From 971db7c53064cffe58470165547675c1039acc37 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Sun, 4 Sep 2016 15:18:55 +0100 Subject: [PATCH 1/1] 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] --- changelog | 264 ++++++++++++++++++ compat | 1 + control | 83 ++++++ copyright | 58 ++++ docs | 1 + gbp.conf | 5 + ...b61eab2e92525c2497294d3be40e361507c4e.diff | 21 ++ ...531a2894e69383f75e6a9b97586e74759ab1b.diff | 17 ++ ...ed182c4b4583c9a2ed3c1fc01764941560c72.diff | 27 ++ patches/jaunty-dsc-patch-nodbg | 1 + patches/karmic-dsc-patch-nodbg | 1 + patches/lenny-dsc-patch-nodbg | 37 +++ patches/lucid-dsc-patch-nodbg | 1 + patches/lucid-dsc-patch-nodoc | 60 ++++ patches/series | 3 + pycompat | 1 + python-nipy-doc.docs | 1 + python-nipy-doc.examples | 1 + python-nipy-doc.links | 2 + python-nipy-doc.lintian-overrides | 4 + python-nipy.docs | 1 + pyversions | 1 + rules | 106 +++++++ source/format | 1 + source/options | 1 + upstream/metadata | 11 + watch | 4 + 27 files changed, 714 insertions(+) create mode 100644 changelog create mode 100644 compat create mode 100644 control create mode 100644 copyright create mode 100644 docs create mode 100644 gbp.conf create mode 100644 patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff create mode 100644 patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff create mode 100644 patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff create mode 120000 patches/jaunty-dsc-patch-nodbg create mode 120000 patches/karmic-dsc-patch-nodbg create mode 100644 patches/lenny-dsc-patch-nodbg create mode 120000 patches/lucid-dsc-patch-nodbg create mode 100644 patches/lucid-dsc-patch-nodoc create mode 100644 patches/series create mode 100644 pycompat create mode 100644 python-nipy-doc.docs create mode 100644 python-nipy-doc.examples create mode 100644 python-nipy-doc.links create mode 100644 python-nipy-doc.lintian-overrides create mode 100644 python-nipy.docs create mode 100644 pyversions create mode 100755 rules create mode 100644 source/format create mode 100644 source/options create mode 100644 upstream/metadata create mode 100644 watch diff --git a/changelog b/changelog new file mode 100644 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 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 --git a/compat b/compat new file mode 100644 index 0000000..7f8f011 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +7 diff --git a/control b/control new file mode 100644 index 0000000..b1da9d9 --- /dev/null +++ b/control @@ -0,0 +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 --git a/copyright b/copyright new file mode 100644 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 +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 --git a/docs b/docs new file mode 100644 index 0000000..e845566 --- /dev/null +++ b/docs @@ -0,0 +1 @@ +README diff --git a/gbp.conf b/gbp.conf new file mode 100644 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 index 0000000..9ba435c --- /dev/null +++ b/patches/changeset_32cb61eab2e92525c2497294d3be40e361507c4e.diff @@ -0,0 +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 --git a/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff b/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff new file mode 100644 index 0000000..68568e4 --- /dev/null +++ b/patches/changeset_751531a2894e69383f75e6a9b97586e74759ab1b.diff @@ -0,0 +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 --git a/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff b/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff new file mode 100644 index 0000000..0b2d7a0 --- /dev/null +++ b/patches/changeset_78ced182c4b4583c9a2ed3c1fc01764941560c72.diff @@ -0,0 +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 --git a/patches/jaunty-dsc-patch-nodbg b/patches/jaunty-dsc-patch-nodbg new file mode 120000 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 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 index 0000000..35ab882 --- /dev/null +++ b/patches/lenny-dsc-patch-nodbg @@ -0,0 +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 --git a/patches/lucid-dsc-patch-nodbg b/patches/lucid-dsc-patch-nodbg new file mode 120000 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 index 0000000..3135a49 --- /dev/null +++ b/patches/lucid-dsc-patch-nodoc @@ -0,0 +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 --git a/patches/series b/patches/series new file mode 100644 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 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 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 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 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 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 index 0000000..ed2ec4c --- /dev/null +++ b/python-nipy.docs @@ -0,0 +1 @@ +debian/upstream diff --git a/pyversions b/pyversions new file mode 100644 index 0000000..b3dc41e --- /dev/null +++ b/pyversions @@ -0,0 +1 @@ +2.5- diff --git a/rules b/rules new file mode 100755 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 + $(MAKE) -C doc clean + dh_clean + + +# We build documentation only for -indep +binary-indep: doc-stamp + +binary: binary-arch binary-indep diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/source/options b/source/options new file mode 100644 index 0000000..558e200 --- /dev/null +++ b/source/options @@ -0,0 +1 @@ +extend-diff-ignore = "(^|/)(nipy/COMMIT_INFO.txt|\.gitignore)$" diff --git a/upstream/metadata b/upstream/metadata new file mode 100644 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 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 -- 2.30.2