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* [SPARK-4023] [MLlib] [PySpark] convert rdd into RDD of VectorDavies Liu2014-10-211-0/+19
| | | | | | | | | | | | | Convert the input rdd to RDD of Vector. cc mengxr Author: Davies Liu <davies@databricks.com> Closes #2870 from davies/fix4023 and squashes the following commits: 1eac767 [Davies Liu] address comments 0871576 [Davies Liu] convert rdd into RDD of Vector
* [SPARK-3867][PySpark] ./python/run-tests failed when it run with Python 2.6 ↵cocoatomo2014-10-111-1/+5
| | | | | | | | | | | | | and unittest2 is not installed ./python/run-tests search a Python 2.6 executable on PATH and use it if available. When using Python 2.6, it is going to import unittest2 module which is not a standard library in Python 2.6, so it fails with ImportError. Author: cocoatomo <cocoatomo77@gmail.com> Closes #2759 from cocoatomo/issues/3867-unittest2-import-error and squashes the following commits: f068eb5 [cocoatomo] [SPARK-3867] ./python/run-tests failed when it run with Python 2.6 and unittest2 is not installed
* [SPARK-3786] [PySpark] speedup testsDavies Liu2014-10-061-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | This patch try to speed up tests of PySpark, re-use the SparkContext in tests.py and mllib/tests.py to reduce the overhead of create SparkContext, remove some test cases, which did not make sense. It also improve the performance of some cases, such as MergerTests and SortTests. before this patch: real 21m27.320s user 4m42.967s sys 0m17.343s after this patch: real 9m47.541s user 2m12.947s sys 0m14.543s It almost cut the time by half. Author: Davies Liu <davies.liu@gmail.com> Closes #2646 from davies/tests and squashes the following commits: c54de60 [Davies Liu] revert change about memory limit 6a2a4b0 [Davies Liu] refactor of tests, speedup 100%
* [SPARK-3491] [MLlib] [PySpark] use pickle to serialize data in MLlibDavies Liu2014-09-191-45/+54
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Currently, we serialize the data between JVM and Python case by case manually, this cannot scale to support so many APIs in MLlib. This patch will try to address this problem by serialize the data using pickle protocol, using Pyrolite library to serialize/deserialize in JVM. Pickle protocol can be easily extended to support customized class. All the modules are refactored to use this protocol. Known issues: There will be some performance regression (both CPU and memory, the serialized data increased) Author: Davies Liu <davies.liu@gmail.com> Closes #2378 from davies/pickle_mllib and squashes the following commits: dffbba2 [Davies Liu] Merge branch 'master' of github.com:apache/spark into pickle_mllib 810f97f [Davies Liu] fix equal of matrix 032cd62 [Davies Liu] add more type check and conversion for user_product bd738ab [Davies Liu] address comments e431377 [Davies Liu] fix cache of rdd, refactor 19d0967 [Davies Liu] refactor Picklers 2511e76 [Davies Liu] cleanup 1fccf1a [Davies Liu] address comments a2cc855 [Davies Liu] fix tests 9ceff73 [Davies Liu] test size of serialized Rating 44e0551 [Davies Liu] fix cache a379a81 [Davies Liu] fix pickle array in python2.7 df625c7 [Davies Liu] Merge commit '154d141' into pickle_mllib 154d141 [Davies Liu] fix autobatchedpickler 44736d7 [Davies Liu] speed up pickling array in Python 2.7 e1d1bfc [Davies Liu] refactor 708dc02 [Davies Liu] fix tests 9dcfb63 [Davies Liu] fix style 88034f0 [Davies Liu] rafactor, address comments 46a501e [Davies Liu] choose batch size automatically df19464 [Davies Liu] memorize the module and class name during pickleing f3506c5 [Davies Liu] Merge branch 'master' into pickle_mllib 722dd96 [Davies Liu] cleanup _common.py 0ee1525 [Davies Liu] remove outdated tests b02e34f [Davies Liu] remove _common.py 84c721d [Davies Liu] Merge branch 'master' into pickle_mllib 4d7963e [Davies Liu] remove muanlly serialization 6d26b03 [Davies Liu] fix tests c383544 [Davies Liu] classification f2a0856 [Davies Liu] mllib/regression d9f691f [Davies Liu] mllib/util cccb8b1 [Davies Liu] mllib/tree 8fe166a [Davies Liu] Merge branch 'pickle' into pickle_mllib aa2287e [Davies Liu] random f1544c4 [Davies Liu] refactor clustering 52d1350 [Davies Liu] use new protocol in mllib/stat b30ef35 [Davies Liu] use pickle to serialize data for mllib/recommendation f44f771 [Davies Liu] enable tests about array 3908f5c [Davies Liu] Merge branch 'master' into pickle c77c87b [Davies Liu] cleanup debugging code 60e4e2f [Davies Liu] support unpickle array.array for Python 2.6
* [PySpark] [SPARK-2954] [SPARK-2948] [SPARK-2910] [SPARK-2101] Python 2.6 FixesJosh Rosen2014-08-111-1/+6
