[scikit-learn] annotated tag 0.5.dfsg created (now 73f9068)
Andreas Tille
tille at debian.org
Wed Dec 28 13:10:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag 0.5.dfsg
in repository scikit-learn.
at 73f9068 (tag)
tagging a3476be23a0e1fc1625be1d28f3ec7fd124cd8f8 (commit)
replaces 0.4
tagged by Yaroslav Halchenko
on Mon Oct 11 09:58:21 2010 -0400
- Log -----------------------------------------------------------------
DFSG copy (removed libsvm, joblib copies) of scikits.learn 0.5
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Alexandre Gramfort (149):
Merge branch 'master' of /Volumes/DAVID/scikit-learn
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
API: changing the way the parameters of Lasso+E-Net are optimized
ENH : imroving documentation of lasso + enet paths function
ENH : add LeavePLabelOut cross-validation generator
ENH : adding support for mean-shift clustering with a flat kernel
ENH: making data contiguous in memory in coordinate descent
ENH: adding affinity propagation algorithm
removing pl.show()
ENH: adding exception raising
Merge branch 'master' of github.com:agramfort/scikit-learn
using staticmethod rather than property
cosmit
setting array as fortran in lasso + enet coordinate descent
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
MISC : renaming affinity propagation example
broke glm to improve model selection
ongoing work on glm with crossval
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
continue improve glm cv
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
fix glm cv
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
fix frozenset
BUG : fix in affinity propagation
BUG : fix in stock market example
BUG : fix with blas on mac os x
ENH : moving bench_glm.py to benchmarks folder
ENH : glm coordinate descent with BLAS
BUG : fix blas support in setup.py with coordinate descent
ENH : adding stratified cross-validation object
ENH : fix doctests in glm, svm and lda
adding grid search code
BUG : fix doctests in neighbors
BUG : fix doctest in datasets/base.py
ENH : using digits in grid search example
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
API : renaming GridSearch to GridSearchCV
API : cross val generator in now given in fit in grid search object
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
ENH : update grid search example
ENH : first draft of RFE
ENH : fix RFE + example
ENH : improve RFE
ENH : adding loss functions in metrics.py
Merge branch 'master' of github.com:agramfort/scikit-learn
Merge branch 'master' of github.com:agramfort/scikit-learn
ENH : fix RFE and RFECV
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
ENH : allow grid search to work with lists of grids
ENH : using BaseEstimator with GNB
cosmit'
ENH : adding BaseClassifier and BaseRegressor base classes
ENH : using mixin rather than base class to bring score methods to estimators
ENH : fix in svc.coef_ + cosmit
ENH : fix in svc.coef_ + cosmit
ENH : using np.logspace instead of np.linspace in paths
ENH : using np.logspace instead of np.linspace in paths (after merge)
API : making Y optional in fit for OneClassSVM
FIX : removing duplicated example
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
ENH : new SVR example
ENH : new SVR example
Merge branch 'temp'
ENH : improve QDA (taken from Matt Perrot)
ENH : improve LDA (taken from Matt Perrot)
ENH : improve LDA QDA example (taken from Matt Perrot)
MISC: cosmit in LDA, QDA
ENH : new example for LDA vs QDA
ENH : removing old example for LDA vs QDA
ENH : attempt to have a default parameter for bandwidth in MeanShift algorithm
ENH : adding doc to clustering module API : adding trailing underscores to estimates in clustering classes
ENH: adding test for RFE and reaching 100% coverage
ENH : adding doc for grid_search module
MISC : cosmit nfeatures -> n_features, nsamples -> n_samples, nclasses -> n_classes
FIX : adding missing doc file
FIX : fix in subplot index in plot_iris.py
ENH : removing unused preprocessing routines
FIX : in Makefile that calls now nosetests directly
FIX: removing useless imports
ENH : more work on LARS (doc + examples)
Merge branch 'master' of github.com:scikit-learn/scikit-learn
ENH : continue refactoring of GLM module (doc, moving files, config etc.)
