- Various Fixes to docs
 - Make data source traits actually interfaces

Based on #4862 but with fixed conflicts.

Author: Reynold Xin <rxin@databricks.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #4868 from marmbrus/pr/4862 and squashes the following commits:

fe091ea [Michael Armbrust] Merge remote-tracking branch 'origin/master' into pr/4862
0208497 [Reynold Xin] Test fixes.
34e0a28 [Reynold Xin] [SPARK-5310][SQL] Various fixes to Spark SQL docs.

Another one from JoshRosen 's wish list. The first commit is much smaller and removes 2 of the 4 Clock classes. The second is much larger, necessary for consolidating the streaming one. I put together implementations in the way that seemed simplest. Almost all the change is standardizing class and method names.

Author: Sean Owen <sowen@cloudera.com>

Closes #4514 from srowen/SPARK-4682 and squashes the following commits:

5ed3a03 [Sean Owen] Javadoc Clock classes; make ManualClock private[spark]
169dd13 [Sean Owen] Add support for legacy org.apache.spark.streaming clock class names
277785a [Sean Owen] Reduce the net change in this patch by reversing some unnecessary syntax changes along the way
b5e53df [Sean Owen] FakeClock -> ManualClock; getTime() -> getTimeMillis()
160863a [Sean Owen] Consolidate Streaming Clock class into common util Clock
7c956b2 [Sean Owen] Consolidate Clocks except for Streaming Clock

Author: Michael Armbrust <michael@databricks.com>

Closes #4642 from marmbrus/docs and squashes the following commits:

d291c34 [Michael Armbrust] python tests
9be66e3 [Michael Armbrust] comments
d56afc2 [Michael Armbrust] fix style
f004747 [Michael Armbrust] fix build
c4a907b [Michael Armbrust] fix tests
42e2b73 [Michael Armbrust] [SQL] Documentation / API Clean-up.

Yarn's config option `spark.yarn.user.classpath.first` does not work the same way as
`spark.files.userClassPathFirst`; Yarn's version is a lot more dangerous, in that it
modifies the system classpath, instead of restricting the changes to the user's class
loader. So this change implements the behavior of the latter for Yarn, and deprecates
the more dangerous choice.

To be able to achieve feature-parity, I also implemented the option for drivers (the existing
option only applies to executors). So now there are two options, each controlling whether
to apply userClassPathFirst to the driver or executors. The old option was deprecated, and
aliased to the new one (`spark.executor.userClassPathFirst`).

The existing "child-first" class loader also had to be fixed. It didn't handle resources, and it
was also doing some things that ended up causing JVM errors depending on how things
were being called.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #3233 from vanzin/SPARK-2996 and squashes the following commits:

9cf9cf1 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
a1499e2 [Marcelo Vanzin] Remove SPARK_HOME propagation.
fa7df88 [Marcelo Vanzin] Remove 'test.resource' file, create it dynamically.
a8c69f1 [Marcelo Vanzin] Review feedback.
cabf962 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
a1b8d7e [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
3f768e3 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
2ce3c7a [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
0e6d6be [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
70d4044 [Marcelo Vanzin] Fix pyspark/yarn-cluster test.
0fe7777 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
0e6ef19 [Marcelo Vanzin] Move class loaders around and make names more meaninful.
fe970a7 [Marcelo Vanzin] Review feedback.
25d4fed [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
3cb6498 [Marcelo Vanzin] Call the right loadClass() method on the parent.
fbb8ab5 [Marcelo Vanzin] Add locking in loadClass() to avoid deadlocks.
2e6c4b7 [Marcelo Vanzin] Mention new setting in documentation.
b6497f9 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
a10f379 [Marcelo Vanzin] Some feedback.
3730151 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
f513871 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
44010b6 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
7b57cba [Marcelo Vanzin] Remove now outdated message.
5304d64 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
35949c8 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
54e1a98 [Marcelo Vanzin] Merge branch 'master' into SPARK-2996
d1273b2 [Marcelo Vanzin] Add test file to rat exclude.
fa1aafa [Marcelo Vanzin] Remove write check on user jars.
89d8072 [Marcelo Vanzin] Cleanups.
a963ea3 [Marcelo Vanzin] Implement spark.driver.userClassPathFirst for standalone cluster mode.
50afa5f [Marcelo Vanzin] Fix Yarn executor command line.
7d14397 [Marcelo Vanzin] Register user jars in executor up front.
7f8603c [Marcelo Vanzin] Fix yarn-cluster mode without userClassPathFirst.
20373f5 [Marcelo Vanzin] Fix ClientBaseSuite.
55c88fa [Marcelo Vanzin] Run all Yarn integration tests via spark-submit.
0b64d92 [Marcelo Vanzin] Add deprecation warning to yarn option.
4a84d87 [Marcelo Vanzin] Fix the child-first class loader.
d0394b8 [Marcelo Vanzin] Add "deprecated configs" to SparkConf.
46d8cf2 [Marcelo Vanzin] Update doc with new option, change name to "userClassPathFirst".
a314f2d [Marcelo Vanzin] Enable driver class path isolation in SparkSubmit.
91f7e54 [Marcelo Vanzin] [yarn] Enable executor class path isolation.
a853e74 [Marcelo Vanzin] Re-work CoarseGrainedExecutorBackend command line arguments.
89522ef [Marcelo Vanzin] Add class path isolation support for Yarn cluster mode.

