From: Yaroslav Halchenko Date: Tue, 13 May 2014 14:07:58 +0000 (+0000) Subject: Import scikit-learn_0.14.1-3.debian.tar.xz X-Git-Tag: archive/raspbian/0.18-5+rpi1~1^2^2~3^2 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=5ab88668eed52076475180f8d8ec1b11cb1cc528;p=scikit-learn.git.old Import scikit-learn_0.14.1-3.debian.tar.xz [dgit import tarball scikit-learn 0.14.1-3 scikit-learn_0.14.1-3.debian.tar.xz] --- 5ab88668eed52076475180f8d8ec1b11cb1cc528 diff --git a/README.source b/README.source new file mode 100644 index 0000000..d81bee6 --- /dev/null +++ b/README.source @@ -0,0 +1,9 @@ +scikit-learn for Debian +----------------------- + +For flexibility and easier interaction with upstream, sources are +obtained directly from upstream git repository, releases "merged" into +dfsg branch while stripping materials already present on Debian system +(e.g. joblib), and packaged into .orig.tar.gz using git-buildpackage. + + -- Yaroslav Halchenko , Mon, 17 Oct 2011 23:48:57 -0400 diff --git a/TODO b/TODO new file mode 100644 index 0000000..f002d86 --- /dev/null +++ b/TODO @@ -0,0 +1,12 @@ +# emacs: -*- mode: org; indent-tabs-mode: nil -*- + +* Modularization +** Use now-available system-wide liblinear? +** Use system-wide atlas? + +ATM Debian carries stable upstream release 3.8.3, while scikits.learn +uses 3.9.25 (current development upstream release is 3.9.32, +see #609287) + +* provide .doc-base file +* provide -dbg package diff --git a/changelog b/changelog new file mode 100644 index 0000000..6e0ab3d --- /dev/null +++ b/changelog @@ -0,0 +1,317 @@ +scikit-learn (0.14.1-3) unstable; urgency=medium + + * Cherry-pick a workaround for FTBFS due to error in current scipy + (Closes: #746096) + + -- Yaroslav Halchenko Tue, 13 May 2014 10:07:58 -0400 + +scikit-learn (0.14.1-2) unstable; urgency=low + + * Disable reporting to google analytics -- we haven't got any permission from + the users allowing to report back to 3rd party services + (thanks Ambrose Andrews, Closes: #730259) + + -- Yaroslav Halchenko Sun, 24 Nov 2013 10:17:29 -0500 + +scikit-learn (0.14.1-1) unstable; urgency=low + + * The freshiest upstream release + - addressed 'clean -a' issue, thus removing the dh_auto_clean override + * debian/rules + - if available cython >= 0.19 -- re-build Cythonized sources while + monitoring for changes using dh_autoreconf + + -- Yaroslav Halchenko Thu, 08 Aug 2013 14:06:48 -0400 + +scikit-learn (0.14-1) UNRELEASED; urgency=low + + * The fresh upstream release + * debian/rules + - overload dh_auto_clean to call "clean" without -a + (see https://github.com/scikit-learn/scikit-learn/issues/2351) + * debian/control + - Build-Depends: + - multilined + - dropped swig (not needed since awhile) + - moved sphinx, PIL, and graphviz to Build-Depends-Indep since + needed only for -doc package + - do not build documentation when sphinx < 1.1.3 due to problems + with unicode in earlier present on older Debian/Ubuntu's versions + - boosted policy to 3.9.4 (no further changes) + - migrate from python-support to dh_python2 + + -- Yaroslav Halchenko Wed, 07 Aug 2013 20:16:04 -0400 + +scikit-learn (0.14~a1+git20-gc9ba2c3-1) UNRELEASED; urgency=low + + * Fresh pre-release snapshot + * debian/control + - python-imaing to build-depends (for documentation) and removed not + needed XS-DM-Upload-Allowed + + -- Yaroslav Halchenko Mon, 05 Aug 2013 10:56:38 -0400 + +scikit-learn (0.13.1-1) unstable; urgency=low + + * "Fresh" bugfix release: + - dropping all cherry picked changesets + + -- Yaroslav Halchenko Sat, 01 Jun 2013 11:36:44 -0400 + +scikit-learn (0.13-3) unstable; urgency=low + + * Upload to unstable + * debian/control + - move joblib to Depends from Recommends (Closes: #709056) + - remove unused AFAIK XB-Python-Version + + -- Yaroslav Halchenko Mon, 20 May 2013 11:01:00 -0400 + +scikit-learn (0.13-2) experimental; urgency=low + + * CP from upstream commits to fix a problem with ROC curves lacking + (0,0), (1,1) trailing points in some cases (gh-1658) + + -- Yaroslav Halchenko Mon, 18 Feb 2013 12:31:57 -0500 + +scikit-learn (0.13-1) experimental; urgency=low + + * Fresh upstream release + - dropping CP-ed changesets and deb_disable_test_spectral_old_scipy patch + * debian/rules + - removing exclusion of tests previously failed + + -- Yaroslav Halchenko Tue, 22 Jan 2013 21:37:24 -0500 + +scikit-learn (0.12.1-1) experimental; urgency=low + + * Fresh upstream bugfix release + - for now excluded some labile tests from testing + - picked up after release fix: 552833 Robustify LARS. Fixes issue #487 + + -- Yaroslav Halchenko Wed, 31 Oct 2012 16:17:41 -0400 + +scikit-learn (0.12.0-1) experimental; urgency=low + + * Fresh upstream release: + - all debian/up_ patches removed, deb_ patched updated + * Boosted policy to 3.9.3 (should be ok without changes) + * patches/deb_disable_test_spectral_old_scipy + - disable unittest on older scipy's due to failure + * debian/control + - removed obsolete (and not used any longer) python-psyco from + Recommends + + -- Yaroslav Halchenko Thu, 06 Sep 2012 21:30:31 -0400 + +scikit-learn (0.11.0-2) unstable; urgency=low + + * Patches to resolve FTBFS'es (Closes: #680246) + - armel: up_inconsistent_numpy_warnings (adopted upstream) + - mipsel: up_MinCovDet_test_seeding (picked up from upstream) + + -- Yaroslav Halchenko Wed, 04 Jul 2012 11:26:24 -0400 + +scikit-learn (0.11.0-1) unstable; urgency=low + + * Fresh upstream release + * Adjusted patches/deb_use_system_joblib to avoid submodule + import + * debian/rules: + - run unittests in verbose mode + - exclude 1 test with known failures (reported upstream) + to avoid FTBFS + + -- Yaroslav Halchenko Mon, 07 May 2012 22:40:04 -0400 + +scikit-learn (0.10.0-1) unstable; urgency=low + + * Snapshot of upstream release branch + - Python 2.5 compatibility dropped + * Dropping .dfsg suffix since it is not adequate. Sources are + repackaged only to remove joblib shipped in a separate package in Debian + main + * Adjusted dfsg and other rules to operate on sklearn directory + * Dropping cherry-picked fix up_release_sv_coef_memory + * Operate on 'requested' not all supported Python versions + * Added 'set -e' to composite cmdline constructs in debian/rules to + prevent swallowing errors. Thanks to Jakub Wilk for citing me the relevant + exerpt from Debian policy ;-) + + -- Yaroslav Halchenko Thu, 12 Jan 2012 22:42:03 -0500 + +scikit-learn (0.9.0.dfsg-1) unstable; urgency=low + + * New upstream release: + - renamed module to sklearn, + scikits.learn adapter was provided to ease migration + - there is no strict dependency on IPython any longer. Thus removed + IPython from build-depends and Suggest it now for binary package + (Closes: #636472) + * Enabled all unittests and ignored failures on doctests: + https://github.com/scikit-learn/scikit-learn/issues/401 + * Adjusted debian/copyright to be fresh DEP5-compliant + + -- Yaroslav Halchenko Mon, 17 Oct 2011 23:49:47 -0400 + +scikit-learn (0.8.1.dfsg-1) unstable; urgency=low + + * New upstream maintenance release + + -- Yaroslav Halchenko Fri, 01 Jul 2011 14:37:28 -0400 + +scikit-learn (0.8.0.dfsg-1) unstable; urgency=low + + * New upstream release + * [97bc011] Boost policy compliance to 3.9.2 -- no changes + * Included post-release fixes: + - [f7d5317] FIX: reflect SVC API change (eps -> tol) in doc/tutorial.rst + * Disabled unittest test_fit_works_on_sequences_of_different_length + due to test failure during build + + -- Yaroslav Halchenko Wed, 11 May 2011 10:08:13 -0400 + +scikit-learn (0.7.1.dfsg-3) unstable; urgency=low + + * Do not build documentation in -a mode, to prevent timeouts on buildd + servers + * Use JOBLIB_MULTIPROCESSING=0 to suppress use of multiprocessing by + joblib while running tests to prevent failures in chroots without + /dev/shm mounted + + -- Yaroslav Halchenko Wed, 13 Apr 2011 17:18:46 -0400 + +scikit-learn (0.7.1.dfsg-2) unstable; urgency=low + + * Upload to unstable + * Exclude objects.inv from being compressed (Closes: #608775) + * Restrict numpy versioned dependency only to -lib package. Thanks Jakub + Wilk + + -- Yaroslav Halchenko Wed, 06 Apr 2011 14:24:35 -0400 + +scikit-learn (0.7.1.dfsg-1) experimental; urgency=low + + * [8972010] New upstream release + + -- Yaroslav Halchenko Sat, 19 Mar 2011 11:31:00 -0400 + +scikit-learn (0.6.0.dfsg-1) experimental; urgency=low + + * [05f0870] Disabled use of system libsvm - scikits.learn has its own + fork + * [104eb54] Adjusted dfsg rule -- do not prune libsvm + * [6b4e757] Updated copyright: DEP5 rev153, entries for cblas/ and + lib{linear/svm} + * [489f3a2] Extended TODO (in emacs-org mode): consider system's + liblinear (need 1.7 with a fix) + * Introduced .dfsg suffix to signal for difference from the pristine + distribution of scikits.learn + * [5dc61b3] Added README.source to describe reason(s) for .dfsg + * [81e7f16] debian/watch: mangle debian version - remove .dfsg for + comparisons + + -- Yaroslav Halchenko Sun, 09 Jan 2011 21:01:33 -0500 + +scikit-learn (0.5-1) experimental; urgency=low + + * New upstream release. Absorbed patches: + - up_libsvm_verbosity_control + - up_system_libsvm_no_svmhdepends + - deb_libsvm_cythoning + * Boost policy compliance to 3.9.1 -- no changes + + -- Yaroslav Halchenko Mon, 11 Oct 2010 10:00:11 -0400 + +scikit-learn (0.5~rc3-1) UNRELEASED; urgency=low + + * New upstream release-candidate + - pruning joblib in favor of external package + added patch deb_use_system_joblib + * New patches for upstream + - up_libsvm_verbosity_control -- API for controlling libsvm verbosity + - up_system_libsvm_no_svmhdepends -- do not use shipped svm.h + * Deprecated patches: + - up_workaround_numpy_cython_issue589652 + - deb_cython_0.12.1 + + -- Yaroslav Halchenko Wed, 06 Oct 2010 15:05:40 -0400 + +scikit-learn (0.4-3) unstable; urgency=low + + * Acknowledging Nico's NMU + * Restricting for Python versions >= 2.5 + + -- Yaroslav Halchenko Fri, 06 Aug 2010 10:12:38 -0400 + +scikit-learn (0.4-2.1) unstable; urgency=low + + * Non-maintainer upload. + * Call dh_numpy from debian/rules to add the correct depends for numpy in + python:Depends (Closes: #590762) + + -- Nico Golde Thu, 05 Aug 2010 13:34:19 +0200 + +scikit-learn (0.4-2) unstable; urgency=low + + * deb_cython_0.12.1 to use code cythoned with up-to-date cython + 0.12.1 + * Build-Depend on python-numpy providing numpy-ext (Closes: #589590) + * Policy compliance 3.9.0: + - providing BSD license verbatim and removing references + to deprecated BSD license file on Debian systems + * Nosetesting without suppressing output from code + * Workaround to allow BFS (Closes: #588595) + + -- Yaroslav Halchenko Mon, 19 Jul 2010 12:32:06 -0400 + +scikit-learn (0.4-1) unstable; urgency=low + + * Fresh upstream release: + - no boost library used any longer (removed from Build-Depends) + * Moving under NeuroDebian umbrella + + -- Yaroslav Halchenko Tue, 29 Jun 2010 09:32:18 -0400 + +scikit-learn (0.3-4) unstable; urgency=low + + * Disabling test_gmm_em unittests while building (Closes: #580879). + Actual reason for failing tests lies within NumPy -- see #581043, + which should be fixed there, but should not prevent building of + this package atm. + + -- Yaroslav Halchenko Mon, 10 May 2010 23:59:49 -0400 + +scikit-learn (0.3-3) unstable; urgency=low + + * Set HOME and MPLCONFIGDIR while unittesting as well (Closes: #580727) + + -- Yaroslav Halchenko Sat, 08 May 2010 12:47:07 -0400 + +scikit-learn (0.3-2) unstable; urgency=low + + * Setting both HOME and MPLCONFIGDIR while building documentation + (slipped through fingers somehow) (Closes: #580727). + + -- Yaroslav Halchenko Sat, 08 May 2010 00:35:59 -0400 + +scikit-learn (0.3-1) unstable; urgency=low + + * Fresh upstream release. + * Switching to use quilt for patches, debian/* tags point to detached + debian branch + * debian/rules: + + build docs after python modules got built + + additional cleanups + * debian/control: + + additional build-depends: python-matplotlib, ipython, swig, + libboost-dev + + -- Yaroslav Halchenko Mon, 03 May 2010 12:25:21 -0400 + +scikit-learn (0.2+svn625-1) unstable; urgency=low + + * Initial Debian release (Closes: #567036) + * First ever package by me to adhere to use fresh and shiny dh. + + -- Yaroslav Halchenko Wed, 07 Apr 2010 23:38:06 -0400 diff --git a/compat b/compat new file mode 100644 index 0000000..7ed6ff8 --- /dev/null +++ b/compat @@ -0,0 +1 @@ +5 diff --git a/control b/control new file mode 100644 index 0000000..79772b2 --- /dev/null +++ b/control @@ -0,0 +1,72 @@ +Source: scikit-learn +Section: python +Priority: optional +Maintainer: NeuroDebian Team +Uploaders: Yaroslav Halchenko , Michael Hanke +Build-Depends: debhelper (>= 7.0.50), dh-autoreconf, + python-all-dev (>= 2.5), + cython (>= 0.12~), + python-setuptools, + python-numpy, python-scipy, + libsvm-dev (>= 2.84.0), + python-nose, + python-matplotlib, + python-joblib (>= 0.4.5), python-support +Build-Depends-Indep: + python-sphinx (>= 1.0), python-imaging, graphviz, +Standards-Version: 3.9.4 +XS-Python-Version: >= 2.6 +Homepage: http://scikit-learn.sourceforge.net +Vcs-Browser: http://github.com/yarikoptic/scikit-learn +Vcs-Git: git://github.com/yarikoptic/scikit-learn.git + +Package: python-sklearn +Replaces: python-scikits-learn (<< 0.9~) +Breaks: python-scikits-learn (<< 0.9~) +Architecture: all +Depends: ${misc:Depends}, ${python:Depends}, python-numpy, python-scipy, python-sklearn-lib(>= ${source:Version}), + python-joblib (>= 0.4.5), +Provides: ${python:Provides} +Recommends: python-nose, python-matplotlib +Suggests: python-dap, python-scikits-optimization, python-sklearn-doc, ipython +Enhances: python-mvpa2, python-mdp +Description: Python modules for machine learning and data mining + scikit-learn is a collection of Python modules relevant to + machine/statistical learning and data mining. Non-exhaustive list of + included functionality: + - Gaussian Mixture Models + - Manifold learning + - kNN + - SVM (via LIBSVM) + + +Package: python-sklearn-doc +Conflicts: python-scikits-learn-doc +Replaces: python-scikits-learn-doc +Architecture: all +Section: doc +Depends: ${misc:Depends}, libjs-jquery +Suggests: python-sklearn +Description: documentation and examples for scikit-learn + This package contains documentation and example scripts for + python-sklearn. + +Package: python-sklearn-lib +Conflicts: python-scikits-learn-lib +Replaces: python-scikits-learn-lib +Architecture: any +Depends: ${misc:Depends}, ${shlibs:Depends}, ${python:Depends}, python-numpy +Provides: ${python:Provides} +Description: low-level implementations and bindings for scikit-learn + This is an add-on package for python-sklearn. It provides + low-level implementations and custom Python bindings for the LIBSVM + library. + + +Package: python-scikits-learn +Depends: python-sklearn, ${misc:Depends}, ${python:Depends} +Architecture: all +Section: oldlibs +Description: transitional compatibility package for scikits.learn -> sklearn migration + Provides old namespace (scikits.learn) and could be removed if + dependent code migrated to use sklearn for clarity of the namespace. diff --git a/copyright b/copyright new file mode 100644 index 0000000..b20162c --- /dev/null +++ b/copyright @@ -0,0 +1,68 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: scikit-learn +Upstream-Contact: Fabian Pedregosa +Source: http://github.com/scikit-learn/scikit-learn + +Files: * +Copyright: 2007-2012, Scikit-Learn Developers +License: BSD-3 + +Files: doc/sphinxext/* +Copyright: 2008, Stefan van der Walt , Pauli Virtanen +License: BSD + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + 2. 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. + +Files: sklearn/src/cblas/* +Copyright: 1996-2006 R. Clint Whaley + 1998 Jeff Horner + 2001 Peter Soendergaard + 1999 Antoine P. Petitet + 2001 Julian Ruhe + 2003 Tim Mattox + 2003 Hank Dietz + 2003 Camm Maguire + 1999 The Australian National University + 2000 Antoine P. Petitet, University of Tennessee, +License: BSD-3 +Comment: Extract from 3.9.25 atlas + +Files: sklearn/svm/src/libsvm + sklearn/svm/src/liblinear +Copyright: 2000-2010, Chih-Chung Chang and Chih-Jen Lin +License: BSD-3 +Comment: Partial fork of the LIBSVM package. + +Files: debian/* +Copyright: 2010-2012, Yaroslav Halchenko +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: + . + a. Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + b. 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. + c. Neither the name of the Scikit-learn Developers nor the names of + its 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 REGENTS 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/gbp.conf b/gbp.conf new file mode 100644 index 0000000..2d1e49d --- /dev/null +++ b/gbp.conf @@ -0,0 +1,26 @@ +[DEFAULT] +# the default build command: +builder = debuild -i'\.(git\.