ENH : more refactoring of GLM module
FIX : fixing __init__ files for examples
ENH : cosmit + fix examples for doc generation
cosmit in examples
Merge branch 'master' of github.com:scikit-learn/scikit-learn
BUG : fix in Lars at the end of path + more tests (not working yet)
ENH : using explained variance as score for regression problems
ENH: on the use of explained_variance in mixin regressor class
FIX : fix in handling of intercept in glm base and ridge
TEST : adding test to ridge with no intercept
ENH : draft of what could be a preprocessing routine (done by hand for now)
FIX : prevent pipeline.score to do a fit which was wrong
FIX : it may happen that pipeline.estimator do not implement predict
moving ridge out of bayes.py
ENH : adding PCA filter
ENH : adding computation of percentage of variance explained by each component
FIX : for doctest in PCA
ENH : adding ledoit-wolf for robust covariance estimation
ENH : adding FastICA class + example
Merge branch 'add_ica' of http://github.com/bthirion/scikit-learn into ica
ENH : more on ICA (examples + doc)
Merge branch 'ica'
FIX : fix ica vs pca example
ENH : adding example + refactor in covariance module
splitting ledoit_wolf.py in two files
oups missing example file
FIX: missing covariance.py
cleaning the handling of the intercept in GLM linear models
ENH : avoiding computing a pinv at each iteration in BayesianRidge
Merge branch 'master' of github.com:scikit-learn/scikit-learn
TEST : bayes
FIX : imports in __init__ of glm
cosmit in ARDRegression
TEST : removing lda.py
COSMIT : PEP 8 in PCA
Merge branch 'master' of github.com:scikit-learn/scikit-learn
FIX : RegressinMix score had flipped y_true and y_pred
EXAMPLE : adding model selection example with train/test error graphical illustration
EXAMPLE : making only one figure in model selection example
Merge branch 'master' of github.com:scikit-learn/scikit-learn
FIX __init__.py of glm.sparse
EXAMPLE: add example of dense vs sparse Lasso on dense and sparse data
FIX : example of dense vs sparse Lasso on dense and sparse data
passing Gram in LARS and LassoLARS
ENH : more doc in lars.py, handling of intercept
Merge branch 'fabian/python_lars_fast_2'
fix doctests in lars.py
more on lasso benchmark
Merge branch 'master' of github.com:scikit-learn/scikit-learn
FIX : preprocessing : scaler should not be allowed with axis=1 (opt removed)
skipping BayesianRidge failing test
using diabetes in lasso/lars examples
removing assert for debug
ENH : speeding up the LARS
BUG: bug fix in LARS Lasso mode + speed improvement (we can still do better)
adding LARS with Gram to benchmark
ENH : speed in LARS by forcing X to be fortran ordered + cosmit (unactive -> inactive)
pretifying the LAR / LARS examples to match with results on wikipedia page
cosmit in docs of glm module
Merge branch 'master' of github.com:scikit-learn/scikit-learn
ENH : improvements in bayes
Merge branch 'master' of github.com:scikit-learn/scikit-learn
fix doc generation on plot_lasso_coordinate_descent_path.py example (pb on my box)
DOC: updating doc on Univariate feature selection
Ariel Rokem (1):
Added description of input parameters in svm.SVC docstring
Bertrand Thirion (10):
introduced gael's implementation of fast_ica and debugged GS orthogonalization
cosmit in fastica, that created a bug -- to be fixed
updates in fastica and more tests
completed and cleaned the tests
improved the tests
solved conflict in test_fastica
added probabilistic PCA and associated tests; works reasonably well
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Merge branch 'master' of github.com:scikit-learn/scikit-learn
fix in ppca
Edouard DUCHESNAY (6):
add pipeline
WIP pipeline
Example of feature selection pipeline
Merge branch 'master' of github.com:vmichel/scikit-learn
Cosmetic on Pipeline
Merge branch 'master' of github.com:vmichel/scikit-learn
Fabian Pedregosa (262):
Add intercept to classes Lasso and ElasticNet
Cosmetic changes in SVM doc.
Start of 0.5 development cycle.
Re-enable code that was removed for the release
Cleanup gmm example. Removed unused modules.
In LAR, normalize only non-zero columns.
Add support in LAR for unnormalized columns.
LAR: add a test for zero coefficients.
Cosmetic changes in glm module.
Add modules to top-level __init__.
Rename ninter --> n_iter in the API guidelines.
Add documentation to svm mdoule.
FIX: bug in blas_opt detection.
Link against compiled cblas in case this is not in the system.
Bug fixing in setup.py
Apply changes made by Olivier.
One more tests on LibSVM with precomputed callable kernel.
Refactoring of LibSVM bindings.
Test for libsvm margin.
More bugfixes for blas detection in setup.py
FIX: numpy 1.4 fixes.
Mark as known to fail some tests in test_hmm.
Use numpy.testing instead of unittest to skip failing tests.
Refine cblas detection on OSX.
FIX: compatibility fixes for py3k.
Initial support for sparse matrices in SVMs (scikits.learn.sparse.svm)
Refine cblas detection on OSX.
FIX: compatibility fixes for py3k.
Initial support for sparse matrices in SVMs (scikits.learn.sparse.svm)
FIX: bug fixing on sparse.svm.
FIX: more bugfixing in sparse.svm.
Doc updates to the svm module.
Remove unused imports in qda module.
Some doc for the svm module.
Add target in to Makefile.
Fix names and missing parameters in LinearSVC.
Add support for sparse matrices in liblinear bindings.
Add a reference to density estimation in GMM docs.
Use relative imports inside scikits.learn.
Remove unused imports from hmm module.
Refinement and bugfixing in the liblinear bindings.
More refactoring and bugfixing with liblinear.
More refactoring in libsvm + liblinear.
remove unused imports from setup.py
run all tests suite through nose.
move liblinear into its own folder
Bug fixing in liblinear bindings.
Added some failing tests.
Bug fixing in liblinear bindings.
XFail tests that fail (or are plainly wrong).
