We should document options in public API doc. Otherwise, it is hard to find out the options without looking at the code. I tried to make `DefaultSource` private and put the documentation to package doc. However, since then there exists no public class under `source.libsvm`, the Java package doc doesn't show up in the generated html file (http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4492654). So I put the doc to `DefaultSource` instead. There are several minor updates in this PR:

1. Do `vectorType == "sparse"` only once.
2. Update `hashCode` and `equals`.
3. Remove inherited doc.
4. Delete temp dir in `afterAll`.

Lewuathe

Author: Xiangrui Meng <meng@databricks.com>

Closes #8699 from mengxr/SPARK-10537.

Add Python API for ```MultilayerPerceptronClassifier```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8067 from yanboliang/SPARK-9773.

LinearRegression and LogisticRegression lack of some Params for Python, and some Params are not shared classes which lead we need to write them for each class. These kinds of Params are list here:
```scala
HasElasticNetParam
HasFitIntercept
HasStandardization
HasThresholds
```
Here we implement them in shared params at Python side and make LinearRegression/LogisticRegression parameters peer with Scala one.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8508 from yanboliang/spark-10026.

[SPARK-10518] [DOCS] Update code examples in spark.ml user guide to use LIBSVM data source instead of MLUtils

I fixed to use LIBSVM data source in the example code in spark.ml instead of MLUtils

Author: y-shimizu <y.shimizu0429@gmail.com>

Closes #8697 from y-shimizu/SPARK-10518.

Previously, project/plugins.sbt explicitly set scalaVersion to 2.10.4. This can cause issues when using a version of sbt that is compiled against a different version of Scala (for example sbt 0.13.9 uses 2.10.5). Removing this explicit setting will cause build files to be compiled and run against the same version of Scala that sbt is compiled against.

Note that this only applies to the project build files (items in project/), it is distinct from the version of Scala we target for the actual spark compilation.

Author: Ahir Reddy <ahirreddy@gmail.com>

Closes #8709 from ahirreddy/sbt-scala-version-fix.

Before this fix, `MyDenseVectorUDT.typeName` gives `mydensevecto`, which is not desirable.

Author: Cheng Lian <lian@databricks.com>

Closes #8640 from liancheng/spark-10472/udt-type-name.

