[SPARK-3790][MLlib] CosineSimilarity Example

Provide example  for `RowMatrix.columnSimilarity()`

Author: Reza Zadeh <rizlar@gmail.com>

Closes #2622 from rezazadeh/dimsumexample and squashes the following commits:

8f20b82 [Reza Zadeh] update comment
379066d [Reza Zadeh] cache rows
792b81c [Reza Zadeh] Address review comments
e573c7a [Reza Zadeh] Average absolute error
b15685f [Reza Zadeh] Use scopt. Distribute evaluation.
eca3dfd [Reza Zadeh] Documentation
ac96fb2 [Reza Zadeh] Compute approximation error, add command line.
4533579 [Reza Zadeh] CosineSimilarity Example
[SPARK-3486][MLlib][PySpark] PySpark support for Word2Vec

mengxr
Added PySpark support for Word2Vec
Change list
(1) PySpark support for Word2Vec
(2) SerDe support of string sequence both on python side and JVM side
(3) Test for SerDe of string sequence on JVM side

Author: Liquan Pei <liquanpei@gmail.com>

Closes #2356 from Ishiihara/Word2Vec-python and squashes the following commits:

476ea34 [Liquan Pei] style fixes
b13a0b9 [Liquan Pei] resolve merge conflicts and minor fixes
8671eba [Liquan Pei] Merge remote-tracking branch 'upstream/master' into Word2Vec-python
daf88a6 [Liquan Pei] modification according to feedback
a73fa19 [Liquan Pei] clean up
3d8007b [Liquan Pei] fix findSynonyms for vector
1bdcd2e [Liquan Pei] minor fixes
cdef9f4 [Liquan Pei] add missing comments
b7447eb [Liquan Pei] modify according to feedback
b9a7383 [Liquan Pei] cache words RDD in fit
89490bf [Liquan Pei] add tests and Word2VecModelWrapper
78bbb53 [Liquan Pei] use pickle for seq string SerDe
a264b08 [Liquan Pei] Merge remote-tracking branch 'upstream/master' into Word2Vec-python
ca1e5ff [Liquan Pei] fix test
68e7276 [Liquan Pei] minor style fixes
48d5e72 [Liquan Pei] Functionality improvement
0ad3ac1 [Liquan Pei] minor fix
c867fdf [Liquan Pei] add Word2Vec to pyspark
[SPARK-3832][MLlib] Upgrade Breeze dependency to 0.10

In Breeze 0.10, the L1regParam can be configured through anonymous function in OWLQN, and each component can be penalized differently. This is required for GLMNET in MLlib with L1/L2 regularization.
https://github.com/scalanlp/breeze/commit/2570911026aa05aa1908ccf7370bc19cd8808a4c

Author: DB Tsai <dbtsai@dbtsai.com>

Closes #2693 from dbtsai/breeze0.10 and squashes the following commits:

7a0c45c [DB Tsai] In Breeze 0.10, the L1regParam can be configured through anonymous function in OWLQN, and each component can be penalized differently. This is required for GLMNET in MLlib with L1/L2 regularization. https://github.com/scalanlp/breeze/commit/2570911026aa05aa1908ccf7370bc19cd8808a4c
[SPARK-3398] [EC2] Have spark-ec2 intelligently wait for specific cluster states

Instead of waiting arbitrary amounts of time for the cluster to reach a specific state, this patch lets `spark-ec2` explicitly wait for a cluster to reach a desired state.

This is useful in a couple of situations:
* The cluster is launching and you want to wait until SSH is available before installing stuff.
* The cluster is being terminated and you want to wait until all the instances are terminated before trying to delete security groups.

This patch removes the need for the `--wait` option and removes some of the time-based retry logic that was being used.

Author: Nicholas Chammas <nicholas.chammas@gmail.com>

Closes #2339 from nchammas/spark-ec2-wait-properly and squashes the following commits:

43a69f0 [Nicholas Chammas] short-circuit SSH check; linear backoff
9a9e035 [Nicholas Chammas] remove extraneous comment
26c5ed0 [Nicholas Chammas] replace print with write()
bb67c06 [Nicholas Chammas] deprecate wait option; remove dead code
7969265 [Nicholas Chammas] fix long line (PEP 8)
126e4cf [Nicholas Chammas] wait for specific cluster states
[SPARK-3829] Make Spark logo image on the header of HistoryPage as a link to HistoryPage's page #1

There is a Spark logo on the header of HistoryPage.
We can have too many HistoryPages if we run 20+ applications. So I think, it's useful if the logo is as a link to the HistoryPage's page number 1.