Refactor layout of developer docs.
Revert unwanted changes (aka ooooops!).
Added tests to trigger failure on classes using liblinear.
Refinement and bugfixing in the liblinear bindings.
More refactoring and bugfixing with liblinear.
More refactoring in libsvm + liblinear.
remove unused imports from setup.py
run all tests suite through nose.
move liblinear into its own folder
Bug fixing in liblinear bindings.
Added some failing tests.
Bug fixing in liblinear bindings.
XFail tests that fail (or are plainly wrong).
Refactor layout of developer docs.
Revert unwanted changes (aka ooooops!).
Added tests to trigger failure on classes using liblinear.
Update the developer docs.
Refactoring & bug solving in liblinear.
FIX: fix liblinear predict in the multiclass case.
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
Add reference to pybrain from the ann docs.
Update numpydoc (sphinx extension).
Update svm rst doc.
Add rst doc for logistic (empty for now).
FIX: fix shape of support vectors in liblinear sparse.
Update git information.
Do not compare LinearSVC and SVC for exactly equal classification.
Update git information in README.rst.
Update sphinxext/docscrape from numpy's trunk.
Refactoring in the svm module.
Re-enable probability estimates in logisitic regression.
Rename failing example in order to build the doc.
FIX: fix generating the examples with some tricky uses of pylab.
Update install information.
Fallback to plain html for image rendering in index.html
Fix bugs in dev docs.
Updates on install doc.
Update mailmap file.
Updates on sparse.svm.SVC
Remove install_requires line.
Update README. Remove unused dependencies.
Use str for printing parameters.
Update setup.py.
Change make setup to run setup.py
Use repr for arrays in representation of classifiers.
Use nosetest as testing tool in README.
Allow setting variable PYTHON, NOSETESTS in Makefile.
Doc: correct size of intercept in svm.
Keep shrinking and probability as booleans in SVM.
Refactoring: put all gmm examples in its own directory.
Some love for the rst docs.
Create new class NuSVR.
Some patches for k_means.
Backport changes in sparsetools to compile under python2.7.
Add a pure-python version of LARS and refactor structure in glm.
add README for gmm examples.
Refactoring and doc for svm module.
FIX: fixes for the lars lasso code.
Fix build system.
Fixes on the Lasso-LARS algorithm.
Add benchmarks for the LARS algorithm.
Change score function and add docstrings.
Some work on the rst docs.
more doc love.
DOC: more work on svm module.
Fix in LARS: specify manually number of interations for full path.
Remove "debugging" traces...
Fix doctests.
DOC: some doc glm module.
Convert to ndarray in Ridge
DOC: glm module.
FIX: fix intercept in LinearRegression.
Doc: Add stub file.
Benchmarks for some Glm classifiers.
DOC: more on glm module.
Fix typo
Backport total_seconds from python2.7 to use in benchmarks
Refactoring in glm.benchmarks.
Rename nSV_ --> n_support_ in svm module.
Some more doc for the glm module.
Update doc svm.NuSVC
Make BSD find happy.
Compat: Add function copysign in the case of numpy < 1.4
Do not import pylab globally in benchmarks
Test for function utils.fixes._copysign.
FIX: fix previous (stupid) commit.
Welcome Virgile Fritsch
Update docstring for BayesianRidge.
DOC: update docstrings in glm.bayes.
Update docstrings in svm and logistic.
FIX: some fixes for bayesian doc in glm.rst
DOC: some more fixes on BayesianRegression doc.
Better error message in fit svm.
Fix failing tests (sparse svm).
Merge http://github.com/GaelVaroquaux/scikit-learn into gael
Be able to do _get_params and _set_params in a recursive way.
Fix imports.
Temporary fix for Table of Contents not showing.
Do not import pyalb in the benchmarks.
LARS refactoring speedup Work In Progress!!!
more on lars optimization
more on lars speedup WIP
LARS with precomputed kernel working.
more work in lars optimization.
More on LARS performance: triangular solving and cholesky deletes.
A more challenging example.
cleanup and fix some tests.
More on LARS.
more optimizations
cleanup
Update CBLAS files: add rotg, rot, trsv, remove tpsv.
Good bye minilearn.
Fixes for ref atlas.
Some fixes for the atlas we ship.
Add missing cblas_dcopy files.
New theme for the web page.
Add what's new page and a nicer sidebar for index page.
Move glm related benchmarks to a common location.
Performance improvements for LARS precomputed Gram matrix.
Remove weight_label keyword from SVR.
Remove Minilearn C sources.
Add some developer information for the CBLAS we ship.
Cosmetic changes to the cblas README.
More love for the new web page theme.
Refactoring in the svm module.
Also remove Windows python extension (.pyd) in make clean.
move sparse.svm into the svm module to match glm.sparse.
Make a reference page in the docs.
Update class reference.
Cleanup in setup scripts.
Bugfixing in setup.py
cosmit.
Cosmetic changes to svm tests.
Correct default value of gamma in the svm docstrings.
