## What changes were proposed in this pull request?
This patch bumps the master branch version to `2.4.0-SNAPSHOT`.
## How was this patch tested?
N/A
Author: gatorsmile <gatorsmile@gmail.com>
Closes#20222 from gatorsmile/bump24.
## What changes were proposed in this pull request?
We need to add some helper code to make testing ML transformers & models easier with streaming data. These tests might help us catch any remaining issues and we could encourage future PRs to use these tests to prevent new Models & Transformers from having issues.
I add a `MLTest` trait which extends `StreamTest` trait, and override `createSparkSession`. So ML testsuite can only extend `MLTest`, to use both ML & Stream test util functions.
I only modify one testcase in `LinearRegressionSuite`, for first pass review.
Link to #19746
## How was this patch tested?
`MLTestSuite` added.
Author: WeichenXu <weichen.xu@databricks.com>
Closes#19843 from WeichenXu123/ml_stream_test_helper.
…build; fix some things that will be warnings or errors in 2.12; restore Scala 2.12 profile infrastructure
## What changes were proposed in this pull request?
This change adds back the infrastructure for a Scala 2.12 build, but does not enable it in the release or Python test scripts.
In order to make that meaningful, it also resolves compile errors that the code hits in 2.12 only, in a way that still works with 2.11.
It also updates dependencies to the earliest minor release of dependencies whose current version does not yet support Scala 2.12. This is in a sense covered by other JIRAs under the main umbrella, but implemented here. The versions below still work with 2.11, and are the _latest_ maintenance release in the _earliest_ viable minor release.
- Scalatest 2.x -> 3.0.3
- Chill 0.8.0 -> 0.8.4
- Clapper 1.0.x -> 1.1.2
- json4s 3.2.x -> 3.4.2
- Jackson 2.6.x -> 2.7.9 (required by json4s)
This change does _not_ fully enable a Scala 2.12 build:
- It will also require dropping support for Kafka before 0.10. Easy enough, just didn't do it yet here
- It will require recreating `SparkILoop` and `Main` for REPL 2.12, which is SPARK-14650. Possible to do here too.
What it does do is make changes that resolve much of the remaining gap without affecting the current 2.11 build.
## How was this patch tested?
Existing tests and build. Manually tested with `./dev/change-scala-version.sh 2.12` to verify it compiles, modulo the exceptions above.
Author: Sean Owen <sowen@cloudera.com>
Closes#18645 from srowen/SPARK-14280.
Remove spark-tag's compile-scope dependency (and, indirectly, spark-core's compile-scope transitive-dependency) on scalatest by splitting test-oriented tags into spark-tags' test JAR.
Alternative to #16303.
Author: Ryan Williams <ryan.blake.williams@gmail.com>
Closes#16311 from ryan-williams/tt.
## What changes were proposed in this pull request?
This patch bumps master branch version to 2.2.0-SNAPSHOT.
## How was this patch tested?
N/A
Author: Reynold Xin <rxin@databricks.com>
Closes#16126 from rxin/SPARK-18695.
https://issues.apache.org/jira/browse/SPARK-16535
## What changes were proposed in this pull request?
When I scan through the pom.xml of sub projects, I found this warning as below and attached screenshot
```
Definition of groupId is redundant, because it's inherited from the parent
```
I've tried to remove some of the lines with groupId definition, and the build on my local machine is still ok.
```
<groupId>org.apache.spark</groupId>
```
As I just find now `<maven.version>3.3.9</maven.version>` is being used in Spark 2.x, and Maven-3 supports versionless parent elements: Maven 3 will remove the need to specify the parent version in sub modules. THIS is great (in Maven 3.1).
ref: http://stackoverflow.com/questions/3157240/maven-3-worth-it/3166762#3166762
## How was this patch tested?
I've tested by re-building the project, and build succeeded.
Author: Xin Ren <iamshrek@126.com>
Closes#14189 from keypointt/SPARK-16535.
## What changes were proposed in this pull request?
After SPARK-16476 (committed earlier today as #14128), we can finally bump the version number.
## How was this patch tested?
N/A
Author: Reynold Xin <rxin@databricks.com>
Closes#14130 from rxin/SPARK-16477.
## What changes were proposed in this pull request?
See https://issues.apache.org/jira/browse/SPARK-15523
This PR replaces PR #13293. It's isolated to a new branch, and contains some more squashed changes.
## How was this patch tested?
1. Executed `mvn clean package` in `mllib` directory
2. Executed `dev/test-dependencies.sh --replace-manifest` in the root directory.
Author: Villu Ruusmann <villu.ruusmann@gmail.com>
Closes#13297 from vruusmann/update-jpmml.
