[SPARK-3309] [PySpark] Put all public API in __all__

Put all public API in __all__, also put them all in pyspark.__init__.py, then we can got all the documents for public API by `pydoc pyspark`. It also can be used by other programs (such as Sphinx or Epydoc) to generate only documents for public APIs.

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

Closes #2205 from davies/public and squashes the following commits:

c6c5567 [Davies Liu] fix message
f7b35be [Davies Liu] put SchemeRDD, Row in pyspark.sql module
7e3016a [Davies Liu] add __all__ in mllib
6281b48 [Davies Liu] fix doc for SchemaRDD
6caab21 [Davies Liu] add public interfaces into pyspark.__init__.py
[SPARK-3263][GraphX] Fix changes made to GraphGenerator.logNormalGraph in PR #720

PR #720 made multiple changes to GraphGenerator.logNormalGraph including:

* Replacing the call to functions for generating random vertices and edges with in-line implementations with different equations. Based on reading the Pregel paper, I believe the in-line functions are incorrect.
* Hard-coding of RNG seeds so that method now generates the same graph for a given number of vertices, edges, mu, and sigma -- user is not able to override seed or specify that seed should be randomly generated.
* Backwards-incompatible change to logNormalGraph signature with introduction of new required parameter.
* Failed to update scala docs and programming guide for API changes
* Added a Synthetic Benchmark in the examples.

This PR:
* Removes the in-line calls and calls original vertex / edge generation functions again
* Adds an optional seed parameter for deterministic behavior (when desired)
* Keeps the number of partitions parameter that was added.
* Keeps compatibility with the synthetic benchmark example
* Maintains backwards-compatible API

Author: RJ Nowling <rnowling@gmail.com>
Author: Ankur Dave <ankurdave@gmail.com>

Closes #2168 from rnowling/graphgenrand and squashes the following commits:

f1cd79f [Ankur Dave] Style fixes
e11918e [RJ Nowling] Fix bad comparisons in unit tests
785ac70 [RJ Nowling] Fix style error
c70868d [RJ Nowling] Fix logNormalGraph scala doc for seed
41fd1f8 [RJ Nowling] Fix logNormalGraph scala doc for seed
799f002 [RJ Nowling] Added test for different seeds for sampleLogNormal
43949ad [RJ Nowling] Added test for different seeds for generateRandomEdges
2faf75f [RJ Nowling] Added unit test for logNormalGraph
82f22397 [RJ Nowling] Add unit test for sampleLogNormal
b99cba9 [RJ Nowling] Make sampleLogNormal private to Spark (vs private) for unit testing
6803da1 [RJ Nowling] Add GraphGeneratorsSuite with test for generateRandomEdges
1c8fc44 [RJ Nowling] Connected components part of SynthBenchmark was failing to call count on RDD before printing
dfbb6dd [RJ Nowling] Fix parameter name in SynthBenchmark docs
b5eeb80 [RJ Nowling] Add optional seed parameter to SynthBenchmark and set default to randomly generate a seed
1ff8d30 [RJ Nowling] Fix bug in generateRandomEdges where numVertices instead of numEdges was used to control number of edges to generate
98bb73c [RJ Nowling] Add documentation for logNormalGraph parameters
d40141a [RJ Nowling] Fix style error
684804d [RJ Nowling] revert PR #720 which introduce errors in logNormalGraph and messed up seeding of RNGs.  Add user-defined optional seed for deterministic behavior
c183136 [RJ Nowling] Fix to deterministic GraphGenerators.logNormalGraph that allows generating graphs randomly using optional seed.
015010c [RJ Nowling] Fixed GraphGenerator logNormalGraph API to make backward-incompatible change in commit 894ecde04
[SPARK-2845] Add timestamps to block manager events.

