Import nipy_0.4.0+git26-gf8d3149-2.debian.tar.xz

[dgit import tarball nipy 0.4.0+git26-gf8d3149-2 nipy_0.4.0+git26-gf8d3149-2.debian.tar.xz]

diff --git a/changelog b/changelog
new file mode 100644 (file)
index 0000000..6b16195
--- /dev/null
+++ b/changelog
@@ -0,0 +1,264 @@
+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
+

diff --git a/compat b/compat
new file mode 100644 (file)
index 0000000..7f8f011
--- /dev/null
+++ b/compat
@@ -0,0 +1 @@
+7

diff --git a/control b/control
new file mode 100644 (file)
index 0000000..b1da9d9
--- /dev/null
+++ b/control
@@ -0,0 +1,83 @@
+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 (>= 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 --git a/copyright b/copyright
new file mode 100644 (file)
index 0000000..bf46a10
--- /dev/null
+++ b/copyright
@@ -0,0 +1,58 @@
+Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
+Upstream-Name: NIPY
+Upstream-Contact: Matthew Brett <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.

diff --git a/docs b/docs
new file mode 100644 (file)
index 0000000..e845566
--- /dev/null
+++ b/docs
@@ -0,0 +1 @@
+README

diff --git a/gbp.conf b/gbp.conf
new file mode 100644 (file)
index 0000000..a51d9b8
--- /dev/null
+++ b/gbp.conf
@@ -0,0 +1,5 @@
+[DEFAULT]
+upstream-branch = master
+debian-branch = debian
+upstream-tag = %(version)s
+debian-tag = debian/%(version)s

diff --git a/patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff b/patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff
new file mode 100644 (file)
index 0000000..9ba435c
--- /dev/null
+++ b/patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff
@@ -0,0 +1,21 @@
+From: Bertrand Thirion <bertrand.thirion@inria.fr>
+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 --git a/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff b/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff
new file mode 100644 (file)
index 0000000..68568e4
--- /dev/null
+++ b/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff
@@ -0,0 +1,17 @@
+From: Yaroslav Halchenko <debian@onerussian.com>
+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 --git a/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff b/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff
new file mode 100644 (file)
index 0000000..0b2d7a0
--- /dev/null
+++ b/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff
@@ -0,0 +1,27 @@
+From: Matthew Brett <matthew.brett@gmail.com>
+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 --git a/patches/jaunty-dsc-patch-nodbg b/patches/jaunty-dsc-patch-nodbg
new file mode 120000 (symlink)
index 0000000..c3570cc
--- /dev/null
+++ b/patches/jaunty-dsc-patch-nodbg
@@ -0,0 +1 @@
+lenny-dsc-patch-nodbg
\ No newline at end of file

diff --git a/patches/karmic-dsc-patch-nodbg b/patches/karmic-dsc-patch-nodbg
new file mode 120000 (symlink)
index 0000000..c3570cc
--- /dev/null
+++ b/patches/karmic-dsc-patch-nodbg
@@ -0,0 +1 @@
+lenny-dsc-patch-nodbg
\ No newline at end of file

diff --git a/patches/lenny-dsc-patch-nodbg b/patches/lenny-dsc-patch-nodbg
new file mode 100644 (file)
index 0000000..35ab882
--- /dev/null
+++ b/patches/lenny-dsc-patch-nodbg
@@ -0,0 +1,37 @@
+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

diff --git a/patches/lucid-dsc-patch-nodbg b/patches/lucid-dsc-patch-nodbg
new file mode 120000 (symlink)
index 0000000..c3570cc
--- /dev/null
+++ b/patches/lucid-dsc-patch-nodbg
@@ -0,0 +1 @@
+lenny-dsc-patch-nodbg
\ No newline at end of file

diff --git a/patches/lucid-dsc-patch-nodoc b/patches/lucid-dsc-patch-nodoc
new file mode 100644 (file)
index 0000000..3135a49
--- /dev/null
+++ b/patches/lucid-dsc-patch-nodoc
@@ -0,0 +1,60 @@
+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

diff --git a/patches/series b/patches/series
new file mode 100644 (file)
index 0000000..af945ce
--- /dev/null
+++ b/patches/series
@@ -0,0 +1,3 @@
+changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff
+changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff
+changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff

diff --git a/pycompat b/pycompat
new file mode 100644 (file)
index 0000000..0cfbf08
--- /dev/null
+++ b/pycompat
@@ -0,0 +1 @@
+2

diff --git a/python-nipy-doc.docs b/python-nipy-doc.docs
new file mode 100644 (file)
index 0000000..8137b04
--- /dev/null
+++ b/python-nipy-doc.docs
@@ -0,0 +1 @@
+doc/build/html

diff --git a/python-nipy-doc.examples b/python-nipy-doc.examples
new file mode 100644 (file)
index 0000000..2c8fad4
--- /dev/null
+++ b/python-nipy-doc.examples
@@ -0,0 +1 @@
+examples/*.py

diff --git a/python-nipy-doc.links b/python-nipy-doc.links
new file mode 100644 (file)
index 0000000..ebefa35
--- /dev/null
+++ b/python-nipy-doc.links
@@ -0,0 +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 --git a/python-nipy-doc.lintian-overrides b/python-nipy-doc.lintian-overrides
new file mode 100644 (file)
index 0000000..636341d
--- /dev/null
+++ b/python-nipy-doc.lintian-overrides
@@ -0,0 +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 --git a/python-nipy.docs b/python-nipy.docs
new file mode 100644 (file)
index 0000000..ed2ec4c
--- /dev/null
+++ b/python-nipy.docs
@@ -0,0 +1 @@
+debian/upstream

diff --git a/pyversions b/pyversions
new file mode 100644 (file)
index 0000000..b3dc41e
--- /dev/null
+++ b/pyversions
@@ -0,0 +1 @@
+2.5-

diff --git a/rules b/rules
new file mode 100755 (executable)
index 0000000..5d8be8c
--- /dev/null
+++ b/rules
@@ -0,0 +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/:$$PATH \
+                  MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \
+     cd doc; $(MAKE) html
+       : # I: Use jquery from Debian package
+       -rm doc/build/html/_static/jquery.js
+       touch $@
+
+
+#override_dh_auto_install:
+#      dh_auto_install
+
+test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+       : # I: Unittest only the default python version for now against "installed" materials
+       cd debian; \
+     PATH=$(CURDIR)/debian/tmp/usr/bin/:$$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 --git a/source/format b/source/format
new file mode 100644 (file)
index 0000000..163aaf8
--- /dev/null
+++ b/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

diff --git a/source/options b/source/options
new file mode 100644 (file)
index 0000000..558e200
--- /dev/null
+++ b/source/options
@@ -0,0 +1 @@
+extend-diff-ignore = "(^|/)(nipy/COMMIT_INFO.txt|\.gitignore)$"

diff --git a/upstream/metadata b/upstream/metadata
new file mode 100644 (file)
index 0000000..8b38d57
--- /dev/null
+++ b/upstream/metadata
@@ -0,0 +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 --git a/watch b/watch
new file mode 100644 (file)
index 0000000..6d3f808
--- /dev/null
+++ b/watch
@@ -0,0 +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