Now you can quickly launch the spark-shell without building an assembly.  For quick development iteration run `build/sbt ~sparkShell` and calling exit will relaunch with any changes.

Author: Michael Armbrust <michael@databricks.com>

Closes #4438 from marmbrus/sparkShellSbt and squashes the following commits:

b4e44fe [Michael Armbrust] [BUILD] Add the ability to launch spark-shell from SBT.

Sorry for that PR #4330 has some mistakes.

I correct it....  so it works correctly now.

Author: OopsOutOfMemory <victorshengli@126.com>

Closes #4389 from OopsOutOfMemory/doc and squashes the following commits:

843eed9 [OopsOutOfMemory] correct hiveconsole imports

This is part (1a) of the updates from the design doc in [https://docs.google.com/document/d/1BH9el33kBX8JiDdgUJXdLW14CA2qhTCWIG46eXZVoJs]

**UPDATE**: Most of the APIs are being kept private[spark] to allow further discussion.  Here is a list of changes which are public:
* new output columns: rawPrediction, probabilities
  * The “score” column is now called “rawPrediction”
* Classifiers now provide numClasses
* Params.get and .set are now protected instead of private[ml].
* ParamMap now has a size method.
* new classes: LinearRegression, LinearRegressionModel
* LogisticRegression now has an intercept.

### Sketch of APIs (most of which are private[spark] for now)

Abstract classes for learning algorithms (+ corresponding Model abstractions):
* Classifier (+ ClassificationModel)
* ProbabilisticClassifier (+ ProbabilisticClassificationModel)
* Regressor (+ RegressionModel)
* Predictor (+ PredictionModel)
* *For all of these*:
 * There is no strongly typed training-time API.
 * There is a strongly typed test-time (prediction) API which helps developers implement new algorithms.

Concrete classes: learning algorithms
* LinearRegression
* LogisticRegression (updated to use new abstract classes)
 * Also, removed "score" in favor of "probability" output column.  Changed BinaryClassificationEvaluator to match. (SPARK-5031)

Other updates:
* params.scala: Changed Params.set/get to be protected instead of private[ml]
 * This was needed for the example of defining a class from outside of the MLlib namespace.
* VectorUDT: Will later change from private[spark] to public.
 * This is needed for outside users to write their own validateAndTransformSchema() methods using vectors.
 * Also, added equals() method.f
* SPARK-4942 : ML Transformers should allow output cols to be turned on,off
 * Update validateAndTransformSchema
 * Update transform
* (Updated examples, test suites according to other changes)

New examples:
* DeveloperApiExample.scala (example of defining algorithm from outside of the MLlib namespace)
 * Added Java version too

Test Suites:
* LinearRegressionSuite
* LogisticRegressionSuite
* + Java versions of above suites

CC: mengxr  etrain  shivaram

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #3637 from jkbradley/ml-api-part1 and squashes the following commits:

405bfb8 [Joseph K. Bradley] Last edits based on code review.  Small cleanups
fec348a [Joseph K. Bradley] Added JavaDeveloperApiExample.java and fixed other issues: Made developer API private[spark] for now. Added constructors Java can understand to specialized Param types.
8316d5e [Joseph K. Bradley] fixes after rebasing on master
fc62406 [Joseph K. Bradley] fixed test suites after last commit
bcb9549 [Joseph K. Bradley] Fixed issues after rebasing from master (after move from SchemaRDD to DataFrame)
9872424 [Joseph K. Bradley] fixed JavaLinearRegressionSuite.java Java sql api
f542997 [Joseph K. Bradley] Added MIMA excludes for VectorUDT (now public), and added DeveloperApi annotation to it
216d199 [Joseph K. Bradley] fixed after sql datatypes PR got merged
f549e34 [Joseph K. Bradley] Updates based on code review.  Major ones are: * Created weakly typed Predictor.train() method which is called by fit() so that developers do not have to call schema validation or copy parameters. * Made Predictor.featuresDataType have a default value of VectorUDT.   * NOTE: This could be dangerous since the FeaturesType type parameter cannot have a default value.
343e7bd [Joseph K. Bradley] added blanket mima exclude for ml package
82f340b [Joseph K. Bradley] Fixed bug in LogisticRegression (introduced in this PR).  Fixed Java suites
0a16da9 [Joseph K. Bradley] Fixed Linear/Logistic RegressionSuites
c3c8da5 [Joseph K. Bradley] small cleanup
934f97b [Joseph K. Bradley] Fixed bugs from previous commit.
1c61723 [Joseph K. Bradley] * Made ProbabilisticClassificationModel into a subclass of ClassificationModel.  Also introduced ProbabilisticClassifier.  * This was to support output column “probabilityCol” in transform().
4e2f711 [Joseph K. Bradley] rat fix
bc654e1 [Joseph K. Bradley] Added spark.ml LinearRegressionSuite
8d13233 [Joseph K. Bradley] Added methods: * Classifier: batch predictRaw() * Predictor: train() without paramMap ProbabilisticClassificationModel.predictProbabilities() * Java versions of all above batch methods + others
1680905 [Joseph K. Bradley] Added JavaLabeledPointSuite.java for spark.ml, and added constructor to LabeledPoint which defaults weight to 1.0
adbe50a [Joseph K. Bradley] * fixed LinearRegression train() to use embedded paramMap * added Predictor.predict(RDD[Vector]) method * updated Linear/LogisticRegressionSuites
58802e3 [Joseph K. Bradley] added train() to Predictor subclasses which does not take a ParamMap.
57d54ab [Joseph K. Bradley] * Changed semantics of Predictor.train() to merge the given paramMap with the embedded paramMap. * remove threshold_internal from logreg * Added Predictor.copy() * Extended LogisticRegressionSuite
e433872 [Joseph K. Bradley] Updated docs.  Added LabeledPointSuite to spark.ml
54b7b31 [Joseph K. Bradley] Fixed issue with logreg threshold being set correctly
0617d61 [Joseph K. Bradley] Fixed bug from last commit (sorting paramMap by parameter names in toString).  Fixed bug in persisting logreg data.  Added threshold_internal to logreg for faster test-time prediction (avoiding map lookup).
601e792 [Joseph K. Bradley] Modified ParamMap to sort parameters in toString.  Cleaned up classes in class hierarchy, before implementing tests and examples.
d705e87 [Joseph K. Bradley] Added LinearRegression and Regressor back from ml-api branch
52f4fde [Joseph K. Bradley] removing everything except for simple class hierarchy for classification
d35bb5d [Joseph K. Bradley] fixed compilation issues, but have not added tests yet
bfade12 [Joseph K. Bradley] Added lots of classes for new ML API:

It seems that `(ScalaUnidoc, unidoc)` is the correct way to overwrite `scalacOptions` in unidoc.

CC: rxin gzm0

Author: Xiangrui Meng <meng@databricks.com>

Closes #4404 from mengxr/SPARK-5620 and squashes the following commits:

f890cf5 [Xiangrui Meng] add -groups to scalacOptions in unidoc

Add `import org.apache.spark.sql.Dsl._` to make DSL query works.
Since queryExecution is not avaliable in DataFrame, so remove it.

Author: OopsOutOfMemory <victorshengli@126.com>
Author: Sheng, Li <OopsOutOfMemory@users.noreply.github.com>

Closes #4330 from OopsOutOfMemory/hiveconsole and squashes the following commits:

46eb790 [Sheng, Li] Update SparkBuild.scala
d23ee9f [OopsOutOfMemory] minor
d4dd593 [OopsOutOfMemory] refine hive console

The only issue is that `analyzeBlock` is removed, which was marked as a developer API. I didn't change other tests in the ALSSuite under `spark.mllib` to ensure that the implementation is correct.

CC: srowen coderxiang

Author: Xiangrui Meng <meng@databricks.com>

Closes #4321 from mengxr/SPARK-5536 and squashes the following commits:

5a3cee8 [Xiangrui Meng] update python tests that are too strict
e840acf [Xiangrui Meng] ignore scala style check for ALS.train
e9a721c [Xiangrui Meng] update mima excludes
9ee6a36 [Xiangrui Meng] merge master
9a8aeac [Xiangrui Meng] update tests
d8c3271 [Xiangrui Meng] remove analyzeBlocks
d68eee7 [Xiangrui Meng] add checkpoint to new ALS
22a56f8 [Xiangrui Meng] wrap old ALS
c387dff [Xiangrui Meng] support random seed
3bdf24b [Xiangrui Meng] make storage level configurable in the new ALS

This PR brings the Python API for Spark Streaming Kafka data source.

```
    class KafkaUtils(__builtin__.object)
     |  Static methods defined here:
     |
     |  createStream(ssc, zkQuorum, groupId, topics, storageLevel=StorageLevel(True, True, False, False,
2), keyDecoder=<function utf8_decoder>, valueDecoder=<function utf8_decoder>)
     |      Create an input stream that pulls messages from a Kafka Broker.
     |
     |      :param ssc:  StreamingContext object
     |      :param zkQuorum:  Zookeeper quorum (hostname:port,hostname:port,..).
     |      :param groupId:  The group id for this consumer.
     |      :param topics:  Dict of (topic_name -> numPartitions) to consume.
     |                      Each partition is consumed in its own thread.
     |      :param storageLevel:  RDD storage level.
     |      :param keyDecoder:  A function used to decode key
     |      :param valueDecoder:  A function used to decode value
     |      :return: A DStream object
```
run the example:

```
bin/spark-submit --driver-class-path external/kafka-assembly/target/scala-*/spark-streaming-kafka-assembly-*.jar examples/src/main/python/streaming/kafka_wordcount.py localhost:2181 test
```