These are not used by the UI but are useful when analysing the
logs from a spark job.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #654 from vanzin/bm-event-tstamp and squashes the following commits:

d5d6e66 [Marcelo Vanzin] Fix tests.
ec06218 [Marcelo Vanzin] Review feedback.
f134dbc [Marcelo Vanzin] Merge branch 'master' into bm-event-tstamp
b495b7c [Marcelo Vanzin] Merge branch 'master' into bm-event-tstamp
7d2fe9e [Marcelo Vanzin] Review feedback.
d6f381c [Marcelo Vanzin] Update tests added after patch was created.
45e3bf8 [Marcelo Vanzin] Fix unit test after merge.
b37a10f [Marcelo Vanzin] Use === in test assertions.
ef72824 [Marcelo Vanzin] Handle backwards compatibility with 1.0.0.
aca1151 [Marcelo Vanzin] Fix unit test to check new fields.
efdda8e [Marcelo Vanzin] Add timestamps to block manager events.
[SPARK-3388] Expose aplication ID in ApplicationStart event, use it in history server.

This change exposes the application ID generated by the Spark Master, Mesos or Yarn
via the SparkListenerApplicationStart event. It then uses that information to expose the
application via its ID in the history server, instead of using the internal directory name
generated by the event logger as an application id. This allows someone who knows
the application ID to easily figure out the URL for the application's entry in the HS, aside
from looking better.

In Yarn mode, this is used to generate a direct link from the RM application list to the
Spark history server entry (thus providing a fix for SPARK-2150).

Note this sort of assumes that the different managers will generate app ids that are
sufficiently different from each other that clashes will not occur.

Author: Marcelo Vanzin <vanzin@cloudera.com>

This patch had conflicts when merged, resolved by
Committer: Andrew Or <andrewor14@gmail.com>

Closes #1218 from vanzin/yarn-hs-link-2 and squashes the following commits:

2d19f3c [Marcelo Vanzin] Review feedback.
6706d3a [Marcelo Vanzin] Implement applicationId() in base classes.
56fe42e [Marcelo Vanzin] Fix cluster mode history address, plus a cleanup.
44112a8 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
8278316 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
a86bbcf [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
a0056e6 [Marcelo Vanzin] Unbreak test.
4b10cfd [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
cb0cab2 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
25f2826 [Marcelo Vanzin] Add MIMA excludes.
f0ba90f [Marcelo Vanzin] Use BufferedIterator.
c90a08d [Marcelo Vanzin] Remove unused code.
3f8ec66 [Marcelo Vanzin] Review feedback.
21aa71b [Marcelo Vanzin] Fix JSON test.
b022bae [Marcelo Vanzin] Undo SparkContext cleanup.
c6d7478 [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
4e3483f [Marcelo Vanzin] Fix test.
57517b8 [Marcelo Vanzin] Review feedback. Mostly, more consistent use of Scala's Option.
311e49d [Marcelo Vanzin] Merge branch 'master' into yarn-hs-link-2
d35d86f [Marcelo Vanzin] Fix yarn backend after rebase.
36dc362 [Marcelo Vanzin] Don't use Iterator::takeWhile().
0afd696 [Marcelo Vanzin] Wait until master responds before returning from start().
abc4697 [Marcelo Vanzin] Make FsHistoryProvider keep a map of applications by id.
26b266e [Marcelo Vanzin] Use Mesos framework ID as Spark application ID.
b3f3664 [Marcelo Vanzin] [yarn] Make the RM link point to the app direcly in the HS.
2fb7de4 [Marcelo Vanzin] Expose the application ID in the ApplicationStart event.
ed10348 [Marcelo Vanzin] Expose application id to spark context.
[Minor] Fix outdated Spark version

This is causing the event logs to include a file called SPARK_VERSION_1.0.0, which is not accurate.

Author: Andrew Or <andrewor14@gmail.com>
Author: andrewor14 <andrewor14@gmail.com>

Closes #2255 from andrewor14/spark-version and squashes the following commits:

1fbdfe9 [andrewor14] Snapshot
805a1c8 [Andrew Or] JK. Update Spark version to 1.2.0 instead.
bffbaab [Andrew Or] Update Spark version to 1.1.0
[SPARK-3345] Do correct parameters for ShuffleFileGroup

In the method `newFileGroup` of class `FileShuffleBlockManager`, the parameters for creating new `ShuffleFileGroup` object is in wrong order.