Missing method of ml.feature are listed here:
```StringIndexer``` lacks of parameter ```handleInvalid```.
```StringIndexerModel``` lacks of method ```labels```.
```VectorIndexerModel``` lacks of methods ```numFeatures``` and ```categoryMaps```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8313 from yanboliang/spark-10027.

[SPARK-10023] [ML] [PySpark] Unified DecisionTreeParams checkpointInterval between Scala and Python API.

"checkpointInterval" is member of DecisionTreeParams in Scala API which is inconsistency with Python API, we should unified them.
```
member of DecisionTreeParams <-> Scala API
shared param for all ML Transformer/Estimator <-> Python API
```
Proposal:
"checkpointInterval" is also used by ALS, so we make it shared params at Scala.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8528 from yanboliang/spark-10023.

ShuffleManager implementations are currently not given type information for
the key, value and combiner classes. Serialization of shuffle objects relies
on objects being JavaSerializable, with methods defined for reading/writing
the object or, alternatively, serialization via Kryo which uses reflection.

Serialization systems like Avro, Thrift and Protobuf generate classes with
zero argument constructors and explicit schema information
(e.g. IndexedRecords in Avro have get, put and getSchema methods).

By serializing the key, value and combiner class names in ShuffleDependency,
shuffle implementations will have access to schema information when
registerShuffle() is called.

Author: Matt Massie <massie@cs.berkeley.edu>

Closes #7403 from massie/shuffle-classtags.

pyspark.sql.types.Row implements ```__getitem__```

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8333 from yanboliang/spark-7544.

This change brings it to par with `branch-1.5` (and 1.5.0 release)

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #8704 from shivaram/ec2-1.5-update.

`LeftOutputIterator` and `RightOutputIterator` are symmetrically identical and can share a lot of code. If someone makes a change in one but forgets to do the same thing in the other we'll end up with inconsistent behavior. This patch also adds inline comments to clarify the intention of the code.

Author: Andrew Or <andrew@databricks.com>

Closes #8596 from andrewor14/smoj-cleanup.

this PR :
1.  Enhance reflection in RBackend. Automatically matching a Java array to Scala Seq when finding methods. Util functions like seq(), listToSeq() in R side can be removed, as they will conflict with the Serde logic that transferrs a Scala seq to R side.

2.  Enhance the SerDe to support transferring  a Scala seq to R side. Data of ArrayType in DataFrame
after collection is observed to be of Scala Seq type.

3.  Support ArrayType in createDataFrame().

Author: Sun Rui <rui.sun@intel.com>

Closes #8458 from sun-rui/SPARK-10049.

This PR includes the following changes:
- Add SQLConf to LocalNode
- Add HashJoinNode
- Add ConvertToUnsafeNode and ConvertToSafeNode.scala to test unsafe hash join.

Author: zsxwing <zsxwing@gmail.com>

Closes #8535 from zsxwing/SPARK-9990.

[SPARK-10514] [MESOS] waiting for min no of total cores acquired by Spark by implementing the sufficientResourcesRegistered method

spark.scheduler.minRegisteredResourcesRatio configuration parameter works for YARN mode but not for Mesos Coarse grained mode.

If the parameter specified default value of 0 will be set for spark.scheduler.minRegisteredResourcesRatio in base class and this method will always return true.

There are no existing test for YARN mode too. Hence not added test for the same.

Author: Akash Mishra <akash.mishra20@gmail.com>

Closes #8672 from SleepyThread/master.

This is a regression introduced in #4960, this commit fixes it and adds a test.

tnachen andrewor14 please review, this should be an easy one.

Author: Iulian Dragos <jaguarul@gmail.com>

Closes #8653 from dragos/issue/mesos/fine-grained-maxExecutorCores.

The architecture is that, in YARN mode, if the driver detects that an executor has disconnected, it asks the ApplicationMaster why the executor died. If the ApplicationMaster is aware that the executor died because of preemption, all tasks associated with that executor are not marked as failed. The executor
is still removed from the driver's list of available executors, however.

There's a few open questions:
1. Should standalone mode have a similar "get executor loss reason" as well? I localized this change as much as possible to affect only YARN, but there could be a valid case to differentiate executor losses in standalone mode as well.
2. I make a pretty strong assumption in YarnAllocator that getExecutorLossReason(executorId) will only be called once per executor id; I do this so that I can remove the metadata from the in-memory map to avoid object accumulation. It's not clear if I'm being overly zealous to save space, however.

cc vanzin specifically for review because it collided with some earlier YARN scheduling work.
cc JoshRosen because it's similar to output commit coordination we did in the past
cc andrewor14 for our discussion on how to get executor exit codes and loss reasons

Author: mcheah <mcheah@palantir.com>

Closes #8007 from mccheah/feature/preemption-handling.

From JIRA:
Add documentation for tungsten-sort.
From the mailing list "I saw a new "spark.shuffle.manager=tungsten-sort" implemented in
https://issues.apache.org/jira/browse/SPARK-7081, but it can't be found its
corresponding description in
http://people.apache.org/~pwendell/spark-releases/spark-1.5.0-rc3-docs/configuration.html(Currenlty
there are only 'sort' and 'hash' two options)."

Author: Holden Karau <holden@pigscanfly.ca>

Closes #8638 from holdenk/SPARK-10469-document-tungsten-sort.

Data Spill with UnsafeRow causes assert failure.