Author: Davies Liu <davies@databricks.com>
Author: Tathagata Das <tdas@databricks.com>

Closes #3715 from davies/kafka and squashes the following commits:

d93bfe0 [Davies Liu] Update make-distribution.sh
4280d04 [Davies Liu] address comments
e6d0427 [Davies Liu] Merge branch 'master' of github.com:apache/spark into kafka
f257071 [Davies Liu] add tests for null in RDD
23b039a [Davies Liu] address comments
9af51c4 [Davies Liu] Merge branch 'kafka' of github.com:davies/spark into kafka
a74da87 [Davies Liu] address comments
dc1eed0 [Davies Liu] Update kafka_wordcount.py
31e2317 [Davies Liu] Update kafka_wordcount.py
370ba61 [Davies Liu] Update kafka.py
97386b3 [Davies Liu] address comment
2c567a5 [Davies Liu] update logging and comment
33730d1 [Davies Liu] Merge branch 'master' of github.com:apache/spark into kafka
adeeb38 [Davies Liu] Merge pull request #3 from tdas/kafka-python-api
aea8953 [Tathagata Das] Kafka-assembly for Python API
eea16a7 [Davies Liu] refactor
f6ce899 [Davies Liu] add example and fix bugs
98c8d17 [Davies Liu] fix python style
5697a01 [Davies Liu] bypass decoder in scala
048dbe6 [Davies Liu] fix python style
75d485e [Davies Liu] add mqtt
07923c4 [Davies Liu] support kafka in Python

This method survived the code review and it has been there since v1.1.0. It exposes jblas types. Let's remove it from the public API. I think no one calls it directly.

Author: Xiangrui Meng <meng@databricks.com>

Closes #4318 from mengxr/SPARK-5540 and squashes the following commits:

586ade6 [Xiangrui Meng] hide ALS.solveLeastSquares

Added the 2 methods to Graph and GraphImpl.  Both make calls to the underlying vertex and edge RDDs.

This is needed for another PR (for LDA): [https://github.com/apache/spark/pull/4047]

Notes:
* getCheckpointedFiles is plural and returns a Seq[String] instead of an Option[String].
* I attempted to test to make sure the methods returned the correct values after checkpointing.  It did not work; I guess that checkpointing does not occur quickly enough?  I noticed that there are not checkpointing tests for RDDs; is it just hard to test well?

CC: rxin

CC: mengxr  (since related to LDA)

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #4253 from jkbradley/graphx-checkpoint and squashes the following commits:

b680148 [Joseph K. Bradley] added class tag to firstParent call in VertexRDDImpl.isCheckpointed, though not needed to compile
250810e [Joseph K. Bradley] In EdgeRDDImple, VertexRDDImpl, added transient back to partitionsRDD, and made isCheckpointed check firstParent instead of partitionsRDD
695b7a3 [Joseph K. Bradley] changed partitionsRDD in EdgeRDDImpl, VertexRDDImpl to be non-transient
cc00767 [Joseph K. Bradley] added overrides for isCheckpointed, getCheckpointFile in EdgeRDDImpl, VertexRDDImpl. The corresponding Graph methods now work.
188665f [Joseph K. Bradley] improved documentation
235738c [Joseph K. Bradley] Added isCheckpointed and getCheckpointFiles to Graph, GraphImpl

We have seen many use cases of `treeAggregate`/`treeReduce` outside the ML domain. Maybe it is time to move them to Core. pwendell

Author: Xiangrui Meng <meng@databricks.com>

Closes #4228 from mengxr/SPARK-5430 and squashes the following commits:

20ad40d [Xiangrui Meng] exclude tree* from mima
e89a43e [Xiangrui Meng] fix compile and update java doc
3ae1a4b [Xiangrui Meng] add treeReduce/treeAggregate to Python
6f948c5 [Xiangrui Meng] add treeReduce/treeAggregate to JavaRDDLike
d600b6c [Xiangrui Meng] move treeReduce and treeAggregate to core

Author: Ryan Williams <ryan.blake.williams@gmail.com>

Closes #4211 from ryan-williams/sbt0.13.7 and squashes the following commits:

e28476d [Ryan Williams] bump sbt to version to 0.13.7

This pull request redesigns the existing Spark SQL dsl, which already provides data frame like functionalities.

