We should standardize the text format used to represent vectors and labeled points. The proposed formats are the following:

1. dense vector: `[v0,v1,..]`
2. sparse vector: `(size,[i0,i1],[v0,v1])`
3. labeled point: `(label,vector)`

where "(..)" indicates a tuple and "[...]" indicate an array. `loadLabeledPoints` is added to pyspark's `MLUtils`. I didn't add `loadVectors` to pyspark because `RDD.saveAsTextFile` cannot stringify dense vectors in the proposed format automatically.

`MLUtils#saveLabeledData` and `MLUtils#loadLabeledData` are deprecated. Users should use `RDD#saveAsTextFile` and `MLUtils#loadLabeledPoints` instead. In Scala, `MLUtils#loadLabeledPoints` is compatible with the format used by `MLUtils#loadLabeledData`.

CC: @mateiz, @srowen

Author: Xiangrui Meng <meng@databricks.com>

Closes #685 from mengxr/labeled-io and squashes the following commits:

2d1116a [Xiangrui Meng] make loadLabeledData/saveLabeledData deprecated since 1.0.1
297be75 [Xiangrui Meng] change LabeledPoint.parse to LabeledPointParser.parse to maintain binary compatibility
d6b1473 [Xiangrui Meng] Merge branch 'master' into labeled-io
56746ea [Xiangrui Meng] replace # by .
623a5f0 [Xiangrui Meng] merge master
f06d5ba [Xiangrui Meng] add docs and minor updates
640fe0c [Xiangrui Meng] throw SparkException
5bcfbc4 [Xiangrui Meng] update test to add scientific notations
e86bf38 [Xiangrui Meng] remove NumericTokenizer
050fca4 [Xiangrui Meng] use StringTokenizer
6155b75 [Xiangrui Meng] merge master
f644438 [Xiangrui Meng] remove parse methods based on eval from pyspark
a41675a [Xiangrui Meng] python loadLabeledPoint uses Scala's implementation
ce9a475 [Xiangrui Meng] add deserialize_labeled_point to pyspark with tests
e9fcd49 [Xiangrui Meng] add serializeLabeledPoint and tests
aea4ae3 [Xiangrui Meng] minor updates
810d6df [Xiangrui Meng] update tokenizer/parser implementation
7aac03a [Xiangrui Meng] remove Scala parsers
c1885c1 [Xiangrui Meng] add headers and minor changes
b0c50cb [Xiangrui Meng] add customized parser
d731817 [Xiangrui Meng] style update
63dc396 [Xiangrui Meng] add loadLabeledPoints to pyspark
ea122b5 [Xiangrui Meng] Merge branch 'master' into labeled-io
cd6c78f [Xiangrui Meng] add __str__ and parse to LabeledPoint
a7a178e [Xiangrui Meng] add stringify to pyspark's Vectors
5c2dbfa [Xiangrui Meng] add parse to pyspark's Vectors
7853f88 [Xiangrui Meng] update pyspark's SparseVector.__str__
e761d32 [Xiangrui Meng] make LabelPoint.parse compatible with the dense format used before v1.0 and deprecate loadLabeledData and saveLabeledData
9e63a02 [Xiangrui Meng] add loadVectors and loadLabeledPoints
19aa523 [Xiangrui Meng] update toString and add parsers for Vectors and LabeledPoint

Author: Reynold Xin <rxin@apache.org>

Closes #871 from rxin/mllib-pep8 and squashes the following commits:

848416f [Reynold Xin] Fixed a typo in the previous cleanup (c -> sc).
a8db4cd [Reynold Xin] Fix PEP8 violations in Python mllib.

Make loading/saving labeled data easier for pyspark users.

Also changed type check in `SparseVector` to allow numpy integers.

Author: Xiangrui Meng <meng@databricks.com>

Closes #672 from mengxr/pyspark-mllib-util and squashes the following commits:

2943fa7 [Xiangrui Meng] format docs
d61668d [Xiangrui Meng] add loadLibSVMFile and saveAsLibSVMFile to pyspark

This PR adds a SparseVector class in PySpark and updates all the regression, classification and clustering algorithms and models to support sparse data, similar to MLlib. I chose to add this class because SciPy is quite difficult to install in many environments (more so than NumPy), but I plan to add support for SciPy sparse vectors later too, and make the methods work transparently on objects of either type.

On the Scala side, we keep Python sparse vectors sparse and pass them to MLlib. We always return dense vectors from our models.

Some to-do items left:
- [x] Support SciPy's scipy.sparse matrix objects when SciPy is available. We can easily add a function to convert these to our own SparseVector.
- [x] MLlib currently uses a vector with one extra column on the left to represent what we call LabeledPoint in Scala. Do we really want this? It may get annoying once you deal with sparse data since you must add/subtract 1 to each feature index when training. We can remove this API in 1.0 and use tuples for labeling.
- [x] Explain how to use these in the Python MLlib docs.

CC @mengxr, @joshrosen

Author: Matei Zaharia <matei@databricks.com>

Closes #341 from mateiz/py-ml-update and squashes the following commits:

d52e763 [Matei Zaharia] Remove no-longer-needed slice code and handle review comments
ea5a25a [Matei Zaharia] Fix remaining uses of copyto() after merge
b9f97a3 [Matei Zaharia] Fix test
1e1bd0f [Matei Zaharia] Add MLlib logistic regression example in Python
88bc01f [Matei Zaharia] Clean up inheritance of LinearModel in Python, and expose its parametrs
37ab747 [Matei Zaharia] Fix some examples and docs due to changes in MLlib API
da0f27e [Matei Zaharia] Added a MLlib K-means example and updated docs to discuss sparse data
c48e85a [Matei Zaharia] Added some tests for passing lists as input, and added mllib/tests.py to run-tests script.
a07ba10 [Matei Zaharia] Fix some typos and calculation of initial weights
74eefe7 [Matei Zaharia] Added LabeledPoint class in Python
889dde8 [Matei Zaharia] Support scipy.sparse matrices in all our algorithms and models
ab244d1 [Matei Zaharia] Allow SparseVectors to be initialized using a dict
a5d6426 [Matei Zaharia] Add linalg.py to run-tests script
0e7a3d8 [Matei Zaharia] Keep vectors sparse in Java when reading LabeledPoints
eaee759 [Matei Zaharia] Update regression, classification and clustering models for sparse data
2abbb44 [Matei Zaharia] Further work to get linear models working with sparse data
154f45d [Matei Zaharia] Update docs, name some magic values
881fef7 [Matei Zaharia] Added a sparse vector in Python and made Java-Python format more compact