| | | | | | | | | | | | | | | | | - Modify python/run-tests to test with Python 2.6 - Use unittest2 when running on Python 2.6. - Fix issue with namedtuple. - Skip TestOutputFormat.test_newhadoop on Python 2.6 until SPARK-2951 is fixed. - Fix MLlib _deserialize_double on Python 2.6. Closes #1868. Closes #1042. Author: Josh Rosen <joshrosen@apache.org> Closes #1874 from JoshRosen/python2.6 and squashes the following commits: 983d259 [Josh Rosen] [SPARK-2954] Fix MLlib _deserialize_double on Python 2.6. 5d18fd7 [Josh Rosen] [SPARK-2948] [SPARK-2910] [SPARK-2101] Python 2.6 fixes
* [SPARK-2627] [PySpark] have the build enforce PEP 8 automaticallyNicholas Chammas2014-08-061-4/+7
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | As described in [SPARK-2627](https://issues.apache.org/jira/browse/SPARK-2627), we'd like Python code to automatically be checked for PEP 8 compliance by Jenkins. This pull request aims to do that. Notes: * We may need to install [`pep8`](https://pypi.python.org/pypi/pep8) on the build server. * I'm expecting tests to fail now that PEP 8 compliance is being checked as part of the build. I'm fine with cleaning up any remaining PEP 8 violations as part of this pull request. * I did not understand why the RAT and scalastyle reports are saved to text files. I did the same for the PEP 8 check, but only so that the console output style can match those for the RAT and scalastyle checks. The PEP 8 report is removed right after the check is complete. * Updates to the ["Contributing to Spark"](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) guide will be submitted elsewhere, as I don't believe that text is part of the Spark repo. Author: Nicholas Chammas <nicholas.chammas@gmail.com> Author: nchammas <nicholas.chammas@gmail.com> Closes #1744 from nchammas/master and squashes the following commits: 274b238 [Nicholas Chammas] [SPARK-2627] [PySpark] minor indentation changes 983d963 [nchammas] Merge pull request #5 from apache/master 1db5314 [nchammas] Merge pull request #4 from apache/master 0e0245f [Nicholas Chammas] [SPARK-2627] undo erroneous whitespace fixes bf30942 [Nicholas Chammas] [SPARK-2627] PEP8: comment spacing 6db9a44 [nchammas] Merge pull request #3 from apache/master 7b4750e [Nicholas Chammas] merge upstream changes 91b7584 [Nicholas Chammas] [SPARK-2627] undo unnecessary line breaks 44e3e56 [Nicholas Chammas] [SPARK-2627] use tox.ini to exclude files b09fae2 [Nicholas Chammas] don't wrap comments unnecessarily bfb9f9f [Nicholas Chammas] [SPARK-2627] keep up with the PEP 8 fixes 9da347f [nchammas] Merge pull request #2 from apache/master aa5b4b5 [Nicholas Chammas] [SPARK-2627] follow Spark bash style for if blocks d0a83b9 [Nicholas Chammas] [SPARK-2627] check that pep8 downloaded fine dffb5dd [Nicholas Chammas] [SPARK-2627] download pep8 at runtime a1ce7ae [Nicholas Chammas] [SPARK-2627] space out test report sections 21da538 [Nicholas Chammas] [SPARK-2627] it's PEP 8, not PEP8 6f4900b [Nicholas Chammas] [SPARK-2627] more misc PEP 8 fixes fe57ed0 [Nicholas Chammas] removing merge conflict backups 9c01d4c [nchammas] Merge pull request #1 from apache/master 9a66cb0 [Nicholas Chammas] resolving merge conflicts a31ccc4 [Nicholas Chammas] [SPARK-2627] miscellaneous PEP 8 fixes beaa9ac [Nicholas Chammas] [SPARK-2627] fail check on non-zero status 723ed39 [Nicholas Chammas] always delete the report file 0541ebb [Nicholas Chammas] [SPARK-2627] call Python linter from run-tests 12440fa [Nicholas Chammas] [SPARK-2627] add Scala linter 61c07b9 [Nicholas Chammas] [SPARK-2627] add Python linter 75ad552 [Nicholas Chammas] make check output style consistent
* [SPARK-2478] [mllib] DecisionTree Python APIJoseph K. Bradley2014-08-021-0/+36
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Added experimental Python API for Decision Trees. API: * class DecisionTreeModel ** predict() for single examples and RDDs, taking both feature vectors and LabeledPoints ** numNodes() ** depth() ** __str__() * class DecisionTree ** trainClassifier() ** trainRegressor() ** train() Examples and testing: * Added example testing classification and regression with batch prediction: examples/src/main/python/mllib/tree.py * Have also tested example usage in doc of python/pyspark/mllib/tree.py which tests single-example prediction with dense and sparse vectors Also: Small bug fix in python/pyspark/mllib/_common.py: In _linear_predictor_typecheck, changed check for RDD to use isinstance() instead of type() in order to catch RDD subclasses. CC mengxr manishamde Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com> Closes #1727 from jkbradley/decisiontree-python-new and squashes the following commits: 3744488 [Joseph K. Bradley] Renamed test tree.py to decision_tree_runner.py Small updates based on github review. 