TODOs:
With the exception of Python support, other tasks can be done in separate, follow-up PRs.
- [ ] Audit of the API
- [ ] Documentation
- [ ] More test cases to cover the new API
- [x] Python support
- [ ] Type alias SchemaRDD

Author: Reynold Xin <rxin@databricks.com>
Author: Davies Liu <davies@databricks.com>

Closes #4173 from rxin/df1 and squashes the following commits:

0a1a73b [Reynold Xin] Merge branch 'df1' of github.com:rxin/spark into df1
23b4427 [Reynold Xin] Mima.
828f70d [Reynold Xin] Merge pull request #7 from davies/df
257b9e6 [Davies Liu] add repartition
6bf2b73 [Davies Liu] fix collect with UDT and tests
e971078 [Reynold Xin] Missing quotes.
b9306b4 [Reynold Xin] Remove removeColumn/updateColumn for now.
a728bf2 [Reynold Xin] Example rename.
e8aa3d3 [Reynold Xin] groupby -> groupBy.
9662c9e [Davies Liu] improve DataFrame Python API
4ae51ea [Davies Liu] python API for dataframe
1e5e454 [Reynold Xin] Fixed a bug with symbol conversion.
2ca74db [Reynold Xin] Couple minor fixes.
ea98ea1 [Reynold Xin] Documentation & literal expressions.
2b22684 [Reynold Xin] Got rid of IntelliJ problems.
02bbfbc [Reynold Xin] Tightening imports.
ffbce66 [Reynold Xin] Fixed compilation error.
59b6d8b [Reynold Xin] Style violation.
b85edfb [Reynold Xin] ALS.
8c37f0a [Reynold Xin] Made MLlib and examples compile
6d53134 [Reynold Xin] Hive module.
d35efd5 [Reynold Xin] Fixed compilation error.
ce4a5d2 [Reynold Xin] Fixed test cases in SQL except ParquetIOSuite.
66d5ef1 [Reynold Xin] SQLContext minor patch.
c9bcdc0 [Reynold Xin] Checkpoint: SQL module compiles!

Support for transposing local matrices added. The `.transpose` function creates a new object re-using the backing array(s) but switches `numRows` and `numCols`. Operations check the flag `.isTransposed` to see whether the indexing in `values` should be modified.

This PR will pave the way for transposing `BlockMatrix`.

Author: Burak Yavuz <brkyvz@gmail.com>

Closes #4109 from brkyvz/SPARK-5321 and squashes the following commits:

87ab83c [Burak Yavuz] fixed scalastyle
caf4438 [Burak Yavuz] addressed code review v3
c524770 [Burak Yavuz] address code review comments 2
77481e8 [Burak Yavuz] fixed MiMa
f1c1742 [Burak Yavuz] small refactoring
ccccdec [Burak Yavuz] fixed failed test
dd45c88 [Burak Yavuz] addressed code review
a01bd5f [Burak Yavuz] [SPARK-5321] Fixed MiMa issues
2a63593 [Burak Yavuz] [SPARK-5321] fixed bug causing failed gemm test
c55f29a [Burak Yavuz] [SPARK-5321] Support for transposing local matrices cleaned up
c408c05 [Burak Yavuz] [SPARK-5321] Support for transposing local matrices added

`reduceByWindow` for Java API is actually not Java compatible, change to make it Java compatible.

Current solution is to deprecate the old one and add a new API, but since old API actually is not correct, so is keeping the old one meaningful? just to keep the binary compatible? Also even adding new API still need to add to Mima exclusion, I'm not sure to change the API, or deprecate the old API and add a new one, which is the best solution?

Author: jerryshao <saisai.shao@intel.com>

Closes #4104 from jerryshao/SPARK-5315 and squashes the following commits:

5bc8987 [jerryshao] Address the comment
c7aa1b4 [jerryshao] Deprecate the old one to keep binary compatible
8e9dc67 [jerryshao] Fix JavaDStream reduceByWindow signature error

Current Java file stream doesn't support custom key/value type because of loss of type information, details can be seen in [SPARK-5297](https://issues.apache.org/jira/browse/SPARK-5297). Fix this problem by getting correct `ClassTag` from `Class[_]`.

Author: jerryshao <saisai.shao@intel.com>

Closes #4101 from jerryshao/SPARK-5297 and squashes the following commits:

e022ca3 [jerryshao] Add Mima exclusion
ecd61b8 [jerryshao] Fix Java fileInputStream type erasure problem

Pretty minor, but submitted for consideration -- this would at least help people make this check in the most efficient way I know.

Author: Sean Owen <sowen@cloudera.com>

Closes #4074 from srowen/SPARK-5270 and squashes the following commits:

66885b8 [Sean Owen] Add note that JavaRDDLike should not be implemented by user code
2e9b490 [Sean Owen] More tests, and Mima-exclude the new isEmpty method in JavaRDDLike
28395ff [Sean Owen] Add isEmpty to Java, Python
7dd04b7 [Sean Owen] Add efficient RDD.isEmpty()

This makes it possible to compile spark as an external `ProjectRef` where as now we throw a `FileNotFoundException`

Author: Michael Armbrust <michael@databricks.com>

Closes #3905 from marmbrus/effectivePom and squashes the following commits:

fd63aae [Michael Armbrust] Use sbt tasks instead of vals to get hadoop version.

