From 34bf45f883526e6f440e6e6021e6d87ac359806f Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 19 Feb 2018 16:06:56 +0000 Subject: [PATCH 1/1] Import nipy_0.4.2-1.debian.tar.xz [dgit import tarball nipy 0.4.2-1 nipy_0.4.2-1.debian.tar.xz] --- TODO | 1 + changelog | 292 +++++++++++++++++++++++ compat | 1 + control | 84 +++++++ copyright | 58 +++++ docs | 1 + gbp.conf | 5 + patches/deb_no_ipython_console_highlight | 21 ++ patches/deb_no_texext | 37 +++ 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 | 2 + 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, 736 insertions(+) create mode 100644 TODO 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/deb_no_ipython_console_highlight create mode 100644 patches/deb_no_texext 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/TODO b/TODO new file mode 100644 index 0000000..d7c174c --- /dev/null +++ b/TODO @@ -0,0 +1 @@ +- package https://github.com/matthew-brett/texext used in the documentation diff --git a/changelog b/changelog new file mode 100644 index 0000000..38d3d23 --- /dev/null +++ b/changelog @@ -0,0 +1,292 @@ +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 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 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 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 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..ec63514 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +9 diff --git a/control b/control new file mode 100644 index 0000000..25ed06e --- /dev/null +++ b/control @@ -0,0 +1,84 @@ +Source: nipy +Section: python +Priority: extra +Maintainer: NeuroDebian Team +Uploaders: Yaroslav Halchenko , Michael Hanke +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: 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/deb_no_ipython_console_highlight b/patches/deb_no_ipython_console_highlight new file mode 100644 index 0000000..ef61622 --- /dev/null +++ b/patches/deb_no_ipython_console_highlight @@ -0,0 +1,21 @@ +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 += [ diff --git a/patches/deb_no_texext b/patches/deb_no_texext new file mode 100644 index 0000000..3469e9b --- /dev/null +++ b/patches/deb_no_texext @@ -0,0 +1,37 @@ +From: Yaroslav Halchenko +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 + 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..e7a44f3 --- /dev/null +++ b/patches/series @@ -0,0 +1,2 @@ +deb_no_texext +deb_no_ipython_console_highlight 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..1d26f62 --- /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