6b86a9d [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new affceb9 [Joseph K. Bradley] * Fixed bug in doc tests in pyspark/mllib/util.py caused by change in loadLibSVMFile behavior. (It used to threshold labels at 0 to make them 0/1, but it now leaves them as they are.) * Fixed small bug in loadLibSVMFile: If a data file had no features, then loadLibSVMFile would create a single all-zero feature. 67a29bc [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new cf46ad7 [Joseph K. Bradley] Python DecisionTreeModel * predict(empty RDD) returns an empty RDD instead of an error. * Removed support for calling predict() on LabeledPoint and RDD[LabeledPoint] * predict() does not cache serialized RDD any more. aa29873 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new bf21be4 [Joseph K. Bradley] removed old run() func from DecisionTree fa10ea7 [Joseph K. Bradley] Small style update 7968692 [Joseph K. Bradley] small braces typo fix e34c263 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new 4801b40 [Joseph K. Bradley] Small style update to DecisionTreeSuite db0eab2 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix2' into decisiontree-python-new 6873fa9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new 225822f [Joseph K. Bradley] Bug: In DecisionTree, the method sequentialBinSearchForOrderedCategoricalFeatureInClassification() indexed bins from 0 to (math.pow(2, featureCategories.toInt - 1) - 1). This upper bound is the bound for unordered categorical features, not ordered ones. The upper bound should be the arity (i.e., max value) of the feature. 93953f1 [Joseph K. Bradley] Likely done with Python API. 6df89a9 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new 4562c08 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new 665ba78 [Joseph K. Bradley] Small updates towards Python DecisionTree API 188cb0d [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new 6622247 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new b8fac57 [Joseph K. Bradley] Finished Python DecisionTree API and example but need to test a bit more. 2b20c61 [Joseph K. Bradley] Small doc and style updates 1b29c13 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new 584449a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new dab0b67 [Joseph K. Bradley] Added documentation for DecisionTree internals 8bb8aa0 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix 978cfcf [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix 6eed482 [Joseph K. Bradley] In DecisionTree: Changed from using procedural syntax for functions returning Unit to explicitly writing Unit return type. 376dca2 [Joseph K. Bradley] Updated meaning of maxDepth by 1 to fit scikit-learn and rpart. * In code, replaced usages of maxDepth <-- maxDepth + 1 * In params, replace settings of maxDepth <-- maxDepth - 1 e06e423 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new bab3f19 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new 59750f8 [Joseph K. Bradley] * Updated Strategy to check numClassesForClassification only if algo=Classification. * Updates based on comments: ** DecisionTreeRunner *** Made dataFormat arg default to libsvm ** Small cleanups ** tree.Node: Made recursive helper methods private, and renamed them. 52e17c5 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix f5a036c [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new da50db7 [Joseph K. Bradley] Added one more test to DecisionTreeSuite: stump with 2 continuous variables for binary classification. Caused problems in past, but fixed now. 8e227ea [Joseph K. Bradley] Changed Strategy so it only requires numClassesForClassification >= 2 for classification cd1d933 [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new 8ea8750 [Joseph K. Bradley] Bug fix: Off-by-1 when finding thresholds for splits for continuous features. 8a758db [Joseph K. Bradley] Merge branch 'decisiontree-bugfix' into decisiontree-python-new 5fe44ed [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-python-new 2283df8 [Joseph K. Bradley] 2 bug fixes. 73fbea2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into decisiontree-bugfix 5f920a1 [Joseph K. Bradley] Demonstration of bug before submitting fix: Updated DecisionTreeSuite so that 3 tests fail. Will describe bug in next commit. f825352 [Joseph K. Bradley] Wrote Python API and example for DecisionTree. Also added toString, depth, and numNodes methods to DecisionTreeModel.