Refactoring in sparse SVM and bug solving (default value of gamma).
Refactor svm tests.
Fix doctest failing by last bug fixing.
Add target test-doc to Makefile to test the RST docs.
Remove obsolete debugging code from grid_search.
Remove obsolete comments from doc.
Cosmetic changes to grid_search_digits.
Reduce import time.
Polynomial kernel also uses keyword gamma.
Fix typo in svm docs.
Fix wrong link in doc.
DOC: update doc about LARS.
Add LARS, LassoLARS to class reference.
Update funding info.
Update API changes in feature_selection doc.
Remove the ann module.
Remove obsolte css code from the docs.
Update docs on sparse svm.
Correct spelling errors in svm documentation.
Fix spelling errors in glm.rst
Remove non ASCII characters from the docs (problem in latex output)
Fix non-html (latex) generation of the docs.
Fix RST (numpydoc) markup.
Update organization in index.rst
Update doc of neighbors module.
Update links in svm doc.
Update theme in web page (sidebar color)
Fix malformed RST in BallTree.cpp
Change doctests that are machine dependent.
Update joblib to 0.4.5
Comment out fragile joblib tests.
Add test.py script that runs nose.
Remvoe printing statements from tests.
Adopt numpy naming scheme for __version__ attribute.
Compatibility fixes for utils.graph.
Use by default np.unique.
Compatibility fixes for scipy <= 0.7 and numpy <= 1.4
Compatibility fixes for old scipy.sparse.
Do not include Makefile in final release.
Add missing files to setup.py
Add missing images
Rename features --> feature_extraction to match module feature_selection.
Update information on testing.
FIX: bug in setup.py file from glm/sparse/
Update web page.
FIX: fix imports in example for renamed modules.
Add function template for doc.
Update web page theme.
Update mailmap file.
Add Feature Selection classes to the reference docs.
0.5 changelog (Work in progres).
DOC: better link that literalinclude.
Combine user guide into a single file.
Update changelog.
Add png logo.
Update MANIFES.in file.
Update test.py and README.
Simplify test machinery.
Use ELLIPSIS for machine-dependent results in joblib.
Comment out machine-dependent tests from joblib.
Update Makefile
Welcome Mathieu Blondel.
Fix doctests from the tutorial.
0.5 release candidate.
FIX: some setuptools oddities.
0.5.rc2 release.
Still fixing distutils oddities ...
0.5.rc3 release.
Web page update.
Add sparse ti glm/__init__
Fix typo in docstring.
Fix typo
Fix doctests from RST docs.
Fix links in about page.
Cosmetic changes in install.rst
You want the truth well here it is.
Add a link to the PDF version of the docs.
0.5 final release.
Gael Varoquaux (240):
MISC: Make sure that the tests pass on numpy 1.2
MISC: Comsit + replace some global seeds with RandomSate
MISC: Rename to let the underscore RULE!
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
API: Create a base estimator class.
ENH: improve base class
ENH: Temporarily remove the typing for the base_estimator
TEST/BUG: Test the BaseEstimator class and fix the repr
Merge branch 'master' of http://github.com/agramfort/scikit-learn
Cosmit
MISC: Remove the #$! import *
ENH: convert all GLM estimators to the BaseEstimator class
BUG: Fix the OLS regression
BUG: Fix constructors with arguments.
BUG: Syntax error
BUG: str of linear models now working.
API: Change the type of params: turn this into a frozenset: unmutable and
Merge branch 'master' of http://github.com/agramfort/scikit-learn
ENH: Change _params to frozenset
API: Change argument controling whether intercept should be fitted
Cosmit in tests
Merge branch 'master' of http://github.com/agramfort/scikit-learn
API: Change the BaseEstimator and parameter signature logic.
Cosmit
Cosmit
ENH: Convert LDA and clustering to use the new BaseEstimator
MISC: Change the title of the documentation.
Cosmit
ENH: Make the clustering more usable
ENH: Add an example of playing with the stock market
ENH: Make SVNs fit to the BaseEstimator API.
ENH: Make SVNs fit to the BaseEstimator API.
Cosmit
MISC: Put the nearest neighbors estimator to the BaseEstimator
MISC: rename base_estimator.py to base.py
BUG: Make sure that the docs still build with recent versions of numpy
BUG: Make sure the docs still build with recent versions of numpy
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
BUG: Adapt the sparse SVM to the rename of base_estimator.
MISC: Remove warning when compiling docs.
MISC: Adding titles to examples.
DOC: Document best practices/coding guidelines to make it easier for
Cosmit
MISC: Put the nearest neighbors estimator to the BaseEstimator
MISC: rename base_estimator.py to base.py
BUG: Make sure that the docs still build with recent versions of numpy
BUG: Make sure the docs still build with recent versions of numpy
BUG: Adapt the sparse SVM to the rename of base_estimator.
MISC: Remove warning when compiling docs.
MISC: Adding titles to examples.
