[SPARK-3361] Expand PEP 8 checks to include EC2 script and Python examples

This PR resolves [SPARK-3361](https://issues.apache.org/jira/browse/SPARK-3361) by expanding the PEP 8 checks to cover the remaining Python code base:
* The EC2 script
* All Python / PySpark examples

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

Closes #2297 from nchammas/pep8-rulez and squashes the following commits:

1e5ac9a [Nicholas Chammas] PEP 8 fixes to Python examples
c3dbeff [Nicholas Chammas] PEP 8 fixes to EC2 script
65ef6e8 [Nicholas Chammas] expand PEP 8 checks
[SPARK-3409][SQL] Avoid pulling in Exchange operator itself in Exchange's closures.

This is a tiny teeny optimization to move the if check of sortBasedShuffledOn to outside the closures so the closures don't need to pull in the entire Exchange operator object.

Author: Reynold Xin <rxin@apache.org>

Closes #2282 from rxin/SPARK-3409 and squashes the following commits:

1de3f88 [Reynold Xin] [SPARK-3409][SQL] Avoid pulling in Exchange operator itself in Exchange's closures.
[EC2] don't duplicate default values

This PR makes two minor changes to the `spark-ec2` script:

1. The script's input parameter default values are duplicated into the help text. This is unnecessary. This PR replaces the duplicated info with the appropriate `optparse`  placeholder.
2. The default Spark version currently needs to be updated by hand during each release, which is known to be a faulty process. This PR places that default value in an easy-to-spot place.

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

Closes #2290 from nchammas/spark-ec2-default-version and squashes the following commits:

0c6d3bb [Nicholas Chammas] don't duplicate default values
[SPARK-2419][Streaming][Docs] More updates to the streaming programming guide

- Improvements to the kinesis integration guide from @cfregly
- More information about unified input dstreams in main guide

Author: Tathagata Das <tathagata.das1565@gmail.com>
Author: Chris Fregly <chris@fregly.com>

Closes #2307 from tdas/streaming-doc-fix1 and squashes the following commits:

ec40b5d [Tathagata Das] Updated figure with kinesis
fdb9c5e [Tathagata Das] Fixed style issues with kinesis guide
036d219 [Chris Fregly] updated kinesis docs and added an arch diagram
24f622a [Tathagata Das] More modifications.
Spark-3406 add a default storage level to python RDD persist API

Author: Holden Karau <holden@pigscanfly.ca>

Closes #2280 from holdenk/SPARK-3406-Python-RDD-persist-api-does-not-have-default-storage-level and squashes the following commits:

33eaade [Holden Karau] As Josh pointed out, sql also override persist. Make persist behave the same as in the underlying RDD as well
e658227 [Holden Karau] Fix the test I added
e95a6c5 [Holden Karau] The Python persist function did not have a default storageLevel unlike the Scala API. Noticed this issue because we got a bug report back from the book where we had documented it as if it was the same as the Scala API
[SPARK-3397] Bump pom.xml version number of master branch to 1.2.0-SNAPSHOT

Author: GuoQiang Li <witgo@qq.com>

Closes #2268 from witgo/SPARK-3397 and squashes the following commits:

eaf913f [GuoQiang Li] Bump pom.xml version number of master branch to 1.2.0-SNAPSHOT
[SPARK-3273][SPARK-3301]We should read the version information from the same place

Author: GuoQiang Li <witgo@qq.com>

Closes #2175 from witgo/SPARK-3273 and squashes the following commits:

cf9c65a [GuoQiang Li] We should read the version information from the same place
2a44e2f [GuoQiang Li] The spark version in the welcome message of pyspark is not correct
[SPARK-2334] fix AttributeError when call PipelineRDD.id()

The underline JavaRDD for PipelineRDD is created lazily, it's delayed until call _jrdd.

The id of JavaRDD is cached as `_id`, it saves a RPC call in py4j for later calls.

closes #1276

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

Closes #2296 from davies/id and squashes the following commits:

e197958 [Davies Liu] fix style
9721716 [Davies Liu] fix id of PipelineRDD
[SPARK-3353] parent stage should have lower stage id.

Previously parent stages had higher stage id, but parent stages are executed first. This pull request changes the behavior so parent stages would have lower stage id.

