--- /dev/null
--- /dev/null
++- package https://github.com/matthew-brett/texext used in the documentation
--- /dev/null
--- /dev/null
++nipy (0.4.2-2) unstable; urgency=medium
++
++ * Cherry picked a number of fixes from upstream/PRs to become a part of the
++ next release (Closes: #906388)
++ * debian/control
++ - fixed up Vcs fields to point to salsa
++
++ -- Yaroslav Halchenko <debian@onerussian.com> Thu, 10 Jan 2019 11:05:31 -0500
++
++nipy (0.4.2-1) unstable; urgency=medium
++
++ * Fresh upstream release
++ * debian/patches
++ - dropped changesets - upstreamed
++ - deb_no_ipython_console_highlight for now to not require that sphinx
++ extension
++
++ -- Yaroslav Halchenko <debian@onerussian.com> Mon, 19 Feb 2018 11:06:56 -0500
++
++nipy (0.4.1-2) unstable; urgency=medium
++
++ * Boost statement of policy compliance to 4.1.2
++ * Boost debhelper compat from 7 to 9
++ - $@ should come before the options (like --buildsystem=python_distutils)
++ * debian/patches
++ - picked up few patches from upstream to avoid infinite recursion in sympy
++
++ -- Yaroslav Halchenko <debian@onerussian.com> Mon, 18 Dec 2017 10:01:44 -0500
++
++nipy (0.4.1-1) unstable; urgency=medium
++
++ * Fresh upstream release
++ - should resolve some failing tests (Closes: #848745)
++ - dropping absorbed changeset* patches
++
++ -- Yaroslav Halchenko <debian@onerussian.com> Sun, 30 Jul 2017 21:20:58 -0400
++
++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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <debian@onerussian.com> 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 <akumar@debian.org> 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<ver> for all gfortran using modules. (Closes:
++ #535699)
++
++ -- Kumar Appaiah <akumar@debian.org> 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 <debian@onerussian.com> Fri, 12 Jun 2009 16:56:54 -0400
++
++nipy (0.1.2+1741-1) unstable; urgency=low
++
++ * Initial release (Closes: #522353)
++
++ -- Experimental Psychology Maintainers <pkg-exppsy-maintainers@lists.alioth.debian.org> Tue, 14 Apr 2009 18:21:44 -0400
++
--- /dev/null
--- /dev/null
++9
--- /dev/null
--- /dev/null
++Source: nipy
++Section: python
++Priority: extra
++Maintainer: NeuroDebian Team <team@neuro.debian.net>
++Uploaders: Yaroslav Halchenko <debian@onerussian.com>, Michael Hanke <michael.hanke@gmail.com>
++Build-Depends: debhelper (>=9), 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-numpydoc,
++ 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: 4.1.2
++Homepage: http://neuroimaging.scipy.org
++Vcs-Browser: https://salsa.debian.org/neurodebian-team/nipy
++Vcs-Git: https://salsa.debian.org/neurodebian-team/nipy -b debian
++
++
++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
--- /dev/null
--- /dev/null
++Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
++Upstream-Name: NIPY
++Upstream-Contact: Matthew Brett <matthew.brett@gmail.com>
++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 <fuzzyman AT voidspace DOT org DOT uk>
++ 2005-2006, Nicola Larosa <nico AT tekNico DOT net>
++License: BSD-3
++
++Files: nipy/algorithms/statistics/models
++Copyright: 2006, Jonathan E. Taylor
++License: BSD-3
++
++Files: debian/*
++Copyright: 2009-2012, Yaroslav Halchenko <debian@onerussian.com>
++ 2009-2010, Michael Hanke <michael.hanke@gmail.com>
++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.
--- /dev/null
--- /dev/null
++README
--- /dev/null
--- /dev/null
++[DEFAULT]
++upstream-branch = master
++debian-branch = debian
++upstream-tag = %(version)s
++debian-tag = debian/%(version)s
--- /dev/null
--- /dev/null
++From: Matthew Brett <matthew.brett@gmail.com>
++Subject: BF: fix for division error gh-446
++ Thanks to @Amiiir for tracking down this error.
++
++Closes gh-446.
