++ * New upstream snapshot from 0.3.0-261-ge34a388 ++ * debian/patches ++ - deb_use_internal_ipythonsphinx_extensions -- dropped, upstream uses ++ sphinx's copy now ++ * debian/upstream moved into debian/upstream/metadata ++ * debian/{control,rules} ++ - use libjs-underscore for underscore.js ++ ++ -- Yaroslav Halchenko Fri, 03 Oct 2014 16:50:34 -0400 ++ ++nipy (0.3.0-2) UNRELEASED; urgency=medium ++ ++ * debian/patches ++ - deb_use_internal_ipythonsphinx_extensions to use sphinx-provided ++ inheritance_diagram (Closes: #706532) ++ - up_relax_assertion - relax assertion to almost_equal, permittable ++ (Closes: #729594) ++ * debian/{control,rules} ++ - switch away from pysupport ++ - policy boost to 3.9.6 ++ ++ -- Yaroslav Halchenko Fri, 03 Oct 2014 08:30:13 -0400 ++ ++nipy (0.3.0-1) unstable; urgency=low ++ ++ * New upstream release ++ * debian/watch ++ - fixed up for the recent github changes ++ * debian/rules ++ - add scripts/ into PATH while testing and building documentation ++ - generate manpages for the scripts ++ ++ -- Yaroslav Halchenko Sun, 03 Feb 2013 11:36:54 -0500 ++ ++nipy (0.2.0-1) unstable; urgency=low ++ ++ * New upstream release: documentation and example improvements and ++ functionality fixes since rc2. ++ * Updated debian/patches/lucid-dsc-patch-nodoc to build no -doc package ++ on older releases ++ ++ -- Yaroslav Halchenko Sun, 22 Jul 2012 10:50:06 -0400 ++ ++nipy (0.2.0~rc2+git27-g7b9b5a5-1) unstable; urgency=low ++ ++ * New upstream pre-release snapshot from origin/master at ++ 0.2.0rc2-27-g7b9b5a5 ++ ++ -- Yaroslav Halchenko Sat, 30 Jun 2012 00:02:45 -0400 ++ ++nipy (0.2.0~rc2-1) unstable; urgency=low ++ ++ * Fresh RC (Closes: #673489) ++ - addresses python 2.5 compatibility ++ * debian/watch ++ - added to fetch from github tags ++ ++ -- Yaroslav Halchenko Tue, 19 Jun 2012 21:03:28 -0400 ++ ++nipy (0.2.0~rc1+git170-g5d2dc33-1) unstable; urgency=low ++ ++ * Yet another development release snapshot not intended for public ++ - based on current master 6fc3af4 ++ with pull requests #171 and #183 merged ++ * Boosted policy compliance to 3.9.3 -- no changes ++ * debian/copyright: removed obsolete entries, adjusted for DEP5 ++ ++ -- Yaroslav Halchenko Sat, 12 May 2012 22:19:00 -0400 ++ ++nipy (0.2.0~rc1-1) experimental; urgency=low ++ ++ * Release candidate ++ * Add epoch to versioned depends on numpy (Closes: #658372) ++ (Thanks Jakub Wilk for the report and patch) ++ ++ -- Yaroslav Halchenko Mon, 30 Apr 2012 11:36:17 -0400 ++ ++nipy (0.1.999-2) unstable; urgency=low ++ ++ * Recommend sympy (thanks Chris Filo Gorgolewski for the report) ++ * Respect PYTHONPATH while running tests ++ ++ -- Yaroslav Halchenko Sun, 12 Feb 2012 10:59:44 -0500 ++ ++nipy (0.1.999-1) unstable; urgency=low ++ ++ * Alpha release in preparation for upcoming 0.2.0 release (Closes: #581394) ++ * No changes within upstream codebase (Closes: #643225) ++ * Do not unittest if nocheck is provided (Closes: #649620) ++ * Boosted policy compliance to 3.9.2 -- no changes ++ * Patch lucid-dsc-patch-nodoc to avoid trying to build -doc on lucid ++ due to the failure to install needed build-depends ++ ++ -- Yaroslav Halchenko Sun, 27 Nov 2011 22:06:21 -0500 ++ ++nipy (0.1.2+201100720-2) unstable; urgency=low ++ ++ * Merged commits from upstream contributed by Matthew Brett to fix failing ++ unittests on big-endians. Current upstream point: ++ upstream/0.1.2+20110404-74-g698b432 ++ ++ -- Yaroslav Halchenko