```
java.lang.AssertionError: assertion failed
	at scala.Predef$.assert(Predef.scala:165)
	at org.apache.spark.sql.execution.UnsafeRowSerializerInstance$$anon$2.writeKey(UnsafeRowSerializer.scala:75)
	at org.apache.spark.storage.DiskBlockObjectWriter.write(DiskBlockObjectWriter.scala:180)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$writePartitionedFile$2$$anonfun$apply$1.apply(ExternalSorter.scala:688)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$writePartitionedFile$2$$anonfun$apply$1.apply(ExternalSorter.scala:687)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$writePartitionedFile$2.apply(ExternalSorter.scala:687)
	at org.apache.spark.util.collection.ExternalSorter$$anonfun$writePartitionedFile$2.apply(ExternalSorter.scala:683)
	at scala.collection.Iterator$class.foreach(Iterator.scala:727)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
	at org.apache.spark.util.collection.ExternalSorter.writePartitionedFile(ExternalSorter.scala:683)
	at org.apache.spark.shuffle.sort.SortShuffleWriter.write(SortShuffleWriter.scala:80)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
	at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
	at org.apache.spark.scheduler.Task.run(Task.scala:88)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
```

To reproduce that with code (thanks andrewor14):
```scala
bin/spark-shell --master local
  --conf spark.shuffle.memoryFraction=0.005
  --conf spark.shuffle.sort.bypassMergeThreshold=0