++
++--- a/nipy/algorithms/clustering/tests/test_vmm.py
+++++ b/nipy/algorithms/clustering/tests/test_vmm.py
++@@ -12,8 +12,13 @@ from ..von_mises_fisher_mixture import (
++ select_vmm,
++ select_vmm_cv)
++
++-
++ from nose.tools import assert_true, assert_equal
+++from numpy.testing import decorators
+++
+++from nibabel.optpkg import optional_package
+++
+++matplotlib, HAVE_MPL, _ = optional_package('matplotlib')
+++needs_mpl = decorators.skipif(not HAVE_MPL, "Test needs matplotlib")
++
++
++ def test_spherical_area():
++@@ -38,6 +43,18 @@ def test_von_mises_fisher_density():
++ < 1e-2)
++
++
+++@needs_mpl
+++def test_von_mises_fisher_show():
+++ # Smoke test for VonMisesMixture.show
+++ x = np.random.randn(100, 3)
+++ x = (x.T/np.sqrt(np.sum(x**2, 1))).T
+++ vmd = VonMisesMixture(1, 1)
+++ # Need to estimate to avoid error in show
+++ vmd.estimate(x)
+++ # Check that show does not raise an error
+++ vmd.show(x)
+++
+++
++ def test_dimension_selection_bic():
++ # Tests whether dimension selection yields correct results
++ x1 = [0.6, 0.48, 0.64]
++--- a/nipy/algorithms/clustering/von_mises_fisher_mixture.py
+++++ b/nipy/algorithms/clustering/von_mises_fisher_mixture.py
++@@ -233,8 +233,13 @@ class VonMisesMixture(object):
++
++ Parameters
++ ----------
++- x: array fo shape(n,3)
+++ x: array of shape (n, 3)
++ should be on the unit sphere
+++
+++ Notes
+++ -----
+++
+++ Uses ``matplotlib``.
++ """
++ # label the data
++ z = np.argmax(self.responsibilities(x), 1)
++@@ -243,7 +248,7 @@ class VonMisesMixture(object):
++ fig = pylab.figure()
++ ax = p3.Axes3D(fig)
++ colors = (['b', 'g', 'r', 'c', 'm', 'y', 'k', 'w'] * \
++- (1 + (1 + self.k) / 8))[:self.k + 1]
+++ (1 + (1 + self.k) // 8))[:self.k + 1]
++ if (self.null_class) and (z == 0).any():
++ ax.plot3D(x[z == 0, 0], x[z == 0, 1], x[z == 0, 2], '.',
++ color=colors[0])
--- /dev/null
--- /dev/null
++From: Yaroslav Halchenko <debian@onerussian.com>
++Subject: BF: import nosetester explicitely for a doctest
++ Otherwise it leads to failures with fresh numpy where testing.nosetester is
++not automatically imported. See e.g.
++https://travis-ci.org/nipy/nipy/jobs/442714642
++
++--- a/nipy/fixes/numpy/testing/nosetester.py
+++++ b/nipy/fixes/numpy/testing/nosetester.py
++@@ -21,7 +21,8 @@ def get_package_name(filepath):
++
++ Examples
++ --------
++- >>> np.testing.nosetester.get_package_name('nonsense')
+++ >>> from numpy.testing import nosetester
+++ >>> nosetester.get_package_name('nonsense')
++ 'numpy'
++
++ """
--- /dev/null
--- /dev/null
++From: Yaroslav Halchenko <debian@onerussian.com>
++Subject: BF: do not check sympy implementation details (ie for _imp_)
++
++--- a/nipy/modalities/fmri/tests/test_aliases.py
+++++ b/nipy/modalities/fmri/tests/test_aliases.py
++@@ -42,9 +42,8 @@ def test_implemented_function():
++ assert_equal(l2(3), np.sqrt(3))
++ # check that we can pass in a sympy function as input
++ func = sympy.Function('myfunc')
++- assert_false(hasattr(func, '_imp_'))
++ f = implemented_function(func, lambda x: 2*x)
++- assert_true(hasattr(func, '_imp_'))
+++ assert(f)
++
++
++ def test_lambdify():
--- /dev/null
--- /dev/null
--- /dev/null
--- /dev/null
++Index: nipy-0.4.2/doc/conf.py
++===================================================================
++--- nipy-0.4.2.orig/doc/conf.py
+++++ nipy-0.4.2/doc/conf.py
++@@ -45,10 +45,15 @@ extensions = [
++ 'numpydoc',
++ 'sphinx.ext.inheritance_diagram',
++ 'matplotlib.sphinxext.plot_directive',
++- 'IPython.sphinxext.ipython_console_highlighting',
++ ]
++
++ try:
+++ import IPython.sphinxext.ipython_console_highlighting
+++ extensions += ['IPython.sphinxext.ipython_console_highlighting']
+++except ImportError:
+++ pass
+++
+++try:
++ import texext.mathcode
++ import texext.math_dollar
++ extensions += [
--- /dev/null
--- /dev/null
++From: Yaroslav Halchenko <debian@onerussian.com>
++Subject: depends on not yet packaged https://github.com/matthew-brett/texext
++
++Origin: NeuroDebian
++Last-Update: 2018-02-19
++
++--- a/doc/conf.py
+++++ b/doc/conf.py