For example, command:
```scala
sc.parallelize(1 to 10).map(x=>(x,x)).reduceByKey(_+_).count
```
breaks down into 2 stages.

The old web UI:
![screen shot 2014-09-04 at 12 42 44 am](https://cloud.githubusercontent.com/assets/323388/4146177/60fb4f42-3407-11e4-819f-853eb0e22b25.png)

Web UI with this patch:
![screen shot 2014-09-04 at 12 44 55 am](https://cloud.githubusercontent.com/assets/323388/4146178/62e08e62-3407-11e4-867b-a36b10534464.png)

Author: Reynold Xin <rxin@apache.org>

Closes #2273 from rxin/lower-stage-id and squashes the following commits:

abbb4c6 [Reynold Xin] Fixed SparkListenerSuite.
0e02379 [Reynold Xin] Updated DAGSchedulerSuite.
54ccea3 [Reynold Xin] [SPARK-3353] parent stage should have lower stage id.
[SPARK-3394] [SQL] Fix crash in TakeOrdered when limit is 0

This resolves https://issues.apache.org/jira/browse/SPARK-3394

Author: Eric Liang <ekl@google.com>

Closes #2264 from ericl/spark-3394 and squashes the following commits:

c87355b [Eric Liang] refactor
bfb6140 [Eric Liang] change RDD takeOrdered instead
7a51528 [Eric Liang] fix takeordered when limit = 0
[SQL] Update SQL Programming Guide

Author: Michael Armbrust <michael@databricks.com>
Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #2258 from marmbrus/sqlDocUpdate and squashes the following commits:

f3d450b [Michael Armbrust] fix brackets
bea3bfa [Michael Armbrust] Davies suggestions
3a29fe2 [Michael Armbrust] tighten visibility
a71aa36 [Michael Armbrust] Draft of doc updates
52932c0 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into sqlDocUpdate
1e8c849 [Yin Huai] Update the example used for applySchema.
9457c39 [Yin Huai] Update doc.
31ba240 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeDoc
29bc668 [Yin Huai] Draft doc for data type and schema APIs.
[SPARK-3408] Fixed Limit operator so it works with sort-based shuffle.

Author: Reynold Xin <rxin@apache.org>

Closes #2281 from rxin/sql-limit-sort and squashes the following commits:

1ef7780 [Reynold Xin] [SPARK-3408] Fixed Limit operator so it works with sort-based shuffle.
[SPARK-3415] [PySpark] removes SerializingAdapter code

This code removes the SerializingAdapter code that was copied from PiCloud

Author: Ward Viaene <ward.viaene@bigdatapartnership.com>

Closes #2287 from wardviaene/feature/pythonsys and squashes the following commits:

5f0d426 [Ward Viaene] SPARK-3415: modified test class to do dump and load
5f5d559 [Ward Viaene] SPARK-3415: modified test class name and call cloudpickle.dumps instead using StringIO
afc4a9a [Ward Viaene] SPARK-3415: added newlines to pass lint
aaf10b7 [Ward Viaene] SPARK-3415: removed references to SerializingAdapter and rewrote test
65ffeff [Ward Viaene] removed duplicate test
a958866 [Ward Viaene] SPARK-3415: test script
e263bf5 [Ward Viaene] SPARK-3415: removes legacy SerializingAdapter code
Fixed typos in make-distribution.sh

`hadoop.version` and `yarn.version` are properties rather then profiles, should use `-D` instead of `-P`.

/cc pwendell

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

Closes #2121 from liancheng/fix-make-dist and squashes the following commits:

4c49158 [Cheng Lian] Also mentions Hadoop version related Maven profiles
ed5b42a [Cheng Lian] Fixed typos in make-distribution.sh
[HOTFIX] Fix broken Mima tests on the master branch

By merging #2268, which bumped the Spark version to 1.2.0-SNAPSHOT, I inadvertently broke the Mima binary compatibility tests.  The issue is that we were comparing 1.2.0-SNAPSHOT against Spark 1.0.0 without using any Mima excludes.  The right long-term fix for this is probably to publish nightly snapshots on Maven central and change the master branch to test binary compatibility against the current release candidate branch's snapshots until that release is finalized.