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

Closes #2690 from sarutak/SPARK-3829 and squashes the following commits:

908c109 [Kousuke Saruta] Removed extra space.
00bfbd7 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3829
dd87480 [Kousuke Saruta] Made header Spark log image as a link to History Server's top page.
[SPARK-3412] [PySpark] Replace Epydoc with Sphinx to generate Python API docs

Retire Epydoc, use Sphinx to generate API docs.

Refine Sphinx docs, also convert some docstrings into Sphinx style.

It looks like:
![api doc](https://cloud.githubusercontent.com/assets/40902/4538272/9e2d4f10-4dec-11e4-8d96-6e45a8fe51f9.png)

Author: Davies Liu <davies.liu@gmail.com>

Closes #2689 from davies/docs and squashes the following commits:

bf4a0a5 [Davies Liu] fix links
3fb1572 [Davies Liu] fix _static in jekyll
65a287e [Davies Liu] fix scripts and logo
8524042 [Davies Liu] Merge branch 'master' of github.com:apache/spark into docs
d5b874a [Davies Liu] Merge branch 'master' of github.com:apache/spark into docs
4bc1c3c [Davies Liu] refactor
746d0b6 [Davies Liu] @param -> :param
240b393 [Davies Liu] replace epydoc with sphinx doc
[SPARK-3836] [REPL] Spark REPL optionally propagate internal exceptions

Optionally have the repl throw exceptions generated by interpreted code, instead of swallowing the exception and returning it as text output. This is useful when embedding the repl, otherwise it's not possible to know when user code threw an exception.

Author: Ahir Reddy <ahirreddy@gmail.com>

Closes #2695 from ahirreddy/repl-throw-exceptions and squashes the following commits:

bad25ee [Ahir Reddy] Style Fixes
f0e5b44 [Ahir Reddy] Fixed style
0d4413d [Ahir Reddy] propogate excetions from repl
[SPARK-3710] Fix Yarn integration tests on Hadoop 2.2.

It seems some dependencies are not declared when pulling the 2.2
test dependencies, so we need to add them manually for the Yarn
cluster to come up.

These don't seem to be necessary for 2.3 and beyond, so restrict
them to the hadoop-2.2 profile.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2682 from vanzin/SPARK-3710 and squashes the following commits:

701d4fb [Marcelo Vanzin] Add comment.
0540bdf [Marcelo Vanzin] [SPARK-3710] Fix Yarn integration tests on Hadoop 2.2.
[SPARK-3788] [yarn] Fix compareFs to do the right thing for HDFS namespaces.

HA and viewfs use namespaces instead of host names, so you can't
resolve them since that will fail. So be smarter to avoid doing
unnecessary work.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #2649 from vanzin/SPARK-3788 and squashes the following commits:

fedbc73 [Marcelo Vanzin] Update comment.
c938845 [Marcelo Vanzin] Use Objects.equal() to avoid issues with ==.
9f7b571 [Marcelo Vanzin] [SPARK-3788] [yarn] Fix compareFs to do the right thing for HA, federation.
[SPARK-3848] yarn alpha doesn't build on master

yarn alpha build was broken by #2432
as it added an argument to YarnAllocator but not to yarn/alpha YarnAllocationHandler
commit https://github.com/apache/spark/commit/79e45c9323455a51f25ed9acd0edd8682b4bbb88

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

Closes #2715 from sarutak/SPARK-3848 and squashes the following commits:

bafb8d1 [Kousuke Saruta] Fixed parameters for the default constructor of alpha/YarnAllocatorHandler.
HOTFIX: Use correct Hadoop profile in build
[SPARK-3841] [mllib] Pretty-print params for ML examples

Provide a parent class for the Params case classes used in many MLlib examples, where the parent class pretty-prints the case class fields:
Param1Name	Param1Value
Param2Name	Param2Value
...
Using this class will make it easier to print test settings to logs.

Also, updated DecisionTreeRunner to print a little more info.