After the following patches, the main (Scala) API is now usable for Java users directly.

https://github.com/apache/spark/pull/4056
https://github.com/apache/spark/pull/4054
https://github.com/apache/spark/pull/4049
https://github.com/apache/spark/pull/4030
https://github.com/apache/spark/pull/3965
https://github.com/apache/spark/pull/3958

Author: Reynold Xin <rxin@databricks.com>

Closes #4065 from rxin/sql-java-api and squashes the following commits:

b1fd860 [Reynold Xin] Fix Mima
6d86578 [Reynold Xin] Ok one more attempt in fixing Python...
e8f1455 [Reynold Xin] Fix Python again...
3e53f91 [Reynold Xin] Fixed Python.
83735da [Reynold Xin] Fix BigDecimal test.
e9f1de3 [Reynold Xin] Use scala BigDecimal.
500d2c4 [Reynold Xin] Fix Decimal.
ba3bfa2 [Reynold Xin] Updated javadoc for RowFactory.
c4ae1c5 [Reynold Xin] [SPARK-5193][SQL] Remove Spark SQL Java-specific API.

`TaskContext.attemptId` is misleadingly-named, since it currently returns a taskId, which uniquely identifies a particular task attempt within a particular SparkContext, instead of an attempt number, which conveys how many times a task has been attempted.

This patch deprecates `TaskContext.attemptId` and add `TaskContext.taskId` and `TaskContext.attemptNumber` fields.  Prior to this change, it was impossible to determine whether a task was being re-attempted (or was a speculative copy), which made it difficult to write unit tests for tasks that fail on early attempts or speculative tasks that complete faster than original tasks.

Earlier versions of the TaskContext docs suggest that `attemptId` behaves like `attemptNumber`, so there's an argument to be made in favor of changing this method's implementation.  Since we've decided against making that change in maintenance branches, I think it's simpler to add better-named methods and retain the old behavior for `attemptId`; if `attemptId` behaved differently in different branches, then this would cause confusing build-breaks when backporting regression tests that rely on the new `attemptId` behavior.

Most of this patch is fairly straightforward, but there is a bit of trickiness related to Mesos tasks: since there's no field in MesosTaskInfo to encode the attemptId, I packed it into the `data` field alongside the task binary.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #3849 from JoshRosen/SPARK-4014 and squashes the following commits:

89d03e0 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4014
5cfff05 [Josh Rosen] Introduce wrapper for serializing Mesos task launch data.
38574d4 [Josh Rosen] attemptId -> taskAttemptId in PairRDDFunctions
a180b88 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4014
1d43aa6 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4014
eee6a45 [Josh Rosen] Merge remote-tracking branch 'origin/master' into SPARK-4014
0b10526 [Josh Rosen] Use putInt instead of putLong (silly mistake)
8c387ce [Josh Rosen] Use local with maxRetries instead of local-cluster.
cbe4d76 [Josh Rosen] Preserve attemptId behavior and deprecate it:
b2dffa3 [Josh Rosen] Address some of Reynold's minor comments
9d8d4d1 [Josh Rosen] Doc typo
1e7a933 [Josh Rosen] [SPARK-4014] Change TaskContext.attemptId to return attempt number instead of task ID.
fd515a5 [Josh Rosen] Add failing test for SPARK-4014

Having two versions of the data type APIs (one for Java, one for Scala) requires downstream libraries to also have two versions of the APIs if the library wants to support both Java and Scala. I took a look at the Scala version of the data type APIs - it can actually work out pretty well for Java out of the box.

As part of the PR, I created a sql.types package and moved all type definitions there. I then removed the Java specific data type API along with a lot of the conversion code.

This subsumes https://github.com/apache/spark/pull/3925

Author: Reynold Xin <rxin@databricks.com>

Closes #3958 from rxin/SPARK-5123-datatype-2 and squashes the following commits:

66505cc [Reynold Xin] [SPARK-5123] Expose only one version of the data type APIs (i.e. remove the Java-specific API).

Since GraphX is no longer alpha as of 1.2, MimaExcludes should not exclude GraphX for 1.3

Here are the individual excludes I had to add + the associated commits:

```
            // SPARK-4444
            ProblemFilters.exclude[IncompatibleResultTypeProblem](
              "org.apache.spark.graphx.EdgeRDD.fromEdges"),
            ProblemFilters.exclude[MissingMethodProblem]("org.apache.spark.graphx.EdgeRDD.filter"),
            ProblemFilters.exclude[IncompatibleResultTypeProblem](
              "org.apache.spark.graphx.impl.EdgeRDDImpl.filter"),
```
[https://github.com/apache/spark/commit/9ac2bb18ede2e9f73c255fa33445af89aaf8a000]

```
            // SPARK-3623
            ProblemFilters.exclude[MissingMethodProblem]("org.apache.spark.graphx.Graph.checkpoint")
```
[https://github.com/apache/spark/commit/e895e0cbecbbec1b412ff21321e57826d2d0a982]

```
            // SPARK-4620
            ProblemFilters.exclude[MissingMethodProblem]("org.apache.spark.graphx.Graph.unpersist"),
```
[https://github.com/apache/spark/commit/8817fc7fe8785d7b11138ca744f22f7e70f1f0a0]

CC: rxin

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #3856 from jkbradley/graphx-mima and squashes the following commits:

1eea2f6 [Joseph K. Bradley] moved cleanup to run-tests
527ccd9 [Joseph K. Bradley] fixed jenkins script to remove ivy2 cache
802e252 [Joseph K. Bradley] Removed GraphX MIMA excludes and added line to clear spark from .m2 dir before Jenkins tests.  This may not work yet...
30f8bb4 [Joseph K. Bradley] added individual mima excludes for graphx
a3fea42 [Joseph K. Bradley] removed graphx mima exclude for 1.3

This PR is a fixed version of the original PR #3237 by watermen and scwf.
This adds the ability to specify how many elements to print in `DStream.print`.