* Fix PEP8 violations in Python mllib.Reynold Xin2014-05-251-17/+10
| | | | | | | | | Author: Reynold Xin <rxin@apache.org> Closes #871 from rxin/mllib-pep8 and squashes the following commits: 848416f [Reynold Xin] Fixed a typo in the previous cleanup (c -> sc). a8db4cd [Reynold Xin] Fix PEP8 violations in Python mllib.
* fix bugs of dot in pythonXusen Yin2014-04-221-4/+4
| | | | | | | | | | | | | | If there are no `transpose()` in `self.theta`, a *ValueError: matrices are not aligned* is occurring. The former test case just ignore this situation. Author: Xusen Yin <yinxusen@gmail.com> Closes #463 from yinxusen/python-naive-bayes and squashes the following commits: fcbe3bc [Xusen Yin] fix bugs of dot in python
* [WIP] SPARK-1430: Support sparse data in Python MLlibMatei Zaharia2014-04-151-0/+302
This PR adds a SparseVector class in PySpark and updates all the regression, classification and clustering algorithms and models to support sparse data, similar to MLlib. I chose to add this class because SciPy is quite difficult to install in many environments (more so than NumPy), but I plan to add support for SciPy sparse vectors later too, and make the methods work transparently on objects of either type. On the Scala side, we keep Python sparse vectors sparse and pass them to MLlib. We always return dense vectors from our models. Some to-do items left: - [x] Support SciPy's scipy.sparse matrix objects when SciPy is available. We can easily add a function to convert these to our own SparseVector. - [x] MLlib currently uses a vector with one extra column on the left to represent what we call LabeledPoint in Scala. Do we really want this? It may get annoying once you deal with sparse data since you must add/subtract 1 to each feature index when training. We can remove this API in 1.0 and use tuples for labeling. - [x] Explain how to use these in the Python MLlib docs. CC @mengxr, @joshrosen Author: Matei Zaharia <matei@databricks.com> Closes #341 from mateiz/py-ml-update and squashes the following commits: d52e763 [Matei Zaharia] Remove no-longer-needed slice code and handle review comments ea5a25a [Matei Zaharia] Fix remaining uses of copyto() after merge b9f97a3 [Matei Zaharia] Fix test 1e1bd0f [Matei Zaharia] Add MLlib logistic regression example in Python 88bc01f [Matei Zaharia] Clean up inheritance of LinearModel in Python, and expose its parametrs 37ab747 [Matei Zaharia] Fix some examples and docs due to changes in MLlib API da0f27e [Matei Zaharia] Added a MLlib K-means example and updated docs to discuss sparse data c48e85a [Matei Zaharia] Added some tests for passing lists as input, and added mllib/tests.py to run-tests script. a07ba10 [Matei Zaharia] Fix some typos and calculation of initial weights 74eefe7 [Matei Zaharia] Added LabeledPoint class in Python 889dde8 [Matei Zaharia] Support scipy.sparse matrices in all our algorithms and models ab244d1 [Matei Zaharia] Allow SparseVectors to be initialized using a dict a5d6426 [Matei Zaharia] Add linalg.py to run-tests script 0e7a3d8 [Matei Zaharia] Keep vectors sparse in Java when reading LabeledPoints eaee759 [Matei Zaharia] Update regression, classification and clustering models for sparse data 2abbb44 [Matei Zaharia] Further work to get linear models working with sparse data 154f45d [Matei Zaharia] Update docs, name some magic values 881fef7 [Matei Zaharia] Added a sparse vector in Python and made Java-Python format more compact
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