CC: mengxr

Author: Joseph K. Bradley <joseph.kurata.bradley@gmail.com>

Closes #2700 from jkbradley/dtrunner-update and squashes the following commits:

cff873f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dtrunner-update
7a08ae4 [Joseph K. Bradley] code review comment updates
b4d2043 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dtrunner-update
d8228a7 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dtrunner-update
0fc9c64 [Joseph K. Bradley] Added abstract TestParams class for mllib example parameters
12b7798 [Joseph K. Bradley] Added abstract class TestParams for pretty-printing Params values
5f84f03 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dtrunner-update
f7441b6 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dtrunner-update
19eb6fc [Joseph K. Bradley] Updated DecisionTreeRunner to print training time.
[SPARK-3843][Minor] Cleanup scalastyle.txt at the end of running dev/scalastyle

dev/scalastyle create a log file 'scalastyle.txt'. it is overwrote per running but never deleted even though dev/mima and dev/lint-python delete their log files.

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

Closes #2702 from sarutak/scalastyle-txt-cleanup and squashes the following commits:

d6e238e [Kousuke Saruta] Fixed dev/scalastyle to cleanup scalastyle.txt
[SPARK-3831] [SQL] Filter rule Improvement and bool expression optimization.

If we write the filter which is always FALSE like

    SELECT * from person WHERE FALSE;

200 tasks will run. I think, 1 task is enough.

And current optimizer cannot optimize the case NOT is duplicated like

    SELECT * from person WHERE NOT ( NOT (age > 30));

The filter rule above should be simplified

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

Closes #2692 from sarutak/SPARK-3831 and squashes the following commits:

25f3e20 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3831
23c750c [Kousuke Saruta] Improved unsupported predicate test case
a11b9f3 [Kousuke Saruta] Modified NOT predicate test case in PartitionBatchPruningSuite
8ea872b [Kousuke Saruta] Fixed the number of tasks when the data of  LocalRelation is empty.
[SPARK-3713][SQL] Uses JSON to serialize DataType objects

This PR uses JSON instead of `toString` to serialize `DataType`s. The latter is not only hard to parse but also flaky in many cases.

Since we already write schema information to Parquet metadata in the old style, we have to reserve the old `DataType` parser and ensure downward compatibility. The old parser is now renamed to `CaseClassStringParser` and moved into `object DataType`.

JoshRosen davies Please help review PySpark related changes, thanks!

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #2563 from liancheng/datatype-to-json and squashes the following commits:

fc92eb3 [Cheng Lian] Reverts debugging code, simplifies primitive type JSON representation
438c75f [Cheng Lian] Refactors PySpark DataType JSON SerDe per comments
6b6387b [Cheng Lian] Removes debugging code
6a3ee3a [Cheng Lian] Addresses per review comments
dc158b5 [Cheng Lian] Addresses PEP8 issues
99ab4ee [Cheng Lian] Adds compatibility est case for Parquet type conversion
a983a6c [Cheng Lian] Adds PySpark support
f608c6e [Cheng Lian] De/serializes DataType objects from/to JSON
[SQL][Doc] Keep Spark SQL README.md up to date

marmbrus
Update README.md to be consistent with Spark 1.1

Author: Liquan Pei <liquanpei@gmail.com>

Closes #2706 from Ishiihara/SparkSQL-readme and squashes the following commits:

33b9d4b [Liquan Pei] keep README.md up to date
[SPARK-3707] [SQL] Fix bug of type coercion in DIV

Calling `BinaryArithmetic.dataType` will throws exception until it's resolved, but in type coercion rule `Division`, seems doesn't follow this.

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

Closes #2559 from chenghao-intel/type_coercion and squashes the following commits:

199a85d [Cheng Hao] Simplify the divide rule
dc55218 [Cheng Hao] fix bug of type coercion in div
[SPARK-3810][SQL] Makes PreInsertionCasts handle partitions properly

Includes partition keys into account when applying `PreInsertionCasts` rule.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #2672 from liancheng/fix-pre-insert-casts and squashes the following commits:

def1a1a [Cheng Lian] Makes PreInsertionCasts handle partitions properly
[SQL] Prevents per row dynamic dispatching and pattern matching when inserting Hive values

Builds all wrappers at first according to object inspector types to avoid per row costs.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #2592 from liancheng/hive-value-wrapper and squashes the following commits:

9696559 [Cheng Lian] Passes all tests
4998666 [Cheng Lian] Prevents per row dynamic dispatching and pattern matching when inserting Hive values
[SPARK-3857] Create joins package for various join operators.

Author: Reynold Xin <rxin@apache.org>

Closes #2719 from rxin/sql-join-break and squashes the following commits:

0c0082b [Reynold Xin] Fix line length.
cbc664c [Reynold Xin] Rename join -> joins package.
a070d44 [Reynold Xin] Fix line length in HashJoin
a39be8c [Reynold Xin] [SPARK-3857] Create a join package for various join operators.