As a short-term fix until 1.1.0 is published on Maven central, I've configured the build to test the master branch for binary compatibility against the 1.1.0-RC4 jars.  I'll loop back and remove the Apache staging repo as soon as 1.1.0 final is available.

Author: Josh Rosen <joshrosen@apache.org>

Closes #2315 from JoshRosen/mima-fix and squashes the following commits:

776bc2c [Josh Rosen] Add two excludes to workaround Mima annotation issues.
ec90e21 [Josh Rosen] Add deploy and graphx to 1.2 MiMa excludes.
57569be [Josh Rosen] Fix MiMa tests in master branch; test against 1.1.0 RC.
[SPARK-3280] Made sort-based shuffle the default implementation

Sort-based shuffle has lower memory usage and seems to outperform hash-based in almost all of our testing.

Author: Reynold Xin <rxin@apache.org>

Closes #2178 from rxin/sort-shuffle and squashes the following commits:

713d341 [Reynold Xin] Fixed test failures by setting spark.shuffle.compress to the same value as spark.shuffle.spill.compress.
85165e6 [Reynold Xin] Fixed a comment typo.
aa0d372 [Reynold Xin] [SPARK-3280] Made sort-based shuffle the default implementation
[SPARK-938][doc] Add OpenStack Swift support

See compiled doc at
http://people.apache.org/~rxin/tmp/openstack-swift/_site/storage-openstack-swift.html

This is based on #1010. Closes #1010.

Author: Reynold Xin <rxin@apache.org>
Author: Gil Vernik <gilv@il.ibm.com>

Closes #2298 from rxin/openstack-swift and squashes the following commits:

ff4e394 [Reynold Xin] Two minor comments from Patrick.
279f6de [Reynold Xin] core-sites -> core-site
dfb8fea [Reynold Xin] Updated based on Gil's suggestion.
846f5cb [Reynold Xin] Added a link from overview page.
0447c9f [Reynold Xin] Removed sample code.
e9c3761 [Reynold Xin] Merge pull request #1010 from gilv/master
9233fef [Gil Vernik] Fixed typos
6994827 [Gil Vernik] Merge pull request #1 from rxin/openstack
ac0679e [Reynold Xin] Fixed an unclosed tr.
47ce99d [Reynold Xin] Merge branch 'master' into openstack
cca7192 [Gil Vernik] Removed white spases from pom.xml
99f095d [Reynold Xin] Pending openstack changes.
eb22295 [Reynold Xin] Merge pull request #1010 from gilv/master
39a9737 [Gil Vernik] Spark integration with Openstack Swift
c977658 [Gil Vernik] Merge branch 'master' of https://github.com/gilv/spark
2aba763 [Gil Vernik] Fix to docs/openstack-integration.md
9b625b5 [Gil Vernik] Merge branch 'master' of https://github.com/gilv/spark
eff538d [Gil Vernik] SPARK-938 - Openstack Swift object storage support
ce483d7 [Gil Vernik] SPARK-938 - Openstack Swift object storage support
b6c37ef [Gil Vernik] Openstack Swift support
[HOTFIX] A left over version change. It should make mima happy.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #2317 from ScrapCodes/hotfix and squashes the following commits:

b6472d4 [Prashant Sharma] [HOTFIX] for hotfixes, a left over version change.
[SPARK-3086] [SPARK-3043] [SPARK-3156] [mllib]  DecisionTree aggregation improvements

Summary:
1. Variable numBins for each feature [SPARK-3043]
2. Reduced data reshaping in aggregation [SPARK-3043]
3. Choose ordering for ordered categorical features adaptively [SPARK-3156]
4. Changed nodes to use 1-indexing [SPARK-3086]
5. Small clean-ups

Note: This PR looks bigger than it is since I moved several functions from inside findBestSplitsPerGroup to outside of it (to make it clear what was being serialized in the aggregation).

Speedups: This update helps most when many features use few bins but a few features use many bins.  Some example results on speedups with 2M examples, 3.5K features (15-worker EC2 cluster):
* Example where old code was reasonably efficient (1/2 continuous, 1/4 binary, 1/4 20-category): 164.813 --> 116.491 sec
* Example where old code wasted many bins (1/10 continuous, 81/100 binary, 9/100 20-category): 128.701 --> 39.334 sec

Details:

(1) Variable numBins for each feature [SPARK-3043]

DecisionTreeMetadata now computes a variable numBins for each feature.  It also tracks numSplits.