Because in current codes, the parameters `shuffleId` and `fileId` are not used. So it doesn't cause problem now. However it should be corrected for readability and avoid future problem.

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #2235 from viirya/correct_shufflefilegroup_params and squashes the following commits:

fe72567 [Liang-Chi Hsieh] Do correct parameters for ShuffleFileGroup.
[SPARK-2419][Streaming][Docs] Updates to the streaming programming guide

Updated the main streaming programming guide, and also added source-specific guides for Kafka, Flume, Kinesis.

Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: Jacek Laskowski <jacek@japila.pl>

Closes #2254 from tdas/streaming-doc-fix and squashes the following commits:

e45c6d7 [Jacek Laskowski] More fixes from an old PR
5125316 [Tathagata Das] Fixed links
dc02f26 [Tathagata Das] Refactored streaming kinesis guide and made many other changes.
acbc3e3 [Tathagata Das] Fixed links between streaming guides.
cb7007f [Tathagata Das] Added Streaming + Flume integration guide.
9bd9407 [Tathagata Das] Updated streaming programming guide with additional information from SPARK-2419.
[SPARK-3303][core] fix SparkContextSchedulerCreationSuite test error

run test with the master branch with this command when mesos native lib is set
sbt/sbt -Phive "test-only org.apache.spark.SparkContextSchedulerCreationSuite"

get this error:
[info] SparkContextSchedulerCreationSuite:
[info] - bad-master
[info] - local
[info] - local-*
[info] - local-n
[info] - local--n-failures
[info] - local-n-failures
[info] - bad-local-n
[info] - bad-local-n-failures
[info] - local-default-parallelism
[info] - simr
[info] - local-cluster
[info] - yarn-cluster
[info] - yarn-standalone
[info] - yarn-client
[info] - mesos fine-grained
[info] - mesos coarse-grained ** FAILED ***
[info] Executor Spark home `spark.mesos.executor.home` is not set!

Since `executorSparkHome` only used in `createCommand`, move `val executorSparkHome...` to `createCommand` to fix this issue.

Author: scwf <wangfei1@huawei.com>
Author: wangfei <wangfei_hello@126.com>

Closes #2199 from scwf/SparkContextSchedulerCreationSuite and squashes the following commits:

ef1de22 [scwf] fix code fomate
19d26f3 [scwf] fix conflict
d9a8a60 [wangfei] fix SparkContextSchedulerCreationSuite test error
[SPARK-3233] Executor never stop its SparnEnv, BlockManager, ConnectionManager etc.

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

Closes #2138 from sarutak/SPARK-3233 and squashes the following commits:

c0205b7 [Kousuke Saruta] Merge branch 'SPARK-3233' of github.com:sarutak/spark into SPARK-3233
064679d [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3233
d3005fd [Kousuke Saruta] Modified Class definition format of BlockManagerMaster
039b747 [Kousuke Saruta] Modified style
889e2d1 [Kousuke Saruta] Modified BlockManagerMaster to be able to be past isDriver flag
4da8535 [Kousuke Saruta] Modified BlockManagerMaster#stop to send StopBlockManagerMaster message when sender is Driver
6518c3a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3233
d5ab19a [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3233
6bce25c [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into SPARK-3233
6058a58 [Kousuke Saruta] Modified Executor not to invoke SparkEnv#stop in local mode
e5ad9d3 [Kousuke Saruta] Modified Executor to stop SparnEnv at the end of itself
[SPARK-2973][SQL] Lightweight SQL commands without distributed jobs when calling .collect()

By overriding `executeCollect()` in physical plan classes of all commands, we can avoid to kick off a distributed job when collecting result of a SQL command, e.g. `sql("SET").collect()`.

Previously, `Command.sideEffectResult` returns a `Seq[Any]`, and the `execute()` method in sub-classes of `Command` typically convert that to a `Seq[Row]` then parallelize it to an RDD. Now with this PR, `sideEffectResult` is required to return a `Seq[Row]` directly, so that `executeCollect()` can directly leverage that and be factored to the `Command` parent class.

