From 5ab88668eed52076475180f8d8ec1b11cb1cc528 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Tue, 13 May 2014 14:07:58 +0000 Subject: [PATCH] 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] --- README.source | 9 + TODO | 12 + changelog | 317 ++++++++++++++++++ compat | 1 + control | 72 ++++ copyright | 68 ++++ gbp.conf | 26 ++ ...a287b29f3d039b8ecb5194dae1c47cf24641a.diff | 12 + patches/deb_no_google_analytics | 35 ++ patches/deb_use_system_joblib | 40 +++ patches/deb_use_system_libraries | 19 ++ patches/series | 3 + pycompat | 1 + python-sklearn-doc.docs | 1 + python-sklearn-doc.examples | 1 + python-sklearn-doc.links | 1 + rules | 114 +++++++ source/format | 1 + watch | 3 + 19 files changed, 736 insertions(+) create mode 100644 README.source create mode 100644 TODO create mode 100644 changelog create mode 100644 compat create mode 100644 control create mode 100644 copyright create mode 100644 gbp.conf create mode 100644 patches/changeset_36ba287b29f3d039b8ecb5194dae1c47cf24641a.diff create mode 100644 patches/deb_no_google_analytics create mode 100644 patches/deb_use_system_joblib create mode 100644 patches/deb_use_system_libraries create mode 100644 patches/series create mode 100644 pycompat create mode 100644 python-sklearn-doc.docs create mode 100644 python-sklearn-doc.examples create mode 100644 python-sklearn-doc.links create mode 100755 rules create mode 100644 source/format create mode 100644 watch 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]+) -- 2.30.2