Sat, 23 Jul 2011 22:34:15 -0400 ++ ++nipy (0.1.2+201100720-1) unstable; urgency=low ++ ++ * Fresh upstream snapshot: 2c11ae604762105a4adaa46c57e95dc1998485eb ++ - might address FTBFS due to tests on some architectures ++ ++ -- Yaroslav Halchenko Wed, 20 Jul 2011 10:01:30 -0400 ++ ++nipy (0.1.2+20110404-1) unstable; urgency=low ++ ++ * Fresh upstream snapshot: c213cc2421686b5485e43db54ec2ac8a5fa06ea6 ++ - Relies on external nibabel module instead of internal outdated ++ copy. Should close 611316, which would be done upon successfull ++ build across the architectures. ++ - Does not use PyNIfTI any longer, so it is removed from *Depends ++ now ++ - Absorbed all Debian patches ++ * No cdbs was used since nearly a year ago -- removed it from Build-Depends ++ ++ -- Yaroslav Halchenko Mon, 04 Apr 2011 09:54:56 -0400 ++ ++nipy (0.1.2+20110114-1) unstable; urgency=low ++ ++ * Fresh upstream snapshot: 136acf09beff315226e4cfa07066b1f5998e9d5e ++ * Carries numpydoc compatible with sphinx >= 1.0 (Closes: #588625) ++ * Do not compress objects.inv necessary for intersphinx (Closes: #608763) ++ * Added few patches (submitted upstream) to fix building of documentation ++ - 0001-make-few-classes-new-style-derive-from-object.patch ++ - 0002-make-classes-without-new-style-derive-from-object.patch ++ - 0003-import-similarity_measures-as-_sms-in-histogram_regi.patch ++ * Adjusted debian/rules: ++ - run unittests now against default python version ++ on the installed version of nipy. Skipped unittests due to known ++ failures or non-labile tests subject to random data: ++ test_slice_from_3d, test_screen, test_lips3_disjoint, test_mu2tet, ++ test_input_effects, test_same_basis, test_fullrank, test_ec, ++ test_apply_affine, test_lips1_disjoint, test_dtrsm ++ - assure Agg matplotlib backend during documentation build and unittests ++ * Added *-dsc-patch-nodbg backport-dsc patches to avoid building of -dbg ++ package since python-scipy-dbg is missing on lenny or ubuntu releases ++ prior maverick (not sufficient anyways due to other missing versioned ++ build-dependencies atm -- matplotlib, sympy) ++ * Versioned Build-Dependency sympy >= 0.6.6 ++ ++ -- Yaroslav Halchenko Fri, 14 Jan 2011 19:33:28 -0500 ++ ++nipy (0.1.2+20101206-1) UNRELEASED; urgency=low ++ ++ * Fresh upstream snapshot: a0fd6c6c62d91315cdeb8bc81e19f355b12f8013 ++ Never officially released, thus changelogs moved upstairs ++ ++ -- Yaroslav Halchenko Thu, 13 Jan 2011 21:02:35 -0500 ++ ++nipy (0.1.2+20100526-2) unstable; urgency=medium ++ ++ * Strict version dependency on NumPy to assure ABI compatibility in the ++ future (Closes: #590737). Thanks Kumar Appaiah for the reminder. ++ * debian/copyright: ++ - Added missing copyrights/licenses ++ - Adjusted formatting to match DEP5 rev 135 ++ - Citing BSD-3 license verbatim to be compliant with 3.9.0 ++ * Boosted policy compliance to 3.9.1 (BSD-3 license verbatim) ++ * Medium urgency for faster propagation of RC bug fix into squeeze ++ * Added gbp.conf file for easy building using g-b-p ++ ++ -- Yaroslav Halchenko Fri, 06 Aug 2010 11:17:05 -0400 ++ ++nipy (0.1.2+20100526-1) unstable; urgency=low ++ ++ * Fresh upstream snapshot -- needed a new orig.tar.gz since some ++ files were moved/removed ++ * Switching to dh from cdbs: ++ - Assure no documentation is built during binary-arch builds ++ (closes: #581204, #581783) ++ - Build for all supported Python versions ++ - Expanded Build-Depends with all necessary -dbg packages ++ (e.g. cython-dbg, python-all-dbg) ++ - Added dvipng into Build-Depends for avoiding problems during ++ documentation build ++ ++ -- Yaroslav Halchenko Tue, 11 May 2010 21:17:20 -0400 ++ ++nipy (0.1.2+20100505-1) unstable; urgency=low ++ ++ * Fresh upstream snapshot (Closes: #577898). Switching from bzr rev to ++ git dated versioning for nipy for now ++ * Debian packaging moved to be on top of a newly created ++ git repository for nipy upstream ++ * Adhering to a new deb source format 3.0 (quilt) ++ * Policy compliance to 3.8.4 (no changes due) ++ * Switching over to NeuroDebian team ++ * -doc: no pdf's for Documentation (removed texlive, ++ texlive-latex-extra from Build-Depends) (Closes: #567757) ++ * Confirming (and refactoring) NMUs from Kumar (THANKS!): ++ + As promised, closing the issue with absent i386 builds (Closes: #562246) ++ + Adding both PATH= and MPLCONFIGDIR= for building docs ++ + Addressed fortran binding issue with patchless solution: ++ unexport of LDFLAGS in debian/rules which brings -shared back ++ to game (see #535699 for more information) ++ ++ -- Yaroslav Halchenko Tue, 04 May 2010 23:01:12 -0400 ++ ++nipy (0.1.2+1741-2.2) unstable; urgency=low ++ ++ * Non-maintainer upload. ++ * Use $(CURDIR) instead of $(PWD) in debian/rules. (Closes: #535699) ++ ++ -- Kumar Appaiah Sun, 31 Jan 2010 08:40:11 -0600 ++ ++nipy (0.1.2+1741-2.1) unstable; urgency=medium ++ ++ * Non-maintainer upload. ++ * Fix "FTBFS: Tries to write to $HOME during build" using Peter Green's ++ patch. ++ * In addition, make package buildable by hacking the build system to use ++ -shared and -lpython for all gfortran using modules. (Closes: ++ #535699) ++ ++ -- Kumar Appaiah Sun, 31 Jan 2010 00:40:11 -0600 ++ ++nipy (0.1.2+1741-2) unstable; urgency=low ++ ++ * Adjusted long descriptions to follow the guidelines and to become ++ complete sentences with redundant prefixes (closes: #532860) ++ ++ -- Yaroslav Halchenko Fri, 12 Jun 2009 16:56:54 -0400 ++ ++nipy (0.1.2+1741-1) unstable; urgency=low ++ ++ * Initial release (Closes: #522353) ++ ++ -- Experimental Psychology Maintainers Tue, 14 Apr 2009 18:21:44 -0400 ++ diff --cc debian/compat index 0000000,0000000..7f8f011 new file mode 100644 --- /dev/null +++ b/debian/compat @@@ -1,0 -1,0 +1,1 @@@ ++7 diff --cc debian/control index 0000000,0000000..b1da9d9 new file mode 100644 --- /dev/null +++ b/debian/control @@@ -1,0 -1,0 +1,83 @@@ ++Source: nipy ++Section: python ++Priority: extra ++Maintainer: NeuroDebian Team ++Uploaders: Yaroslav Halchenko , Michael Hanke ++Build-Depends: debhelper (>= 7.0.50~), python-all-dev (>= 2.5), ++ python-scipy (>= 0.5), python-numpy (>= 1:1.2), python-matplotlib (>= 0.98.3), ++ python-sphinx (>= 0.6), cython, ++ python-nibabel, python-nose, python-sympy (>= 0.6.6), ++ liblapack-dev, ++ python-all-dbg, python-numpy-dbg, python-scipy-dbg, cython-dbg, ++ graphviz, dvipng, ++ help2man, ++Standards-Version: 3.9.6 ++Homepage: http://neuroimaging.scipy.org ++Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/nipy.git ++Vcs-Git: git://git.debian.org/git/pkg-exppsy/nipy.git ++ ++ ++Package: python-nipy ++Architecture: all ++Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, ++ python-scipy, python-numpy (>= 1:1.2), ++ python-nibabel, ++ python-nipy-lib (>= ${source:Version}), ++Recommends: python-matplotlib, ++ mayavi2, ++ python-sympy, ++Suggests: python-mvpa ++Provides: ${python:Provides} ++XB-Python-Version: ${python:Versions} ++Description: Analysis of structural and functional neuroimaging data ++ NiPy is a Python-based framework for the analysis of structural and ++ functional neuroimaging data. It provides functionality for ++ - General linear model (GLM) statistical analysis ++ - Combined slice time correction and motion correction ++ - General image registration routines with flexible cost functions, ++ optimizers and re-sampling schemes ++ - Image segmentation ++ - Basic visualization of results in 2D and 3D ++ - Basic time series diagnostics ++ - Clustering and activation pattern analysis across subjects ++ - Reproducibility analysis for group studies ++ ++ ++Package: python-nipy-lib ++Architecture: any ++Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} ++Provides: ${python:Provides} ++XB-Python-Version: ${python:Versions} ++Description: Analysis of structural and functional neuroimaging data ++ NiPy is a Python-based framework for the analysis of structural and ++ functional neuroimaging data. ++ . ++ This package provides architecture-dependent builds of the libraries. ++ ++ ++Package: python-nipy-lib-dbg ++Architecture: any ++Section: debug ++Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, ++ python-nipy-lib (= ${binary:Version}) ++Provides: ${python:Provides} ++XB-Python-Version: ${python:Versions} ++Description: Analysis of structural and functional neuroimaging data ++ NiPy is a Python-based framework for the analysis of structural and ++ functional neuroimaging data. ++ . ++ This package provides debugging symbols for architecture-dependent ++ builds of the libraries. ++ ++ ++Package: python-nipy-doc ++Architecture: all ++Section: doc ++Depends: ${misc:Depends}, libjs-jquery, libjs-underscore ++Recommends: python-nipy ++Description: documentation and examples for NiPy ++ This package contains NiPy documentation in various formats (HTML, ++ TXT) including ++ * User manual ++ * Developer guidelines ++ * API documentation diff --cc debian/copyright index 0000000,0000000..bf46a10 new file mode 100644 --- /dev/null +++ b/debian/copyright @@@ -1,0 -1,0 +1,58 @@@ ++Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 ++Upstream-Name: NIPY ++Upstream-Contact: Matthew Brett ++Source: http://github.com/nipy/nipy ++ ++ ++Files: * ++Copyright: 2006-2012, NIPY Developers ++License: BSD-3 ++ ++Files: nipy/testing/lightunit.py ++Copyright: 2009, The IPython Development Team ++License: BSD-3 ++ ++Files: nipy/labs/* ++Copyright: 2003-2012, CEA-INRIA-INSERM ++License: BSD-3 ++ ++Files: nipy/externals/configobj.py ++Copyright: 2005-2006, Michael Foord ++ 2005-2006, Nicola Larosa ++License: BSD-3 ++ ++Files: nipy/algorithms/statistics/models ++Copyright: 2006, Jonathan E. Taylor ++License: BSD-3 ++ ++Files: debian/* ++Copyright: 2009-2012, Yaroslav Halchenko ++ 2009-2010, Michael Hanke ++License: BSD-3 ++ ++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 NIPY 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. diff --cc debian/docs index 0000000,0000000..e845566 new file mode 100644 --- /dev/null +++ b/debian/docs @@@ -1,0 -1,0 +1,1 @@@ ++README diff --cc debian/gbp.conf index 0000000,0000000..a51d9b8 new file mode 100644 --- /dev/null +++ b/debian/gbp.conf @@@ -1,0 -1,0 +1,5 @@@ ++[DEFAULT] ++upstream-branch = master ++debian-branch = debian ++upstream-tag = %(version)s ++debian-tag = debian/%(version)s diff --cc debian/patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff index 0000000,0000000..9ba435c new file mode 100644 --- /dev/null +++ b/debian/patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff @@@ -1,0 -1,0 +1,21 @@@ ++From: Bertrand Thirion ++Subject: fixed failing doctest ++ ++--- a/nipy/algorithms/statistics/mixed_effects_stat.py +++++ b/nipy/algorithms/statistics/mixed_effects_stat.py ++@@ -12,12 +12,11 @@ Author: Bertrand Thirion, 2012. ++ ++ >>> N, P = 15, 500 ++ >>> V1 = np.random.randn(N, P) ** 2 ++->>> effects = np.random.randn(P) > 0 +++>>> effects = np.ones(P) ++ >>> Y = generate_data(np.ones(N), effects, .25, V1) ++ >>> T1 = one_sample_ttest(Y, V1, n_iter=5) ++->>> T1 = [T1[effects == x] for x in np.unique(effects)] ++->>> T2 = [t_stat(Y)[effects == x] for x in np.unique(effects)] ++->>> assert np.array([t1.std() < t2.std() for t1, t2 in zip(T1, T2)]).all() +++>>> T2 = t_stat(Y) +++>>> assert(T1.std() < T2.std()) ++ """ ++ from __future__ import absolute_import ++ from __future__ import print_function diff --cc debian/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff index 0000000,0000000..68568e4 new file mode 100644 --- /dev/null +++ b/debian/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff @@@ -1,0 -1,0 +1,17 @@@ ++From: Yaroslav Halchenko ++Subject: BF: allow for generic IOError-based exception to be thrown when loading non existing file ++ ++--- a/nipy/io/tests/test_image_io.py +++++ b/nipy/io/tests/test_image_io.py ++@@ -41,7 +41,10 @@ def load_template_img(): ++ ++ def test_badfile(): ++ filename = "bad_file.foo" ++- assert_raises(ImageFileError, load_image, filename) +++ # nibabel prior 2.1.0 was throwing ImageFileError and then more specific +++ # FileNotFileNotFoundError which should be a subclass of IOError. +++ # To not mess with version specific imports, checking for IOError +++ assert_raises((ImageFileError, IOError), load_image, filename) ++ ++ ++ @if_templates diff --cc debian/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff index 0000000,0000000..0b2d7a0 new file mode 100644 --- /dev/null +++ b/debian/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff @@@ -1,0 -1,0 +1,27 @@@ ++From: Matthew Brett ++Subject: TST: relax test precision a little for 32-bit ++ 32-bit giving test precision error:: ++ ++ line 154, in test_mu2tet ++ assert_equal(intvol.mu2_tet(0,0,0,0,1,0,0,1,0,1), (3./2 + ++ np.sqrt(3./4))/2) ++ AssertionError: 1.1830127018922194 != 1.1830127018922192 ++ ++See: https://travis-ci.org/MacPython/nipy-wheels/jobs/140268243#L451 ++ ++--- a/nipy/algorithms/statistics/tests/test_intrinsic_volumes.py +++++ b/nipy/algorithms/statistics/tests/test_intrinsic_volumes.py ++@@ -151,8 +151,11 @@ def test_mu1tri(): ++ ++ ++ def test_mu2tet(): ++- assert_equal(intvol.mu2_tet(0,0,0,0,1,0,0,1,0,1), (3./2 + np.sqrt(3./4))/2) ++- +++ # 15 digit precision error found on 32-bit Linux +++ # https://travis-ci.org/MacPython/nipy-wheels/jobs/140268248#L725 +++ assert_almost_equal(intvol.mu2_tet(0,0,0,0,1,0,0,1,0,1), +++ (3./2 + np.sqrt(3./4))/2, +++ 15) ++ ++ def pts2mu1_tet(d, a, b, c): ++ """ Accept point coordinates for calling mu1_tet diff --cc debian/patches/jaunty-dsc-patch-nodbg index 0000000,0000000..c3570cc new file mode 120000 --- /dev/null +++ b/debian/patches/jaunty-dsc-patch-nodbg @@@ -1,0 -1,0 +1,1 @@@ ++lenny-dsc-patch-nodbg diff --cc debian/patches/karmic-dsc-patch-nodbg index 0000000,0000000..c3570cc new file mode 120000 --- /dev/null +++ b/debian/patches/karmic-dsc-patch-nodbg @@@ -1,0 -1,0 +1,1 @@@ ++lenny-dsc-patch-nodbg diff --cc debian/patches/lenny-dsc-patch-nodbg index 0000000,0000000..35ab882 new file mode 100644 --- /dev/null +++ b/debian/patches/lenny-dsc-patch-nodbg @@@ -1,0 -1,0 +1,37 @@@ ++From: Yaroslav Halchenko ++Subject: Disable building of -dbg packages since distribution lacks scipy-dbg ++ ++Vendor: Debian ++ ++--- a/debian/control +++++ b/debian/control ++@@ -8,7 +8,6 @@ ++ python-sphinx (>= 0.6), cython, ++ python-nibabel, python-nose, python-sympy (>= 0.6.6), ++ liblapack-dev, ++- python-all-dbg, python-numpy-dbg, python-scipy-dbg, cython-dbg, ++ graphviz, dvipng ++ Standards-Version: 3.9.2 ++ Homepage: http://neuroimaging.scipy.org ++@@ -52,21 +51,6 @@ ++ This package provides architecture-dependent builds of the libraries. ++ ++ ++-Package: python-nipy-lib-dbg ++-Architecture: any ++-Section: debug ++-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, ++- python-nipy-lib (= ${binary:Version}) ++-Provides: ${python:Provides} ++-XB-Python-Version: ${python:Versions} ++-Description: Analysis of structural and functional neuroimaging data ++- NiPy is a Python-based framework for the analysis of structural and ++- functional neuroimaging data. ++- . ++- This package provides debugging symbols for architecture-dependent ++- builds of the libraries. ++- ++- ++ Package: python-nipy-doc ++ Architecture: all ++ Section: doc diff --cc debian/patches/lucid-dsc-patch-nodbg index 0000000,0000000..c3570cc new file mode 120000 --- /dev/null +++ b/debian/patches/lucid-dsc-patch-nodbg @@@ -1,0 -1,0 +1,1 @@@ ++lenny-dsc-patch-nodbg diff --cc debian/patches/lucid-dsc-patch-nodoc index 0000000,0000000..3135a49 new file mode 100644 --- /dev/null +++ b/debian/patches/lucid-dsc-patch-nodoc @@@ -1,0 -1,0 +1,60 @@@ ++From: Yaroslav Halchenko ++Subject: Do not build -doc package on older releases lacking necessary build-depends ++Origin: Debian ++Last-Update: 2012-07-22 ++ ++diff --git a/debian/control b/debian/control ++index 5387753..4689327 100644 ++--- a/debian/control +++++ b/debian/control ++@@ -5,11 +5,10 @@ Maintainer: NeuroDebian Team ++ Uploaders: Yaroslav Halchenko , Michael Hanke ++ Build-Depends: debhelper (>= 7.0.50~), python-all-dev (>= 2.5), python-support (>= 0.6), ++ python-scipy (>= 0.5), python-numpy (>= 1:1.2), python-matplotlib (>= 0.98.3), ++- python-sphinx (>= 0.6), cython, +++ cython, ++ python-nibabel, python-nose, python-sympy (>= 0.6.6), ++ liblapack-dev, ++ python-all-dbg, python-numpy-dbg, python-scipy-dbg, cython-dbg, ++- graphviz, dvipng ++ Standards-Version: 3.9.3 ++ Homepage: http://neuroimaging.scipy.org ++ Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/nipy.git ++@@ -67,16 +66,3 @@ Description: Analysis of structural and functional neuroimaging data ++ . ++ This package provides debugging symbols for architecture-dependent ++ builds of the libraries. ++- ++- ++-Package: python-nipy-doc ++-Architecture: all ++-Section: doc ++-Depends: ${misc:Depends}, libjs-jquery ++-Recommends: python-nipy ++-Description: documentation and examples for NiPy ++- This package contains NiPy documentation in various formats (HTML, ++- TXT) including ++- * User manual ++- * Developer guidelines ++- * API documentation ++diff --git a/debian/rules b/debian/rules ++index 908535e..c37d763 100755 ++--- a/debian/rules +++++ b/debian/rules ++@@ -29,7 +29,7 @@ doc-stamp: ++ : # I: Generate documentation ++ export PYTHONPATH=$$PWD/`/bin/ls -d build/lib.