++@@ -38,18 +38,26 @@ needs_sphinx = '1.0'
++ # Add any Sphinx extension module names here, as strings. They can be extensions
++ # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
++ extensions = [
++- 'texext.mathcode',
++ 'sphinx.ext.autodoc',
++ 'sphinx.ext.doctest',
++ 'sphinx.ext.mathjax',
++ 'sphinx.ext.autosummary',
++- 'texext.math_dollar',
++ 'numpydoc',
++ 'sphinx.ext.inheritance_diagram',
++ 'matplotlib.sphinxext.plot_directive',
++ 'IPython.sphinxext.ipython_console_highlighting',
++ ]
++
+++try:
+++ import texext.mathcode
+++ import texext.math_dollar
+++ extensions += [
+++ 'texext.mathcode',
+++ 'texext.math_dollar',
+++ ]
+++except ImportError:
+++ pass
+++
++ # Autosummary on
++ autosummary_generate=True
++
--- /dev/null
--- /dev/null
++lenny-dsc-patch-nodbg
--- /dev/null
--- /dev/null
++lenny-dsc-patch-nodbg
--- /dev/null
--- /dev/null
++From: Yaroslav Halchenko <debian@onerussian.com>
++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
--- /dev/null
--- /dev/null
++lenny-dsc-patch-nodbg
--- /dev/null
--- /dev/null
++From: Yaroslav Halchenko <debian@onerussian.com>
++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 <team@neuro.debian.net>
++ Uploaders: Yaroslav Halchenko <debian@onerussian.com>, Michael Hanke <michael.hanke@gmail.com>
++ 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=$$PWD/`/bin/ls -d build/lib.*$(PYVER)` \
++ MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \
++- cd doc; $(MAKE) html
+++ cd doc; # $(MAKE) html
++ : # I: Use jquery from Debian package
++ -rm doc/build/html/_static/jquery.js
++ touch $@
++@@ -83,6 +83,6 @@ override_dh_clean:
++
++
++ # We build documentation only for -indep
++-binary-indep: doc-stamp
+++binary-indep:
++
++ binary: binary-arch binary-indep
--- /dev/null
--- /dev/null
++changeset_7529ffc4585ba67171219aa29a3f6c5df9963f1d.diff
++changeset_aafe079d3bc2928c159cf2ecaa9fbdb3f6520e027529ffc4585ba67171219aa29a3f6c5df9963f1d.diff
++deb_no_texext
++deb_no_ipython_console_highlight
++changeset_aafe079d3bc2928c159cf2ecaa9fbdb3f6520e02.diff
++changeset_9f435191a420bf416ded3c32123fb2aa1163256a.diff
--- /dev/null
--- /dev/null
++2
--- /dev/null
--- /dev/null
++doc/build/html
--- /dev/null
--- /dev/null
++examples/*.py
--- /dev/null
--- /dev/null
++usr/share/javascript/jquery/jquery.js usr/share/doc/python-nipy-doc/html/_static/jquery.js
++usr/share/javascript/underscore/underscore.js usr/share/doc/python-nipy-doc/html/_static/underscore.js
--- /dev/null
--- /dev/null
++# Explicit license file is desired for the completeness of the documentation
++#
++
++python-nipy-doc binary: extra-license-file usr/share/doc/python-nipy-doc/html/_sources/license.txt
--- /dev/null
--- /dev/null
++debian/upstream
--- /dev/null
--- /dev/null
++2.5-
--- /dev/null
--- /dev/null
++#!/usr/bin/make -f
++# -*- mode: makefile; coding: utf-8 -*-
++
++export DH_VERBOSE=1
++
++debver = $(shell LC_ALL=C dpkg-parsechangelog | grep '^Version:' | cut -d ' ' -f 2,2 )
++uver = $(shell echo $(debver) | sed -e 's,-[^-]*$$,,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/:$$PATH \
++ MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \
++ cd doc; $(MAKE) html
++ : # I: Use jquery from Debian package
++ -rm doc/build/html/_static/jquery.js
++ touch $@
++
++
++#override_dh_auto_install:
++# dh_auto_install
++
++test:
++ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
++ : # I: Unittest only the default python version for now against "installed" materials
++ cd debian; \
++ PATH=$(CURDIR)/debian/tmp/usr/bin/:$$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
++ $(MAKE) -C doc clean
++ dh_clean
++
++
++# We build documentation only for -indep
++binary-indep: doc-stamp
++
++binary: binary-arch binary-indep
--- /dev/null
--- /dev/null
++3.0 (quilt)
--- /dev/null
--- /dev/null
++extend-diff-ignore = "(^|/)(nipy/COMMIT_INFO.txt|\.gitignore)$"
--- /dev/null
--- /dev/null
++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
--- /dev/null
--- /dev/null
++# 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
projects / nipy.git / commitdiff