DOC: Document best practices/coding guidelines to make it easier for
Cosmit
ENH: Make the grid_search take instances of estimators rather than
Add a setup.cfg to specify default nosetests behavior.
MISC: 80 character bordel!
Add a setup.cfg to specify default nosetests behavior.
MISC: 80 character bordel!
Cosmit: rename grid to iter_grid
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
DOC: Beautify example
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
MISC: Beautify examples.
Cosmit
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
Merge branch 'master' of http://github.com/vmichel/scikit-learn
ENH: rework univariate selection to reach a compromise between ease of
ENH: First go at a help for cross-validated evaluation of a score.
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
Merge branch 'master' of http://github.com/agramfort/scikit-learn
ENH: Add an example showing the dependency of SVC+Anova on the number of
ENH: Add joblib as a bundle dependency.
BUG: Fix doctests in pipeline.py
BUG: Fix doctest in GMM
ENH: Add script to update joblib dependency
Cosmit: rename MixinClassif to ClassifMixin
ENH: Make sure that in cross_val_scores the StatifiedKFold is used only
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
MISC: Small change to contribution guidelines, suggested by Mathieu
COSMIT: For the sake of underscores
MISC: comment
ENH: Add parallel computing for cross validation.
BUG: Get the BaseEstimator to work even if there is not __init__
ENH: Make the parallel cross validation more efficient.
BUG: Fix cross_val_scores for unsupervised problems.
ENH: Improve cross_val in parallel
Merge branch 'cross_val_gael' of git at github.com:GaelVaroquaux/scikit-learn
Misc
ENH: Improve the repr for the BaseEstimator
Merge branch 'gael' of http://github.com/agramfort/scikit-learn
BUG: Fix a bug preventing from LinearModelCV to print.
Misc
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
BUG: Fix forgotten import in example
MISC: Remove pointless ellipsis directive (doctest)
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
BUG: Fix lda and qda on 64 bits.
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
Merge branch 'master' of ssh://gvaroquaux@scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
TEST: Make sure that doctests for bundled dependendies pass.
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
BUG: Make sure that joblib does get installed.
ENH: Make sure tests get installed.
ENH: Improve the repr for the BaseEstimator
TEST: Make sure that doctests for bundled dependendies pass.
BUG: Make sure that joblib does get installed.
ENH: Improve the repr for the BaseEstimator
TEST: Re-enable external tests.
BUG: Fix doctests to account for change in BaseEstimator repr
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
Merge branch 'cross_val_gael' of git at github.com:GaelVaroquaux/scikit-learn into cross_val_gael
MISC: Update joblib to 0.4.4
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
ENH: Make sure that the QDA inherits from the ClassifierMixin
Merge branch 'cross_val_gael' of github.com:GaelVaroquaux/scikit-learn into cross_val_gael
ENH: Make sure that the QDA inherits from the ClassifierMixin
ENH: Make sure that the logistic regression does inherit from
ENH: Add image to graph feature-extraction helper, and some basic graph
ENH: Make sure that the logistic regression does inherit from
ENH: Add some code to compute a graph Laplacien on sparse and non sparse
Merge branch 'master' of github.com:scikit-learn/scikit-learn into cross_val_gael
BUG: Temporary fix for 'array does not own memory' in SVM
ENH: First implementation of spectral clustering.
BUG: Temporary fix for 'array does not own memory' in SVM
Merge branch 'master' of github.com:scikit-learn/scikit-learn
ENH: Clean up the image clustering code and add an example on lena.
DOC: Add documentation for spectral clustering.
ENH: Add an estimator object for the spectral clustering.
ENH: Add k-means cluster with clever initialization.
ENH: K-means algorithm with good initialization, more
MISC: Restore an example that is now working again.
API: Change 'clustering' to 'cluster'
Merge branch 'master' of git at github.com:GaelVaroquaux/scikit-learn
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
BUG: Add a forgotten setup.py line
ENH: Backport a fast graph connect component algorithm from scipy.
MISC: Cosmit based on comments from Olivier and Alex
DOC: Add some notes on complexity of clustering algorithms.
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
BUG: Adding missing setup.py file.
BUG: Remove UTF8 character checked in by mistake.
BUG: Make graph laplacian and spectral clustering work in 64 bits.
ENH: For numpy >= 1.5, use np.linalg.slogdet as a fast_logdet
BUG: Fix bug with numpy >= 1.5 introduced by my previous (stupid) commit.
ENH: Remove 'import *' in glm/__init__
BUG: Fix tests broken by last commit
ENH: Make spectral clustering tests more robust
Cosmit (PEP 8)
BUG: Fix glm/setup.py so that the glm sub package installs right.
TEST: make the test location consistent.
API: Add cluster as an import of the main __init__
BUG: Fix warnings module not imported in coordinate_descent. Thanks to
Merge branch 'master' of github.com:scikit-learn/scikit-learn
MISC: Move AUTHORS to AUTHORS.rst so that it displays better on github
BUG: Make sure computations do not get executed at import time, so that
Cosmit
BUG: Remove failing doctest.
