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Commits on Feb 1, 2010
  1. 0.1 Release

    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@396 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Feb 1, 2010
  2. Fix parzen method in Neighbors.

    CKDTree has no query_ball_point method.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@395 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Feb 1, 2010
  3. Building the modules inplace broke installation of binary modules.

    Fix this by removing the setup.cfg file.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@394 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Feb 1, 2010
  4. Fix: some distutils cleaning and import fixing.

    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@393 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Feb 1, 2010
Commits on Jan 29, 2010
  1. Fix import of libsvm in tests.

    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@392 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
  2. Update README.

    Run the test suite with "python setup.py test".
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@391 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
  3. Remove tests that depend on weka.

    This had no sense anymore, since loadarff is now part of scipy and it
    was only making test fail.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@390 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
  4. Remove em2 module.

    I remove temporarily this module because it is not mature enough to be
    included in the release. I've moved the code temporarily to
    http://github.com/fseoane/em2 .
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@389 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
  5. Remove sciktis.optimization as explicit dependece from setup.py.

    At least until scikits.optimization is uploaded to pypi, so that this
    package can be installed via easy_install.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@388 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
  6. Fix classification example in machine.svm.

    Various fixes: wrong key for dataset, wrong name for most imports from
    svm namespace... Also corrected the docstring, since we are not using
    iris dataset but german.
    
    This hopefully fixes issue #9:
    
        https://sourceforge.net/apps/trac/scikit-learn/ticket/9
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@387 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
  7. Fix path in examples/projection.py.

    Prefix files to open with absolute directory so that it can be run
    from any directory.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@386 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 29, 2010
Commits on Jan 28, 2010
  1. Added docstring to cost_function module.

    Docstring written after a message of Matthieu Brucher to the mailing
    list.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@385 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 28, 2010
Commits on Jan 27, 2010
  1. Remove references to deleted submodule common/

    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@384 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
  2. 0.1 beta release

    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@383 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
  3. Refactor test_neighbors.

    Just some name updates.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@382 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
  4. Deleted common/myfunctools.py.

    No need for function partial, since we are using ptython2.5.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@381 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
  5. Clean some setup.py files.

    Remove print statements, dead comments.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@380 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
  6. Fix typo in web page.

    Thanks Yaroslav for reporting this.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@379 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
  7. Deleted MANIFEST.in

    There's no need for MANIFEST.in since we are using distutils. Just
    discovered that there's a git plugin that puts in sdist all that's
    under version control (it does it automatically for svn).
    
    More info on how this works can be found here:
    
    http://peak.telecommunity.com/DevCenter/setuptools#including-data-files
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@378 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 27, 2010
Commits on Jan 25, 2010
  1. Fix bug in knn example.

    In pcolormesh, matrix Z should be transposed (see
    mathplotlib.pyplot.pcolormesh' docstring). This example finally
    produces the expected results.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@377 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 25, 2010
  2. API changes for Neighbors broke some tests.

    Fix them.
    
    All tests under scikits/learn/machine/manifold_learning should run now.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@376 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 25, 2010
  3. Fix imports of scikits.optimization.

    Changed the import from scikits.optimization.optimizers.helpers to
    scikits.optimization.helpers. Also changed the import from toolbox.optimizers (which does not exist) to scikits.optimizer. Import should work fine now.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@375 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 25, 2010
  4. Fix bug in barycenters.

    This function was broken because array passed was not an indices
    array. Note that the tests that we have currently for this functions
    does not compare anything, so it only tells us when a function is
    broken in a way that it raises an error, but not when it outputs a
    wrong result.
    
    Note: this fixes issue #12:
    https://sourceforge.net/apps/trac/scikit-learn/ticket/12
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@374 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 25, 2010
  5. Fix relative imports in manifold_learning/regression/tests.

    Add a __init__.py file to the tests directory to enable relative imports.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@373 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 25, 2010
  6. Remove C header file for neighbors.

    Remove remaining C code for neighbors. See commit 368 "Use KDTree from scipy.spatial in Nearest Neighbors" for a rationale on why this code was removed.
    
    From: Fabian Pedregosa <fabian.pedregosa@inria.fr>
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@372 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 25, 2010
Commits on Jan 22, 2010
  1. Add a MANIFEST.in file.

    The second line is a horrible hack, but I really do not know why this
    file is not included by default since it is referenced from
    scikits/learn/machine/manifold_learning/setup.py
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@371 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  2. Update KNN examples.

    Neighbors.predict now accepts an array as parameter. Use this to make
    the code cleaner (and more efficient).
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@370 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  3. Add tests for Nearest Neighbor Algorithm.

    TODO: a lot more tests are needed.
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@369 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  4. Use KDTree from scipy.spatial in Nearest Neighbors.

    Use cKDTree as underlying algorithm in
    manifold_learning.regression.neighbors. By using this class we do not
    need to mantain the C++ bindings and benefit from a class that is
    mature and well tested.
    
    Also, there is a important speedup. For example, in
    manifold_learning/examples/knn.py (removing the plot statements), time
    command says:
    
    7.71s before this patch, now takes 1.74s, thats over a 600% speed gain.
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@368 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  5. Cosmetic cleanup of setup.py.

    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@367 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  6. Remove references to deleted classes.

    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@366 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  7. Remove genetic algorithms.

    I decided to remove this module for the following reasons: the module
    does not quite fit the package's thematic, has references to scipy.ga
    (which has been removed) and there are already some great genetic
    algorithm frameworks in Python.
    
    This thread discussed the removal:
    http://mail.scipy.org/pipermail/scipy-dev/2010-January/013705.html
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@365 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  8. Add needed files from numpy.testing.

    This tests needed the functions assert_array_almost_euqal (they are
    not present in unittest).
    
    These functions also are not present in older versions of numpy
    (1.1.0), but fortunately they are only needed for testing.
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@364 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  9. Fix typos in setup.py.

    This is more important than just cosmetic changes, as it was throwing
    errors when building for windows.
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@363 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010
  10. Change location of header files.

    They where moved from manifold_learning to
    manifold_learning/src/. Also changed the build scripts to build in the
    same place all the extensions that depend on these headers.
    
    It migh not be a good practice to build extension modules from
    submodules, but in this case we have 3 submodules that share the same
    dependencies and the alternative is to repeat the same code in 3
    places. Anyway, in the future a better structure for this directory
    should be envisaged. For this release, let's leave it like this.
    
    As a side-effect, the $PATH issue in OsX with boost installed
    from MacPorts dissapeared, probably because passing
    numpy.get_include() to include_dirs adds the needed dirs (if numpy is
    installed through MacPorts).
    
    Also corrected some setup.py scripts that where throwing
    error/warnings.
    
    git-svn-id: https://scikit-learn.svn.sourceforge.net/svnroot/scikit-learn/trunk@362 22fbfee3-77ab-4535-9bad-27d1bd3bc7d8
    fabianp committed Jan 22, 2010