Author: Yadong Qi <qiyadong2010@gmail.com>
Author: q00251598 <qiyadong@huawei.com>
Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: wangfei <wangfei1@huawei.com>

Closes #3865 from tdas/print-num and squashes the following commits:

cd34e9e [Tathagata Das] Fix bug
7c09f16 [Tathagata Das] Merge remote-tracking branch 'apache-github/master' into HEAD
bb35d1a [Yadong Qi] Update MimaExcludes.scala
f8098ca [Yadong Qi] Update MimaExcludes.scala
f6ac3cb [Yadong Qi] Update MimaExcludes.scala
e4ed897 [Yadong Qi] Update MimaExcludes.scala
3b9d5cf [wangfei] fix conflicts
ec8a3af [q00251598] move to  Spark 1.3
26a70c0 [q00251598] extend the Python DStream's print
b589a4b [q00251598] add another print function

Re-enable MiMa for Streaming Flume Sink module, now that 1.1.0 is released, per the JIRA TO-DO. That's pretty much all there is to this.

Author: Sean Owen <sowen@cloudera.com>

Closes #3842 from srowen/SPARK-2757 and squashes the following commits:

50ff80e [Sean Owen] Exclude apparent false positive turned up by re-enabling MiMa checks for Streaming Flume Sink
0e5ba5c [Sean Owen] Re-enable MiMa for Streaming Flume Sink module

Meant to merge this in when committing SPARK-3787.

This PR is another solution for When we build with sbt with profile for hadoop and without property for hadoop version like:

    sbt/sbt -Phadoop-2.2 assembly

jar name is always used default version (1.0.4).

When we build with maven with same condition for sbt, default version for each profile is used.
For instance, if we  build like:

    mvn -Phadoop-2.2 package

jar name is used hadoop2.2.0 as a default version of hadoop-2.2.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #3046 from sarutak/fix-assembly-jarname-2 and squashes the following commits:

41ef90e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname-2
50c8676 [Kousuke Saruta] Merge branch 'fix-assembly-jarname-2' of github.com:sarutak/spark into fix-assembly-jarname-2
52a1cd2 [Kousuke Saruta] Fixed comflicts
dd30768 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname2
f1c90bb [Kousuke Saruta] Fixed SparkBuild.scala in order to read `hadoop.version` property from pom.xml
af6b100 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
c81806b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
ad1f96e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
b2318eb [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
5fc1259 [Kousuke Saruta] Fixed typo.
eebbb7d [Kousuke Saruta] Fixed wrong jar name

Author: scwf <wangfei1@huawei.com>

Closes #3743 from scwf/abc and squashes the following commits:

7d98bc8 [scwf] removing spark-staging-1038

SPARK-4814 [CORE] Enable assertions in SBT, Maven tests / AssertionError from Hive's LazyBinaryInteger

This enables assertions for the Maven and SBT build, but overrides the Hive module to not enable assertions.

Author: Sean Owen <sowen@cloudera.com>

Closes #3692 from srowen/SPARK-4814 and squashes the following commits:

caca704 [Sean Owen] Disable assertions just for Hive
f71e783 [Sean Owen] Enable assertions for SBT and Maven build

Sorry if this is a little premature with 1.2 still not out the door, but it will make other work like SPARK-4136 and SPARK-2089 a lot easier.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #3215 from sryza/sandy-spark-4338 and squashes the following commits:

1c5ac08 [Sandy Ryza] Update building Spark docs and remove unnecessary newline
9c1421c [Sandy Ryza] SPARK-4338. Ditch yarn-alpha.

This is #3554 from Lewuathe except that I put both `spark.ml` and `spark.mllib` in the group 'MLlib`.

Closes #3554

jkbradley

Author: lewuathe <lewuathe@me.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #3598 from mengxr/Lewuathe-modify-javadoc-setting and squashes the following commits:

184609a [Xiangrui Meng] merge spark.ml and spark.mllib into the same group in javadoc
f7535e6 [lewuathe] [SPARK-4685] Update JavaDoc settings to include spark.ml and all spark.mllib subpackages in the right sections

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #3058 from ueshin/issues/SPARK-4193 and squashes the following commits:

e096bb1 [Takuya UESHIN] Add a plugin declaration to pluginManagement.
6762ec2 [Takuya UESHIN] Fix usage of -Xdoclint javadoc option.
fdb280a [Takuya UESHIN] Fix Javadoc errors.
4745f3c [Takuya UESHIN] Merge branch 'master' into issues/SPARK-4193
923e2f0 [Takuya UESHIN] Use doclint option `-missing` instead of `none`.
30d6718 [Takuya UESHIN] Fix Javadoc errors.
b548017 [Takuya UESHIN] Disable doclint in Java 8 to prevent from build error.