(2) Reduced data reshaping in aggregation [SPARK-3043]

Added DTStatsAggregator, a wrapper around the aggregate statistics array for easy but efficient indexing.
* Added ImpurityAggregator and ImpurityCalculator classes, to make DecisionTree code more oblivious to the type of impurity.
* Design note: I originally tried creating Impurity classes which stored data and storing the aggregates in an Array[Array[Array[Impurity]]].  However, this led to significant slowdowns, perhaps because of overhead in creating so many objects.

The aggregate statistics are never reshaped, and cumulative sums are computed in-place.

Updated the layout of aggregation functions.  The update simplifies things by (1) dividing features into ordered/unordered (instead of ordered/unordered/continuous) and (2) making use of the DTStatsAggregator for indexing.
For this update, the following functions were refactored:
* updateBinForOrderedFeature
* updateBinForUnorderedFeature
* binaryOrNotCategoricalBinSeqOp
* multiclassWithCategoricalBinSeqOp
* regressionBinSeqOp
The above 5 functions were replaced with:
* orderedBinSeqOp
* someUnorderedBinSeqOp

Other changes:
* calculateGainForSplit now treats all feature types the same way.
* Eliminated extractLeftRightNodeAggregates.

(3) Choose ordering for ordered categorical features adaptively [SPARK-3156]

Updated binsToBestSplit():
* This now computes cumulative sums of stats for ordered features.
* For ordered categorical features, it chooses an ordering for categories. (This uses to be done by findSplitsBins.)
* Uses iterators to shorten code and avoid building an Array[Array[InformationGainStats]].

Side effects:
* In findSplitsBins: A sample of the data is only taken for data with continuous features.  It is not needed for data with only categorical features.
* In findSplitsBins: splits and bins are no longer pre-computed for ordered categorical features since they are not needed.
* TreePoint binning is simpler for categorical features.

(4) Changed nodes to use 1-indexing [SPARK-3086]

Nodes used to be indexed from 0.  Now they are indexed from 1.
Node indexing functions are now collected in object Node (Node.scala).

(5) Small clean-ups

Eliminated functions extractNodeInfo() and extractInfoForLowerLevels() to reduce duplicate code.
Eliminated InvalidBinIndex since it is no longer used.

CC: mengxr  manishamde  Please let me know if you have thoughts on this—thanks!

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

Closes #2125 from jkbradley/dt-opt3alt and squashes the following commits:

42c192a [Joseph K. Bradley] Merge branch 'rfs' into dt-opt3alt
d3cc46b [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3alt
00e4404 [Joseph K. Bradley] optimization for TreePoint construction (pre-computing featureArity and isUnordered as arrays)
425716c [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into rfs
a2acea5 [Joseph K. Bradley] Small optimizations based on profiling
aa4e4df [Joseph K. Bradley] Updated DTStatsAggregator with bug fix (nodeString should not be multiplied by statsSize)
4651154 [Joseph K. Bradley] Changed numBins semantics for unordered features. * Before: numBins = numSplits = (1 << k - 1) - 1 * Now: numBins = 2 * numSplits = 2 * [(1 << k - 1) - 1] * This also involved changing the semantics of: ** DecisionTreeMetadata.numUnorderedBins()
1e3b1c7 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3alt
1485fcc [Joseph K. Bradley] Made some DecisionTree methods private.
92f934f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3alt
e676da1 [Joseph K. Bradley] Updated documentation for DecisionTree
37ca845 [Joseph K. Bradley] Fixed problem with how DecisionTree handles ordered categorical	features.
105f8ab [Joseph K. Bradley] Removed commented-out getEmptyBinAggregates from DecisionTree
062c31d [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3alt
6d32ccd [Joseph K. Bradley] In DecisionTree.binsToBestSplit, changed loops to iterators to shorten code.
807cd00 [Joseph K. Bradley] Finished DTStatsAggregator, a wrapper around the aggregate statistics for easy but hopefully efficient indexing.  Modified old ImpurityAggregator classes and renamed them ImpurityCalculator; added ImpurityAggregator classes which work with DTStatsAggregator but do not store data.  Unit tests all succeed.
f2166fd [Joseph K. Bradley] still working on DTStatsAggregator
92f7118 [Joseph K. Bradley] Added partly written DTStatsAggregator
fd8df30 [Joseph K. Bradley] Moved some aggregation helpers outside of findBestSplitsPerGroup
d7c53ee [Joseph K. Bradley] Added more doc for ImpurityAggregator
a40f8f1 [Joseph K. Bradley] Changed nodes to be indexed from 1.  Tests work.
95cad7c [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3
5f94342 [Joseph K. Bradley] Added treeAggregate since not yet merged from master.  Moved node indexing functions to Node.
61c4509 [Joseph K. Bradley] Fixed bugs from merge: missing DT timer call, and numBins setting.  Cleaned up DT Suite some.
3ba7166 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3
b314659 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt3
9c83363 [Joseph K. Bradley] partial merge but not done yet
45f7ea7 [Joseph K. Bradley] partial merge, not yet done
5fce635 [Joseph K. Bradley] Merge branch 'dt-opt2' into dt-opt3
26d10dd [Joseph K. Bradley] Removed tree/model/Filter.scala since no longer used.  Removed debugging println calls in DecisionTree.scala.
356daba [Joseph K. Bradley] Merge branch 'dt-opt1' into dt-opt2
430d782 [Joseph K. Bradley] Added more debug info on binning error.  Added some docs.
d036089 [Joseph K. Bradley] Print timing info to logDebug.
e66f1b1 [Joseph K. Bradley] TreePoint * Updated doc * Made some methods private
8464a6e [Joseph K. Bradley] Moved TimeTracker to tree/impl/ in its own file, and cleaned it up.  Removed debugging println calls from DecisionTree.  Made TreePoint extend Serialiable
a87e08f [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt1
dd4d3aa [Joseph K. Bradley] Mid-process in bug fix: bug for binary classification with categorical features * Bug: Categorical features were all treated as ordered for binary classification.  This is possible but would require the bin ordering to be determined on-the-fly after the aggregation.  Currently, the ordering is determined a priori and fixed for all splits. * (Temp) Fix: Treat low-arity categorical features as unordered for binary classification. * Related change: I removed most tests for isMulticlass in the code.  I instead test metadata for whether there are unordered features. * Status: The bug may be fixed, but more testing needs to be done.
438a660 [Joseph K. Bradley] removed subsampling for mnist8m from DT
86e217f [Joseph K. Bradley] added cache to DT input
e3c84cc [Joseph K. Bradley] Added stuff fro mnist8m to D T Runner
51ef781 [Joseph K. Bradley] Fixed bug introduced by last commit: Variance impurity calculation was incorrect since counts were swapped accidentally
fd65372 [Joseph K. Bradley] Major changes: * Created ImpurityAggregator classes, rather than old aggregates. * Feature split/bin semantics are based on ordered vs. unordered ** E.g.: numSplits = numBins for all unordered features, and numSplits = numBins - 1 for all ordered features. * numBins can differ for each feature
c1565a5 [Joseph K. Bradley] Small DecisionTree updates: * Simplification: Updated calculateGainForSplit to take aggregates for a single (feature, split) pair. * Internal doc: findAggForOrderedFeatureClassification
b914f3b [Joseph K. Bradley] DecisionTree optimization: eliminated filters + small changes
b2ed1f3 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-opt
0f676e2 [Joseph K. Bradley] Optimizations + Bug fix for DecisionTree
3211f02 [Joseph K. Bradley] Optimizing DecisionTree * Added TreePoint representation to avoid calling findBin multiple times. * (not working yet, but debugging)
f61e9d2 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing
bcf874a [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing
511ec85 [Joseph K. Bradley] Merge remote-tracking branch 'upstream/master' into dt-timing
a95bc22 [Joseph K. Bradley] timing for DecisionTree internals
SPARK-3337 Paranoid quoting in shell to allow install dirs with spaces within.

...

Tested ! TBH, it isn't a great idea to have directory with spaces within. Because emacs doesn't like it then hadoop doesn't like it. and so on...

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #2229 from ScrapCodes/SPARK-3337/quoting-shell-scripts and squashes the following commits:

d4ad660 [Prashant Sharma] SPARK-3337 Paranoid quoting in shell to allow install dirs with spaces within.