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

Closes #2215 from liancheng/lightweight-commands and squashes the following commits:

3fbef60 [Cheng Lian] Factored execute() method of physical commands to parent class Command
5a0e16c [Cheng Lian] Passes test suites
e0e12e9 [Cheng Lian] Refactored Command.sideEffectResult and Command.executeCollect
995bdd8 [Cheng Lian] Cleaned up DescribeHiveTableCommand
542977c [Cheng Lian] Avoids confusion between logical and physical plan by adding package prefixes
55b2aa5 [Cheng Lian] Avoids distributed jobs when execution SQL commands
[SPARK-2961][SQL] Use statistics to prune batches within cached partitions

This PR is based on #1883 authored by marmbrus. Key differences:

1. Batch pruning instead of partition pruning

   When #1883 was authored, batched column buffer building (#1880) hadn't been introduced. This PR combines these two and provide partition batch level pruning, which leads to smaller memory footprints and can generally skip more elements. The cost is that the pruning predicates are evaluated more frequently (partition number multiplies batch number per partition).

1. More filters are supported

   Filter predicates consist of `=`, `<`, `<=`, `>`, `>=` and their conjunctions and disjunctions are supported.

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

Closes #2188 from liancheng/in-mem-batch-pruning and squashes the following commits:

68cf019 [Cheng Lian] Marked sqlContext as @transient
4254f6c [Cheng Lian] Enables in-memory partition pruning in PartitionBatchPruningSuite
3784105 [Cheng Lian] Overrides InMemoryColumnarTableScan.sqlContext
d2a1d66 [Cheng Lian] Disables in-memory partition pruning by default
062c315 [Cheng Lian] HiveCompatibilitySuite code cleanup
16b77bf [Cheng Lian] Fixed pruning predication conjunctions and disjunctions
16195c5 [Cheng Lian] Enabled both disjunction and conjunction
89950d0 [Cheng Lian] Worked around Scala style check
9c167f6 [Cheng Lian] Minor code cleanup
3c4d5c7 [Cheng Lian] Minor code cleanup
ea59ee5 [Cheng Lian] Renamed PartitionSkippingSuite to PartitionBatchPruningSuite
fc517d0 [Cheng Lian] More test cases
1868c18 [Cheng Lian] Code cleanup, bugfix, and adding tests
cb76da4 [Cheng Lian] Added more predicate filters, fixed table scan stats for testing purposes
385474a [Cheng Lian] Merge branch 'inMemStats' into in-mem-batch-pruning
[SPARK-3335] [SQL] [PySpark] support broadcast in Python UDF

After this patch, broadcast can be used in Python UDF.

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

Closes #2243 from davies/udf_broadcast and squashes the following commits:

7b88861 [Davies Liu] support broadcast in UDF
[SPARK-2435] Add shutdown hook to pyspark

Author: Matthew Farrellee <matt@redhat.com>

Closes #2183 from mattf/SPARK-2435 and squashes the following commits:

ee0ee99 [Matthew Farrellee] [SPARK-2435] Add shutdown hook to pyspark
[SPARK-3372] [MLlib] MLlib doesn't pass maven build / checkstyle due to multi-byte character contained in Gradient.scala

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

Closes #2248 from sarutak/SPARK-3372 and squashes the following commits:

73a28b8 [Kousuke Saruta] Replaced UTF-8 hyphen with ascii hyphen
[HOTFIX] [SPARK-3400] Revert 9b225ac "fix GraphX EdgeRDD zipPartitions"

9b225ac3072de522b40b46aba6df1f1c231f13ef has been causing GraphX tests
to fail nondeterministically, which is blocking development for others.

Author: Ankur Dave <ankurdave@gmail.com>

Closes #2271 from ankurdave/SPARK-3400 and squashes the following commits:

10c2a97 [Ankur Dave] [HOTFIX] [SPARK-3400] Revert 9b225ac "fix GraphX EdgeRDD zipPartitions"
[SPARK-2140] Updating heap memory calculation for YARN stable and alpha.
[SPARK-2140] Removing calculateAMMemory functions since they are no longer needed.