MISC: More tests and more docs for preprocessing.
BUG: Cater for NaNs in SelectPercentile.
Cosmit: 2 lines between function definitions
ENH: Make sure that the cross_val_score uses StratifiedKFold for
ENH: GridSearchCV: add an 'iid=True' and open the option to optimize
MISC: 3-Fold cross-val by default
ENH: Make sure that grid_search uses a StratifiedKFold by default on
BUG: Fix doctest
DOC: better example for SVM-Anova
ENH: Make sure docs build on older versions of sphinx
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
DOC: Prettify
DOC: Make first page more compact.
DOC: Update the developer guidelines.
MISC: Tweak front page
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
MISC: Cosmit on PCA tests to get understandable errors from the buildbot.
MISC: Delayed import of pylab, to work on the buildbot
MISC: Relative imports
BUG: Fix tests to be moroe robust
Cosmit
Merge branch 'master' of github.com:scikit-learn/scikit-learn
MISC: Add a warning in the spectral clustering if pymag is not present
Revert "MISC: Add a warning in the spectral clustering if pymag is not present"
Revert "Revert "MISC: Add a warning in the spectral clustering if pymag is not present""
BUG: Import stats explicitely to work with scipy > 0.7
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Fix typo on David's name
Merge branch 'master' of github.com:scikit-learn/scikit-learn
ENH: Add _set_params/_get_params in Pipeline
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
ENH: Implement _reinit on Pipelines.
ENH: Use new pipeline framework in SVN-ANOVA
BUG: Import stats explicitely to work with scipy > 0.7
ENH: Finish the __repr__ for the pipeline
ENH: Add error management to the KFolds
ENH: Port the nipy k-means with some cleanups and enhancements.
ENH: Change the initialisation heuristic for k-means: in general random
BUG: Adapt spectral to new k_means API
Merge branch 'master' of github.com:scikit-learn/scikit-learn into kmeans
ENH: Add error management to the KFolds
Cosmit
Cosmit
Merge branch 'master' of github.com:scikit-learn/scikit-learn into pipeline
ENH: Change pipelines so that they are simpler and address subobjects
BUG: Fix bug introduced by previous commit
BUG: Fix doctests.
DOC: Better docstring.
ENH: Make setting nested parameters on Pipeline really work.
Cosmit
TEST: Add a smoke test for cross_val_score
MISC: Fix spelling.
Merge branch 'master' of github.com:scikit-learn/scikit-learn
DOC: Add more links to the index
DOC: Add forgotten link targets.
DOC: prettify the nearest neighbors docs
DOC: Prettify the SVM docs.
MISC: Add 'Python' in the examples page
DOC: fix the PCA iris example.
MISC: Remove non-necessary lines from PCA example
DOC: Prettify the clustering documentation.
DOC: Fix the reference classes documentation
DOC: Prettify the GLM docs
MISC: Quiet down the tests.
Merge branch 'master' of github.com:scikit-learn/scikit-learn
ENH: Add a tester to the scikit.
ENH: Make doctests pass with numpy tester.
MISC: Make sure tests always run.
MISC/DOC: fix reference
TEST: Fix test_pca sign error.
TEST: Fix whitespace in doctests.
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
ENH: GridsearchCV, Pipelines and cross validation
ENH: Make sure that Pipeline and GridSearch objects are indeed recognized
ENH: Make sure clone works on pipelines
ENH: Implement a score for the GridSearch.
ENH: Make sure that a GridSearchCV has a score
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Merge branch 'cross_val' of github.com:GaelVaroquaux/scikit-learn
Merge branch 'master' of http://github.com/fabianp/scikit-learn
Mathieu Blondel (4):
Added filters to WordNGramAnalyzer.
Added a non-hashing dense vectorizer object.
Added transform() method to Pipeline object.
Updated dense vectorizer to follow transformer API.
Matthieu Brucher (1):
Fixed a typo
Matthieu Perrot (23):
ENH: optional computing of estimated covariance of LDA classifier.
MISC: add an unfinished toy example to compare LDA with a (not yet implemented) QDA.
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
BUG: Fixed example after last API changes
BUG: add missing call to pylab show function
BUG: Fixed pipeline feature selection example after last API changes
MISC: lda: Y -> y
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
BUG: Fixed example after last API changes
BUG: add missing call to pylab show function
BUG: Fixed pipeline feature selection example after last API changes
ENH: add QDA classifier, some docs, examples and tests. LDA has been reworked a bit to follow the API of QDA and avoid useless operations.
Merge branch 'master' of http://github.com/GaelVaroquaux/scikit-learn
Merge branch 'master' of git://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
ENH: optional computing of estimated covariance of LDA classifier.
MISC: add an unfinished toy example to compare LDA with a (not yet implemented) QDA.
MISC: lda: Y -> y
ENH: add QDA classifier, some docs, examples and tests. LDA has been reworked a bit to follow the API of QDA and avoid useless operations.