*$(PYVER)` \ ++ MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \ ++- cd doc; $(MAKE) html +++ cd doc; # $(MAKE) html ++ : # I: Use jquery from Debian package ++ -rm doc/build/html/_static/jquery.js ++ touch $@ ++@@ -83,6 +83,6 @@ override_dh_clean: ++ ++ ++ # We build documentation only for -indep ++-binary-indep: doc-stamp +++binary-indep: ++ ++ binary: binary-arch binary-indep diff --cc debian/patches/series index 0000000,0000000..af945ce new file mode 100644 --- /dev/null +++ b/debian/patches/series @@@ -1,0 -1,0 +1,3 @@@ ++changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff ++changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff ++changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff diff --cc debian/pycompat index 0000000,0000000..0cfbf08 new file mode 100644 --- /dev/null +++ b/debian/pycompat @@@ -1,0 -1,0 +1,1 @@@ ++2 diff --cc debian/python-nipy-doc.docs index 0000000,0000000..8137b04 new file mode 100644 --- /dev/null +++ b/debian/python-nipy-doc.docs @@@ -1,0 -1,0 +1,1 @@@ ++doc/build/html diff --cc debian/python-nipy-doc.examples index 0000000,0000000..2c8fad4 new file mode 100644 --- /dev/null +++ b/debian/python-nipy-doc.examples @@@ -1,0 -1,0 +1,1 @@@ ++examples/*.py diff --cc debian/python-nipy-doc.links index 0000000,0000000..ebefa35 new file mode 100644 --- /dev/null +++ b/debian/python-nipy-doc.links @@@ -1,0 -1,0 +1,2 @@@ ++usr/share/javascript/jquery/jquery.js usr/share/doc/python-nipy-doc/html/_static/jquery.js ++usr/share/javascript/underscore/underscore.js usr/share/doc/python-nipy-doc/html/_static/underscore.js diff --cc debian/python-nipy-doc.lintian-overrides index 0000000,0000000..636341d new file mode 100644 --- /dev/null +++ b/debian/python-nipy-doc.lintian-overrides @@@ -1,0 -1,0 +1,4 @@@ ++# Explicit license file is desired for the completeness of the documentation ++# ++ ++python-nipy-doc binary: extra-license-file usr/share/doc/python-nipy-doc/html/_sources/license.txt diff --cc debian/python-nipy.docs index 0000000,0000000..ed2ec4c new file mode 100644 --- /dev/null +++ b/debian/python-nipy.docs @@@ -1,0 -1,0 +1,1 @@@ ++debian/upstream diff --cc debian/pyversions index 0000000,0000000..b3dc41e new file mode 100644 --- /dev/null +++ b/debian/pyversions @@@ -1,0 -1,0 +1,1 @@@ ++2.5- diff --cc debian/rules index 0000000,0000000..259ec73 new file mode 100755 --- /dev/null +++ b/debian/rules @@@ -1,0 -1,0 +1,106 @@@ ++#!/usr/bin/make -f ++# -*- mode: makefile; coding: utf-8 -*- ++ ++export DH_VERBOSE=1 ++ ++debver = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Version:' | cut -d ' ' -f 2,2 ) ++uver = $(shell echo $(debver) | sed -e 's,-[^-]*$$,,g' ) ++ ++PYVER = $(shell pyversions -vd) ++ ++# To fix distutils fragile nature: when seing LDFLAGS=, which is set ++# by dpkg-buildpackage it stops providing -shared flag, so for the ++# minimalistic fix (alternative to NMU-ed #535699 with explicit ++# -shared) we just unexport LDFLAGS ++unexport LDFLAGS ++ ++# Mega rule ++%: ++ dh --buildsystem=python_distutils --with=python2 $@ ++ ++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 ++ ++manpages: ++ @echo "I: generating manpages" ++ set -e; mkdir -p build/manpages && \ ++ cd scripts && for f in *; do \ ++ descr=$$(grep -h -e "^ *'''" -e 'DESCRIP =' $$f | sed -e "s,.*' *\([^'][^']*\)'.