sc.parallelize(1 to 2 * 1000 * 1000, 10)
  .map { i => (i, i) }.toDF("a", "b").groupBy("b").avg().count()
```

Author: Cheng Hao <hao.cheng@intel.com>

Closes #8635 from chenghao-intel/unsafe_spill.

Author: Cheng Lian <lian@databricks.com>

Closes #8670 from liancheng/spark-10301/address-pr-comments.

Use these in the optimizer as well:

            A and (not(A) or B) => A and B
            not(A and B) => not(A) or not(B)
            not(A or B) => not(A) and not(B)

Author: Yash Datta <Yash.Datta@guavus.com>

Closes #5700 from saucam/bool_simp.

The reason for this extra copy is that we iterate the array twice: calculate elements data size and copy elements to array buffer.

A simple solution is to follow `createCodeForStruct`, we can dynamically grow the buffer when needed and thus don't need to know the data size ahead.

This PR also include some typo and style fixes, and did some minor refactor to make sure `input.primitive` is always variable name not code when generate unsafe code.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #8496 from cloud-fan/avoid-copy.

Location of JIRAError has moved between old and new versions of python-jira package.
Longer term it probably makes sense to pin to specific versions (as mentioned in https://issues.apache.org/jira/browse/SPARK-10498 ) but for now, making release tools works with both new and old versions of python-jira.

Author: Holden Karau <holden@pigscanfly.ca>

Closes #8661 from holdenk/SPARK-10497-release-utils-does-not-work-with-new-jira-python.

Small typo in the example for `LabelledPoint` in the MLLib docs.

Author: Sean Paradiso <seanparadiso@gmail.com>

Closes #8680 from sparadiso/docs_mllib_smalltypo.

Add Python API for ml.feature.VectorSlicer.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8102 from yanboliang/SPARK-9772.

This PR is based on #8383 , thanks to viirya

JIRA: https://issues.apache.org/jira/browse/SPARK-9730

This patch adds the Full Outer Join support for SortMergeJoin. A new class SortMergeFullJoinScanner is added to scan rows from left and right iterators. FullOuterIterator is simply a wrapper of type RowIterator to consume joined rows from SortMergeFullJoinScanner.

Closes #8383

Author: Liang-Chi Hsieh <viirya@appier.com>
Author: Davies Liu <davies@databricks.com>

Closes #8579 from davies/smj_fullouter.

[SPARK-10461] [SQL] make sure `input.primitive` is always variable name not code at `GenerateUnsafeProjection`

When we generate unsafe code inside `createCodeForXXX`, we always assign the `input.primitive` to a temp variable in case `input.primitive` is expression code.

This PR did some refactor to make sure `input.primitive` is always variable name, and some other typo and style fixes.

Author: Wenchen Fan <cloud0fan@outlook.com>

Closes #8613 from cloud-fan/minor.

Throw a more readable exception. Please help review. Thanks

Author: Jeff Zhang <zjffdu@apache.org>

Closes #8649 from zjffdu/SPARK-10481.

It is convenient to implement data source API for LIBSVM format to have a better integration with DataFrames and ML pipeline API.

Two option is implemented.
* `numFeatures`: Specify the dimension of features vector
* `featuresType`: Specify the type of output vector. `sparse` is default.

Author: lewuathe <lewuathe@me.com>

Closes #8537 from Lewuathe/SPARK-10117 and squashes the following commits:

986999d [lewuathe] Change unit test phrase
11d513f [lewuathe] Fix some reviews
21600a4 [lewuathe] Merge branch 'master' into SPARK-10117
9ce63c7 [lewuathe] Rewrite service loader file
1fdd2df [lewuathe] Merge branch 'SPARK-10117' of github.com:Lewuathe/spark into SPARK-10117
ba3657c [lewuathe] Merge branch 'master' into SPARK-10117
0ea1c1c [lewuathe] LibSVMRelation is registered into META-INF
4f40891 [lewuathe] Improve test suites
5ab62ab [lewuathe] Merge branch 'master' into SPARK-10117
8660d0e [lewuathe] Fix Java unit test
b56a948 [lewuathe] Merge branch 'master' into SPARK-10117
2c12894 [lewuathe] Remove unnecessary tag
7d693c2 [lewuathe] Resolv conflict
62010af [lewuathe] Merge branch 'master' into SPARK-10117
a97ee97 [lewuathe] Fix some points
aef9564 [lewuathe] Fix
70ee4dd [lewuathe] Add Java test
3fd8dce [lewuathe] [SPARK-10117] Implement SQL data source API for reading LIBSVM data
40d3027 [lewuathe] Add Java test
7056d4a [lewuathe] Merge branch 'master' into SPARK-10117
99accaa [lewuathe] [SPARK-10117] Implement SQL data source API for reading LIBSVM data

The bulk of the changes are on `transient` annotation on class parameter. Often the compiler doesn't generate a field for this parameters, so the the transient annotation would be unnecessary.
But if the class parameter are used in methods, then fields are created. So it is safer to keep the annotations.

The remainder are some potential bugs, and deprecated syntax.

Author: Luc Bourlier <luc.bourlier@typesafe.com>

Closes #8433 from skyluc/issue/sbt-2.11.

jira: https://issues.apache.org/jira/browse/SPARK-10249

update user guide since python support added.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #8620 from hhbyyh/swPyDocExample.

Adds IndexToString to PySpark.

Author: Holden Karau <holden@pigscanfly.ca>

Closes #7976 from holdenk/SPARK-9654-add-string-indexer-inverse-in-pyspark.

Modified class-level docstrings to mark all feature transformers in pyspark.ml as experimental.

Author: noelsmith <mail@noelsmith.com>

Closes #8623 from noel-smith/SPARK-10094-mark-pyspark-ml-trans-exp.

cc mengxr

Author: Davies Liu <davies@databricks.com>

Closes #8657 from davies/move_since.

Add WeibullGenerator for RandomDataGenerator.
#8611 need use WeibullGenerator to generate random data based on Weibull distribution.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #8622 from yanboliang/spark-10464.

The goal of this PR is to have a weighted least squares implementation that takes the normal equation approach, and hence to be able to provide R-like summary statistics and support IRLS (used by GLMs). The tests match R's lm and glmnet.

There are couple TODOs that can be addressed in future PRs:
* consolidate summary statistics aggregators
* move `dspr` to `BLAS`
* etc

It would be nice to have this merged first because it blocks couple other features.

dbtsai

Author: Xiangrui Meng <meng@databricks.com>

Closes #8588 from mengxr/SPARK-9834.

[SPARK-10071] [STREAMING] Output a warning when writing QueueInputDStream and throw a better exception when reading QueueInputDStream

Output a warning when serializing QueueInputDStream rather than throwing an exception to allow unit tests use it. Moreover, this PR also throws an better exception when deserializing QueueInputDStream to make the user find out the problem easily. The previous exception is hard to understand: https://issues.apache.org/jira/browse/SPARK-8553

Author: zsxwing <zsxwing@gmail.com>

Closes #8624 from zsxwing/SPARK-10071 and squashes the following commits:

847cfa8 [zsxwing] Output a warning when writing QueueInputDStream and throw a better exception when reading QueueInputDStream

Author: Reynold Xin <rxin@databricks.com>

Closes #8660 from rxin/contrib.

Author: Michael Armbrust <michael@databricks.com>

Closes #8659 from marmbrus/testBuildBreak.