Merge branch 'master' of git://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
cosmit in LDA/QDA
MISC: vectorize priors computation for LDA and QDA
Merge branch 'master' of ssh://revilyo@scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
MISC: remove debug
Olivier Grisel (116):
test to reproduce issue 67 on LARS coef shape
Merge branch 'master' into issue-67-LARS-shape
tracking changes from master
follow API change in LARS
Merge branch 'master' into issue-67-LARS-shape
Merge branch 'master' into issue-67-LARS-shape
make sparse coding test pass
more .gitignore
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
started work on document classification: bag of wordsw extraction and hashed tfidf
some tests for the text features extractor
checkpointing work in progress on MLComp dataset integration
remove labels handling from vectorizer code
more work on document classification dataset loader
smaller default dim: faster to load by default, need experimental setting to find good tradeoff
make it easy to find the raw source document
better parameter ordering
example usage of MLComp document classification datasets
use compiled re pattern
small fixes
Merge branches 'master' and 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
typos
add the ability to use stop words for text classification, but does not improve accuracy hence not enabled by default
typo in comments
faster and better accuracy with hinge loss of doc classif example but not sparse anymore since l2 reg...
make the features package a first class citizen
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
ENH: more efficient stopping criterion coordinate descent GLM and comparison with python-glmnet
blas-ification of elastic net + ensure that the gap is initialized and evaluated
cosmit
work in progress on sparse vector extraction for document datasets
exclude scikits.learn.external package from top level nosetests env
missing pl.show() in rfe examples
more missing pl.show() in examples
using a separate class for the sparse version of the hashing vectorizer
readd the dense version of the vectorizer
checkpointing work in progress on the sparse version of the document vectorizer
more scalable TF-IDF computation unfortunately using a python for loop
new example to demonstrate sparse TF-IDF + sparse SVM on 20 newsgroups (too slow right now)
Merge branch 'sparse-documents'
avoid useless allocations in dense_to_sparse conversion
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
experimenting with character n-grams features (basic morphological analyzer)
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
fix one simple import in doctest for GMM
simple Makefile for repetitive dev tasks on POSIX OS
fix broken/unstable sparse SVM tests
even more stability fix for sparse SVM
fix broken doctest in HMM
disabling broken doctest in Gaussian Mixture Models
fix HMM doctests
cosmit
ignore coverage output folder
trailing spaces
skip remaining failing tests in HMM test suite
fix inline comment
Showcase the new LinearSVC wrapper for with sparse liblinear bindings in the 20 newsgroups document classification example
tracking changes in master branch
fix broken test for text features extraction
fix broken test for text features extraction
tracking changes from master and restore broken SparseHashingVectorizer
add ability to compute token ngrams too
fix broken doctests for SVC / NuSVC
Merge branch 'master' into char-ngram-features
cosmit
cosmit + trailing spaces + improved some comments
pep8 spacing
more cosmit
cosmit
Merge branch 'master' of github.com:scikit-learn/scikit-learn into issue-77-sparse-cd
starting boilerplate for sparse coordinate descent
Merge branch 'master' of github.com:scikit-learn/scikit-learn into issue-77-sparse-cd
fix broken test
checkpointing work in progress
avoid confusing cython extension names
fixed various issues with sparse datatype handling in previous checkpoint
better note
first stab at the sparse CD
leave sparse evaluation of the dual gap for later
forgot files from previous checkin
Merge branch 'master' of github.com:scikit-learn/scikit-learn into issue-77-sparse-cd
check that sparse API for coordinate descent also work with dense list-based input
one more test for sparse CD
sparse dual gap too!
Merge branch 'master' of github.com:scikit-learn/scikit-learn into issue-77-sparse-cd
cosmit
Merge branch 'master' of github.com:scikit-learn/scikit-learn
fix broken doctest in cross_val
Merge branch 'master' into issue-77-sparse-cd
more robust tests
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Merge branch 'master' into issue-77-sparse-cd
missing import
added sparse Lasso utility class
OPTIM: fix a typo and some suboptimal cython constructs in dense coordinate descent
Merge branch 'master' of github.com:scikit-learn/scikit-learn
share the same cython impl for both lasso and elastic net CD
make d_w_max early stopping criterion scale invariant
cosmit: s/nsamples/n_samples/g and s/nfeatures/n_features/g
group stopping criterion related boilerplate in the same place for readability
FIX: make CD lasso robust to zero valued columns (useless features)
Merge branch 'master' of github.com:scikit-learn/scikit-learn
add duration to glmnet benchmark output
removed useless includes
make d_w_max threshold independant of the squared norm of y to make it useful in practice
Merge branch 'master' into issue-77-sparse-cd
port latest bugfix and optims from dense CD to sparse CD
fix NORMALIZE_WHITESPACE issues in doctests
more robust and understable CD elastic net test using explained variance score instead of RMSE
forgot to setup the good value of rho in last checkin
Merge branch 'master' into issue-77-sparse-cd
Merge branch 'textextract' of git://github.com/mblondel/scikit-learn
Merge branch 'master' of github.com:scikit-learn/scikit-learn
better docstring + cosmit for the RFE module
pep8
move the RFE module to the feature selection package
Ron Weiss (38):
added hmm code from http://github.com/ronw/gm
removed logging, dependency on abc, and unnecessary imports
added hmm unit tests
cleanup hmm module: made properties compatible with Python 2.5, etc.