*|gbp.conf|gitignore)' +# the default clean command: +cleaner = fakeroot debian/rules clean +# the default branch for upstream sources: +upstream-branch = dfsg +# the default branch for the debian patch: +debian-branch = debian +# the default tag formats used: +upstream-tag = %(version)s +upstream-tree = branch +debian-tag = debian/%(version)s + +# Options only affecting git-buildpackage +[git-buildpackage] +# ignore some any non-gitted files +ignore-new = True +#upstream-branch = dfsgclean +# uncomment this to automatically GPG sign tags +sign-tags = True +# use this for more svn-buildpackage like bahaviour: +export-dir = ../build-area/ +tarball-dir = ../tarballs/ + + diff --git a/patches/changeset_36ba287b29f3d039b8ecb5194dae1c47cf24641a.diff b/patches/changeset_36ba287b29f3d039b8ecb5194dae1c47cf24641a.diff new file mode 100644 index 0000000..dba9a19 --- /dev/null +++ b/patches/changeset_36ba287b29f3d039b8ecb5194dae1c47cf24641a.diff @@ -0,0 +1,12 @@ +From: Gael Varoquaux +Subject: TST: fix test on scipy dev version + +--- a/sklearn/cluster/bicluster/tests/test_utils.py ++++ b/sklearn/cluster/bicluster/tests/test_utils.py +@@ -40,4 +40,6 @@ def test_get_submatrix(): + [6, 7], + [18, 19]]) + submatrix[:] = -1 ++ if issparse(X): ++ X = X.todense() + assert_true(np.all(X != -1)) diff --git a/patches/deb_no_google_analytics b/patches/deb_no_google_analytics new file mode 100644 index 0000000..6f7af6f --- /dev/null +++ b/patches/deb_no_google_analytics @@ -0,0 +1,35 @@ +From: Yaroslav Halchenko +Subject: Disable google analytics referrals in the -doc + + if we were to provide some information from just reading documentation we + had to disclose and seek approval from the user before doing that. + + Thanks Ambrose Andrews for the analysis and report + +Origin: Debian +Bug: 730259 +Bug-Debian: http://bugs.debian.org/730259 +Bug-Ubuntu: https://launchpad.net/bugs/ +Last-Update: 2013-11-24 + +--- a/doc/conf.py ++++ b/doc/conf.py +@@ -122,7 +122,7 @@ html_theme = 'scikit-learn' + # further. For a list of options available for each theme, see the + # documentation. + html_theme_options = {'oldversion': False, 'collapsiblesidebar': True, +- 'google_analytics': True, 'surveybanner': False, ++ 'google_analytics': False, 'surveybanner': False, + 'sprintbanner' : True} + + # Add any paths that contain custom themes here, relative to this directory. +--- a/doc/themes/scikit-learn/theme.conf ++++ b/doc/themes/scikit-learn/theme.conf +@@ -6,6 +6,6 @@ pygments_style = tango + [options] + oldversion = False + collapsiblesidebar = True +-google_analytics = True ++google_analytics = False + surveybanner = False + sprintbanner = True diff --git a/patches/deb_use_system_joblib b/patches/deb_use_system_joblib new file mode 100644 index 0000000..5be10f7 --- /dev/null +++ b/patches/deb_use_system_joblib @@ -0,0 +1,40 @@ +From: Yaroslav Halchenko +Subject: use system-wide joblib and do not attempt to install joblib/test + + Relies on DFSG-ed sources with no joblib present + +--- a/sklearn/externals/setup.py ++++ b/sklearn/externals/setup.py +@@ -5,6 +5,5 @@ def configuration(parent_package='', top + from numpy.distutils.misc_util import Configuration + config = Configuration('externals', parent_package, top_path) + config.add_subpackage('joblib') +- config.add_subpackage('joblib/test') + + return config +--- /dev/null ++++ b/sklearn/externals/joblib/__init__.py +@@ -0,0 +1,3 @@ ++# yoh: use system-wide joblib ++ ++from joblib import * +--- a/sklearn/metrics/pairwise.py ++++ b/sklearn/metrics/pairwise.py +@@ -47,7 +47,7 @@ from ..utils.extmath import safe_sparse_ + from ..preprocessing import normalize + from ..externals.joblib import Parallel + from ..externals.joblib import delayed +-from ..externals.joblib.parallel import cpu_count ++from ..externals.joblib import parallel + + from .pairwise_fast import _chi2_kernel_fast + +@@ -559,7 +559,7 @@ def _parallel_pairwise(X, Y, func, n_job + """Break the pairwise matrix in n_jobs even slices + and compute them in parallel""" + if n_jobs < 0: +- n_jobs = max(cpu_count() + 1 + n_jobs, 1) ++ n_jobs = max(parallel.cpu_count() + 1 + n_jobs, 1) + + if Y is None: + Y = X diff --git a/patches/deb_use_system_libraries b/patches/deb_use_system_libraries new file mode 100644 index 0000000..2391d26 --- /dev/null +++ b/patches/deb_use_system_libraries @@ -0,0 +1,19 @@ +From: Yaroslav Halchenko +Subject: Use system libraries as specified in site.cfg + +--- a/site.cfg ++++ b/site.cfg +@@ -1,9 +1,9 @@ + + # Uncomment to link against system-wide libsvm +-# [libsvm] +-# libraries=svm +-# library_dirs=/usr/lib +-# include_dirs=/usr/include/libsvm-2.0/libsvm ++[libsvm] ++libraries=svm ++library_dirs=/usr/lib ++include_dirs=/usr/include/libsvm-2.0/libsvm + + # Uncomment to link against the MKL library on windows + # [mkl] diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..b67d55e --- /dev/null +++ b/patches/series @@ -0,0 +1,3 @@ +deb_use_system_joblib +deb_no_google_analytics +changeset_36ba287b29f3d039b8ecb5194dae1c47cf24641a.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-sklearn-doc.docs b/python-sklearn-doc.docs new file mode 100644 index 0000000..7123782 --- /dev/null +++ b/python-sklearn-doc.docs @@ -0,0 +1 @@ +doc/_build/html diff --git a/python-sklearn-doc.examples b/python-sklearn-doc.examples new file mode 100644 index 0000000..e39721e --- /dev/null +++ b/python-sklearn-doc.examples @@ -0,0 +1 @@ +examples/* diff --git a/python-sklearn-doc.links b/python-sklearn-doc.links new file mode 100644 index 0000000..83a6aa9 --- /dev/null +++ b/python-sklearn-doc.links @@ -0,0 +1 @@ +usr/share/javascript/jquery/jquery.js usr/share/doc/python-sklearn-doc/html/_static/jquery.js diff --git a/rules b/rules new file mode 100755 index 0000000..ed72058 --- /dev/null +++ b/rules @@ -0,0 +1,114 @@ +#!/usr/bin/make -f +# -*- mode: makefile; coding: utf-8 -*- + +PACKAGE_NAME = python-sklearn +PACKAGE_ROOT_DIR = debian/${PACKAGE_NAME} + +PYVERS = $(shell pyversions -vr) +PYVER = $(shell pyversions -vd) + +SPHINX_VER := $(shell python -c 'from sphinx import __version__; print __version__') +NODOC = $(shell dpkg --compare-versions $(SPHINX_VER) lt 10.1.3 && echo "nodoc" || echo "") +export DEB_BUILD_OPTIONS += $(NODOC) + +CYTHON_VER := $(shell dpkg -l cython 2>/dev/null | awk '/^ii/{print $$3;}' || echo 0) +RECONF = $(shell dpkg --compare-versions $(CYTHON_VER) ge 0.19 && echo ",autoreconf" || echo "") + +# Some tests are known to fail randomly so need to be excluded ATM +NOSEARGS := +# --exclude='test_(sparse_svc_clone_with_callable_kernel|spectral_clustering_sparse|ovr_fit_predict)' + +# Mega rule +%: + : # Explicit build system to avoid use of all-in-1 Makefile + dh $@ --buildsystem=python_distutils --with python2$(RECONF) + +cythonize: + @echo "D: removing previously generated by Cython sources" + find -iname *.c | xargs grep -l 'Generated by Cython' | xargs rm + make cython + +override_dh_autoreconf: + dh_autoreconf debian/rules -- cythonize + +override_dh_clean: + rm -rf build doc/_build doc/auto_examples *-stamp *.egg-info sklearn/datasets/__config__.py + dh_clean + +override_dh_auto_install: ${PYVERS:%=python-install%} ${PYVERS:%=python-test%} +# Per Python version logic -- install, test, move .so into -lib +python-install%: + python$* setup.py install --install-layout=deb --root=$(PACKAGE_ROOT_DIR) + +python-test%: python-install% +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + : # Run unittests here against installed scikits.learn + export PYTHONPATH=`/bin/ls -d $$PWD/$(PACKAGE_ROOT_DIR)/usr/lib/python$*/*/`; \ + export MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \ + export JOBLIB_MULTIPROCESSING=0; \ + cd build/; python$* /usr/bin/nosetests -s -v $(NOSEARGS) sklearn && \ + { python$* /usr/bin/nosetests -v --with-doctest --doctest-extension=rst ../doc/ || : ; } # doctests are failing ATM +else + : # Skip unittests due to nocheck +endif + + +override_dh_installdocs: + : # Build Documentation using installed scikits.learn +ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS))) +ifneq (,$(findstring -a,$(DH_INTERNAL_OPTIONS))) + : # not building documentation in -a +else + export PYTHONPATH=`/bin/ls -d $$PWD/$(PACKAGE_ROOT_DIR)/usr/lib/python$(PYVER)/*`; \ + export MPLCONFIGDIR=$(CURDIR)/build HOME=$(CURDIR)/build; \ + cd doc; $(MAKE) html +endif +else + mkdir -p doc/_build/html + echo "

sklearn documentation was not built.

Please visit http://scikit-learn.org" >| doc/_build/html/index.html +endif + : # Use jquery from Debian package, so prune shipped one + -rm doc/_build/html/_static/jquery.js + dh_installdocs -A AUTHORS.rst README*.rst + +override_dh_installchangelogs: + dh_installchangelogs doc/whats_new.rst + +## move binary libraries into -lib +override_dh_python2: + : # Move platform-specific libraries into -lib + set -e; \ + for lib in $$(find $(PACKAGE_ROOT_DIR)/usr -name '*.so'); do \ + sdir=$$(dirname $$lib) ; \ + tdir=$(PACKAGE_ROOT_DIR)-lib/$${sdir#*$(PACKAGE_NAME)/} ; \ + mkdir -p $$tdir ; \ + echo "Moving '$$lib' into '$$tdir'." ; \ + mv $$lib $$tdir ; \ + done + if [ -x /usr/bin/dh_numpy ]; then dh_numpy -ppython-sklearn-lib; fi + : # Prune scikits/__init__.py to avoid conflicts + find debian -wholename \*scikits/__init__.py -delete + : # Move scikits. space into a compatibility package + set -e; \ + find debian -wholename \*scikits -type d | while read skd; do \ + skbd=$$(dirname $$skd); \ + skbd_=$$(echo $$skbd | sed -e 's/sklearn/scikits-learn/g'); \ + mkdir -p $$skbd_; \ + mv $$skd $$skbd_; \ + done + dh_python2 + +## immediately useable documentation and exemplar scripts/data +override_dh_compress: + dh_compress -X.py -X.html -X.pdf -X.css -X.jpg -X.txt -X.js -X.json -X.rtc -Xobjects.inv + + +## to prepare next Debian upstream source tarball +dfsg: dfsg-releases +dfsg-%: + git checkout dfsg + -git merge --no-commit $* + -git rm -rf sklearn/externals/joblib + # -git rm -f ./sklearn/svm/src/libsvm/svm.* + git commit -m "Merge $* into DFSG (pruning externals: joblib)" -a + git checkout debian diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/watch b/watch new file mode 100644 index 0000000..1933bcd --- /dev/null +++ b/watch @@ -0,0 +1,3 @@ +version=3 +opts="dversionmangle=s/.dfsg$//" \ + http://github.com/scikit-learn/scikit-learn/downloads .*tarball/([\d\.a-z]+)