```scala
    import org.apache.spark.sql.hive.execution.HiveTableScan
    sql("select key, value, key + 1 from src").registerTempTable("abc")
    cacheTable("abc")

    val sparkPlan = sql(
      """select a.key, b.key, c.key from
        |abc a join abc b on a.key=b.key
        |join abc c on a.key=c.key""".stripMargin).queryExecution.sparkPlan

    assert(sparkPlan.collect { case e: InMemoryColumnarTableScan => e }.size === 3) // failed
    assert(sparkPlan.collect { case e: HiveTableScan => e }.size === 0) // failed
```

The actual plan is:

```
== Parsed Logical Plan ==
'Project [unresolvedalias('a.key),unresolvedalias('b.key),unresolvedalias('c.key)]
 'Join Inner, Some(('a.key = 'c.key))
  'Join Inner, Some(('a.key = 'b.key))
   'UnresolvedRelation [abc], Some(a)
   'UnresolvedRelation [abc], Some(b)
  'UnresolvedRelation [abc], Some(c)

== Analyzed Logical Plan ==
key: int, key: int, key: int
Project [key#14,key#61,key#66]
 Join Inner, Some((key#14 = key#66))
  Join Inner, Some((key#14 = key#61))
   Subquery a
    Subquery abc
     Project [key#14,value#15,(key#14 + 1) AS _c2#16]
      MetastoreRelation default, src, None
   Subquery b
    Subquery abc
     Project [key#61,value#62,(key#61 + 1) AS _c2#58]
      MetastoreRelation default, src, None
  Subquery c
   Subquery abc
    Project [key#66,value#67,(key#66 + 1) AS _c2#63]
     MetastoreRelation default, src, None

== Optimized Logical Plan ==
Project [key#14,key#61,key#66]
 Join Inner, Some((key#14 = key#66))
  Project [key#14,key#61]
   Join Inner, Some((key#14 = key#61))
    Project [key#14]
     InMemoryRelation [key#14,value#15,_c2#16], true, 10000, StorageLevel(true, true, false, true, 1), (Project [key#14,value#15,(key#14 + 1) AS _c2#16]), Some(abc)
    Project [key#61]
     MetastoreRelation default, src, None
  Project [key#66]
   MetastoreRelation default, src, None

== Physical Plan ==
TungstenProject [key#14,key#61,key#66]
 BroadcastHashJoin [key#14], [key#66], BuildRight
  TungstenProject [key#14,key#61]
   BroadcastHashJoin [key#14], [key#61], BuildRight
    ConvertToUnsafe
     InMemoryColumnarTableScan [key#14], (InMemoryRelation [key#14,value#15,_c2#16], true, 10000, StorageLevel(true, true, false, true, 1), (Project [key#14,value#15,(key#14 + 1) AS _c2#16]), Some(abc))
    ConvertToUnsafe
     HiveTableScan [key#61], (MetastoreRelation default, src, None)
  ConvertToUnsafe
   HiveTableScan [key#66], (MetastoreRelation default, src, None)
```

Author: Cheng Hao <hao.cheng@intel.com>

Closes #8494 from chenghao-intel/weird_cache.