changed hmm.trainer usage: each hmm object must have a _default_trainer property which can be overridden by passing a different trainer into hmm.train()
changed "train" -> "fit". Removed HMMGMM for now.
removed references to gmm.init() in gmm docstrings
fixed random seed in hmm unittests
removed init() method from hmm classes
minor tweaks to make hmm.GaussianHMM look like gmm.GMM
fixed bug in HMM viterbi logprob
added MultinomialHMM, unit tests
fixed *HMM.fit() to include *all* parameters by default
removed ndim argument from gmm.rvs()
added validate_covars back to gmm.py
added ndim property back to gmm to keep it consistent with HMM
Merge branch 'hmm'
added support for HMMs with GMM emissions
Merge remote branch 'upstream/master'
fixed GMM examples
fixed GMM examples
fixed broken doctests in gmm.py
updated gmm.py to comply with scikit-learn API. fixed pep8, pyflakes errors
DOC: fixed typos in developer documentation
Merge branch 'master' of ssh://scikit-learn.git.sourceforge.net/gitroot/scikit-learn/scikit-learn
BUG: fixed failing test in GMM
remove GMM.lpdf method
merge
update hmm module to comply with scikit-learn API
remove hmm.HMM factory to simplify hmm module's interface
merge hmm_trainers into hmm module
finish merge of hmm_trainers with hmm and remove hmm_trainers
remove extraneous tests from test_hmm.py
speed up hmm unit tests, add test for GaussianHMM with priors
fix GMMHMM bugs. speed up tests
Merge branch 'master' of github.com:scikit-learn/scikit-learn
FIX: failing gmm tests
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Vincent Michel (40):
New feature selection
Last version of univariate selection
Merge branch 'master' of git at github.com:vmichel/scikit-learn
Corrections of indentation in univariate_selection
remove old univariate_selection
Correct nosetets for univariate_selection
Add doc to univariate_selection
Merge branch 'master' of git at github.com:vmichel/scikit-learn
Merge branch 'master' of git at github.com:agramfort/scikit-learn
Merge branch 'master' of git at github.com:agramfort/scikit-learn
Add rfe example
update example
Merge branch 'master' of git at github.com:agramfort/scikit-learn
Merge branch 'master' of git at github.com:agramfort/scikit-learn
Corrections in rfe
Remove feature selection
Add ranking_
Add Crossvalidated version of RFE
Add example of RFE CV
ENH : New version of Bayes Ridge
Merge branch 'master' of git at github.com:vmichel/scikit-learn
Newer (and faster !) version of Bayesian regression.
Merge branch 'master' of https://vmichel@github.com/scikit-learn/scikit-learn
ENH : New version of Bayes Ridge
Newer (and faster !) version of Bayesian regression.
Update tests for bayes
Merge branch 'master' of git at github.com:scikit-learn/scikit-learn
Add first draft of variational bayes
Add variational inference
DOC: Update doc for bayesian regression + examples
Merge branch 'master' of github.com:scikit-learn/scikit-learn
FIX : Remove reference to Variational Bayes
More doc in bayes.py, fix bug in high dimension, add score
Merge branch 'master' of github.com:scikit-learn/scikit-learn
ENH : change the convergence trigger
More coverage for bayes
DOC : create and start doc for cross-validation.
Merge branch 'master' of github.com:scikit-learn/scikit-learn
DOC : add changes in classes.rst
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Virgile Fritsch (9):
DOC: Fix typos in svm module documentation.
Remove Y from fit in OneClassSVM.
Add a reinitialization function for estimators + write test for
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
Change test name for the _reinit() method.
Merge branch 'master' of github.com:scikit-learn/scikit-learn
Merge branch 'master' of github.com:GaelVaroquaux/scikit-learn
DOC: Explain the _set_params method in BaseEstimator class.
Rename PyBallTree* --> BallTree* in BallTree.cpp.
Yaroslav Halchenko (13):
pruning joblib external
Merge commit '8b26c79e7ba67dd614e84c3333ce845ee2edb049' into dfsg
Merge 0.5.rc into DFSG (pruning externals: joblib)
Merge 0.5.rc3 into DFSG (pruning externals: joblib)
removing carried version of libsvm in favor to use systemwide (otherwise svm.h inclusion conflict)
DOC: removing a stale request for subversion write permissions
Allow to build _libsvm.so against system-wide LIBSVM's svm.h
API to control LIBSVM verbosity without patching
recythoning _libsvm.pyx for previous commit
revert change to libsvm -- now verbosity is controlled via API
enable more doc testing for test-doc Makefile rule
adding acknowledgement to Dr.Haxby for my support ;-)
Merge 0.5 into DFSG (pruning externals: joblib)
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