*,\1,g" | head -n 1); \ ++ PYTHONPATH=../ \ ++ help2man -n "$$descr" --no-discard-stderr --no-info --version-string "$(uver)" "python ./$$f" \ ++ >| ../build/manpages/$$f.1; \ ++ done ++ ++# ++# Documentation ++# ++doc-stamp: ++ : # I: Generate documentation ++ export PYTHONPATH=$$PWD/`/bin/ls -d build/lib.*$(PYVER)` \ ++ PATH=$(CURDIR)/debian/tmp/usr/bin/:$$PATH \ ++ MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \ ++ cd doc; $(MAKE) html ++ : # I: Use jquery from Debian package ++ -rm doc/build/html/_static/jquery.js ++ touch $@ ++ ++ ++#override_dh_auto_install: ++# dh_auto_install ++ ++test: ++ifeq (testsuitedisabled,$(filter nocheck,$(DEB_BUILD_OPTIONS))) ++ : # I: Unittest only the default python version for now against "installed" materials ++ cd debian; \ ++ PATH=$(CURDIR)/debian/tmp/usr/bin/:$$PATH \ ++ PYTHONPATH=$$(/bin/ls -d $(CURDIR)/debian/tmp/usr/lib/python$(PYVER)/*-packages):$$PYTHONPATH \ ++ MPLCONFIGDIR=$(CURDIR)/build \ ++ ../tools/nipnost nipy ++else ++ : # Skip unittests due to nocheck ++endif ++ ++override_dh_install: test ++ : # I: Move libraries into the python-nipy-lib and -lib-dbg packages ++ find debian/tmp/ -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,debian/tmp/,debian/python-nipy-lib$$suf/,g"); \ ++ mkdir -p $$d; echo "Moving $$so under $$d"; mv $$so $$d; \ ++ done ++ : # I: Move leftovers into python-nipy ++ mkdir -p debian/python-nipy ++ mv debian/tmp/* debian/python-nipy/ ++ : # I: Fix up interpreter which might be -dbg one ++ sed -i -e 's,/usr/bin/python-dbg,/usr/bin/python,g' debian/python-nipy/usr/bin/* ++ : # I: Assure versioned dependency on NumPy ++ if [ -x /usr/bin/dh_numpy ]; then dh_numpy; fi ++ ++ dh_install ++ -rm debian/python-nipy-doc/usr/share/javascript/underscore/underscore.js ++ ++ ++## immediately useable documentation and exemplar scripts/data ++override_dh_compress: ++ : # I: Avoiding compression of what should not be compressed ++ dh_compress -X.py -X.html -X.pdf -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -Xobjects.inv ++ ++override_dh_installman: manpages ++ dh_installman -ppython-nipy build/manpages/*.1 ++ ++override_dh_clean: ++ : # I: Custom cleaning ++ rm -rf build doc-stamp nipy/neurospin/__config__.py ++ $(MAKE) -C doc clean ++ dh_clean ++ ++ ++# We build documentation only for -indep ++binary-indep: doc-stamp ++ ++binary: binary-arch binary-indep diff --cc debian/source/format index 0000000,0000000..163aaf8 new file mode 100644 --- /dev/null +++ b/debian/source/format @@@ -1,0 -1,0 +1,1 @@@ ++3.0 (quilt) diff --cc debian/source/options index 0000000,0000000..558e200 new file mode 100644 --- /dev/null +++ b/debian/source/options @@@ -1,0 -1,0 +1,1 @@@ ++extend-diff-ignore = "(^|/)(nipy/COMMIT_INFO.txt|\.gitignore)$" diff --cc debian/upstream/metadata index 0000000,0000000..8b38d57 new file mode 100644 --- /dev/null +++ b/debian/upstream/metadata @@@ -1,0 -1,0 +1,11 @@@ ++Name: nipy ++Reference: ++ - Author: K. Jarrod Millman and Matthew Brett ++ Title: Analysis of functional magnetic resonance imaging in Python ++ Publisher: IEEE Computer Society ++ Journal: Computing in Science & Engineering ++ Pages: 52--55 ++ Year: 2007 ++ Volume: 9 ++ Number: 3 ++ eprint: http://jarrodmillman.com/papers/nipy-cise2007.pdf diff --cc debian/watch index 0000000,0000000..6d3f808 new file mode 100644 --- /dev/null +++ b/debian/watch @@@ -1,0 -1,0 +1,4 @@@ ++# Compulsory line, this is a version 3 file ++version=3 ++opts="filenamemangle=s/.*\/(.*)/nipy-$1/" \ ++ http://github.com/nipy/nipy/tags .*archive/(\d[\d\.a-z]+)\.tar\.gz