Before we have a full picture of the operators we want to add, it might be safer to hide `Matrix.transposeMultiply` in 1.2.0. Another update we want to change is `Matrix.randn` and `Matrix.rand`, both of which should take a `Random` implementation. Otherwise, it is very likely to produce inconsistent RDDs. I also added some unit tests for matrix factory methods. All APIs are new in 1.2, so there is no incompatible changes.

brkyvz

Author: Xiangrui Meng <meng@databricks.com>

Closes #3468 from mengxr/SPARK-4614 and squashes the following commits:

3b0e4e2 [Xiangrui Meng] add mima excludes
6bfd8a4 [Xiangrui Meng] hide transposeMultiply; add rng to rand and randn; add unit tests

This pull request revises the programming guide to reflect changes in the GraphX API as well as the deprecated mapReduceTriplets operator.

Author: Joseph E. Gonzalez <joseph.e.gonzalez@gmail.com>

Closes #3359 from jegonzal/GraphXProgrammingGuide and squashes the following commits:

4421964 [Joseph E. Gonzalez] updating documentation for graphx

I tried to build for Scala 2.11 using sbt with the following command:

```
$ sbt/sbt -Dscala-2.11 assembly
```

but it ends with the following error messages:

```
[error] (streaming-kafka/*:update) sbt.ResolveException: unresolved dependency: org.apache.kafka#kafka_2.11;0.8.0: not found
[error] (catalyst/*:update) sbt.ResolveException: unresolved dependency: org.scalamacros#quasiquotes_2.11;2.0.1: not found
```

The reason is:
If system property `-Dscala-2.11` (without value) was set, `SparkBuild.scala` adds `scala-2.11` profile, but also `sbt-pom-reader` activates `scala-2.10` profile instead of `scala-2.11` profile because the activator `PropertyProfileActivator` used by `sbt-pom-reader` internally checks if the property value is empty or not.

The value is set to non-empty value, then no need to add profiles in `SparkBuild.scala` because `sbt-pom-reader` can handle as expected.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #3342 from ueshin/issues/SPARK-4429 and squashes the following commits:

14d86e8 [Takuya UESHIN] Add a comment.
4eef52b [Takuya UESHIN] Remove unneeded condition.
ce98d0f [Takuya UESHIN] Set non-empty value to system property "scala-2.11" if the property exists instead of adding profile.

This is blocking #3353 and other patches.

Author: Andrew Or <andrew@databricks.com>

Closes #3371 from andrewor14/mima-hot-fix and squashes the following commits:

842d059 [Andrew Or] Move excludes to the right section
c4d4f4e [Andrew Or] MIMA hot fix

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #3277 from vanzin/version-1.3 and squashes the following commits:

7c3c396 [Marcelo Vanzin] Added temp repo to sbt build.
5f404ff [Marcelo Vanzin] Add another exclusion.
19457e7 [Marcelo Vanzin] Update old version to 1.2, add temporary 1.2 repo.
3c8d705 [Marcelo Vanzin] Workaround for MIMA checks.
e940810 [Marcelo Vanzin] Bumping version to 1.3.0-SNAPSHOT.

The progress bar will look like this:

![1___spark_job__85_250_finished__4_are_running___java_](https://cloud.githubusercontent.com/assets/40902/4854813/a02f44ac-6099-11e4-9060-7c73a73151d6.png)

In the right corner, the numbers are: finished tasks, running tasks, total tasks.

After the stage has finished, it will disappear.

The progress bar is only showed if logging level is WARN or higher (but progress in title is still showed), it can be turned off by spark.driver.showConsoleProgress.

Author: Davies Liu <davies@databricks.com>

Closes #3029 from davies/progress and squashes the following commits:

95336d5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
fc49ac8 [Davies Liu] address commentse
2e90f75 [Davies Liu] show multiple stages in same time
0081bcc [Davies Liu] address comments
38c42f1 [Davies Liu] fix tests
ab87958 [Davies Liu] disable progress bar during tests
30ac852 [Davies Liu] re-implement progress bar
b3f34e5 [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
6fd30ff [Davies Liu] show progress bar if no task finished in 500ms
e4e7344 [Davies Liu] refactor
e1f524d [Davies Liu] revert unnecessary change
a60477c [Davies Liu] Merge branch 'master' of github.com:apache/spark into progress
5cae3f2 [Davies Liu] fix style
ea49fe0 [Davies Liu] address comments
bc53d99 [Davies Liu] refactor
e6bb189 [Davies Liu] fix logging in sparkshell
7e7d4e7 [Davies Liu] address commments
5df26bb [Davies Liu] fix style
9e42208 [Davies Liu] show progress bar in console and title