## What changes were proposed in this pull request?
(See https://github.com/apache/spark/pull/12416 where most of this was already reviewed and committed; this is just the module structure and move part. This change does not move the annotations into test scope, which was the apparently problem last time.)
Rename `spark-test-tags` -> `spark-tags`; move common annotations like `Since` to `spark-tags`
## How was this patch tested?
Jenkins tests.
Author: Sean Owen <sowen@cloudera.com>
Closes#13074 from srowen/SPARK-15290.
## What changes were proposed in this pull request?
This PR adds `since` tag into the matrix and vector classes in spark-mllib-local.
## How was this patch tested?
Scala-style checks passed.
Author: Pravin Gadakh <prgadakh@in.ibm.com>
Closes#12416 from pravingadakh/SPARK-14613.
## What changes were proposed in this pull request?
Move json4s, breeze dependency declaration into parent
## How was this patch tested?
Should be no functional change, but Jenkins tests will test that.
Author: Sean Owen <sowen@cloudera.com>
Closes#12390 from srowen/SPARK-14612.
## What changes were proposed in this pull request?
In order to separate the linear algebra, and vector matrix classes into a standalone jar, we need to setup the build first. This PR will create a new jar called mllib-local with minimal dependencies.
The previous PR was failing the build because of `spark-core:test` dependency, and that was reverted. In this PR, `FunSuite` with `// scalastyle:ignore funsuite` in mllib-local test was used, similar to sketch.
Thanks.
## How was this patch tested?
Unit tests
mengxr tedyu holdenk
Author: DB Tsai <dbt@netflix.com>
Closes#12298 from dbtsai/dbtsai-mllib-local-build-fix.
## What changes were proposed in this pull request?
In order to separate the linear algebra, and vector matrix classes into a standalone jar, we need to setup the build first. This PR will create a new jar called mllib-local with minimal dependencies. The test scope will still depend on spark-core and spark-core-test in order to use the common utilities, but the runtime will avoid any platform dependency. Couple platform independent classes will be moved to this package to demonstrate how this work.
## How was this patch tested?
Unit tests
Author: DB Tsai <dbt@netflix.com>
Closes#12241 from dbtsai/dbtsai-mllib-local-build.
## What changes were proposed in this pull request?
Remove last usage of jblas, in tests
## How was this patch tested?
Jenkins tests -- the same ones that are being modified.
Author: Sean Owen <sowen@cloudera.com>
Closes#11560 from srowen/SPARK-13715.
This patch changes Spark's build to make Scala 2.11 the default Scala version. To be clear, this does not mean that Spark will stop supporting Scala 2.10: users will still be able to compile Spark for Scala 2.10 by following the instructions on the "Building Spark" page; however, it does mean that Scala 2.11 will be the default Scala version used by our CI builds (including pull request builds).
The Scala 2.11 compiler is faster than 2.10, so I think we'll be able to look forward to a slight speedup in our CI builds (it looks like it's about 2X faster for the Maven compile-only builds, for instance).
After this patch is merged, I'll update Jenkins to add new compile-only jobs to ensure that Scala 2.10 compilation doesn't break.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#10608 from JoshRosen/SPARK-6363.
This change does two things:
- tag a few tests and adds the mechanism in the build to be able to disable those tags,
both in maven and sbt, for both junit and scalatest suites.
- add some logic to run-tests.py to disable some tags depending on what files have
changed; that's used to disable expensive tests when a module hasn't explicitly
been changed, to speed up testing for changes that don't directly affect those
modules.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#8437 from vanzin/test-tags.
Spark's tests currently depend on `mockito-all`, which bundles Hamcrest and Objenesis classes. Instead, it should depend on `mockito-core`, which declares those libraries as Maven dependencies. This is necessary in order to fix a dependency conflict that leads to a NoSuchMethodError when using certain Hamcrest matchers.
See https://github.com/mockito/mockito/wiki/Declaring-mockito-dependency for more details.
Author: Josh Rosen <joshrosen@databricks.com>
Closes#7061 from JoshRosen/mockito-core-instead-of-all and squashes the following commits:
70eccbe [Josh Rosen] Depend on mockito-core instead of mockito-all.
Author: Patrick Wendell <patrick@databricks.com>
Closes#6328 from pwendell/spark-1.5-update and squashes the following commits:
2f42d02 [Patrick Wendell] A few more excludes
4bebcf0 [Patrick Wendell] Update to RC4
61aaf46 [Patrick Wendell] Using new release candidate
55f1610 [Patrick Wendell] Another exclude
04b4f04 [Patrick Wendell] More issues with transient 1.4 changes
36f549b [Patrick Wendell] [SPARK-7801] [BUILD] Updating versions to SPARK 1.5.0
This patch fixes a build break in maven caused by #6441.
Note that this patch reverts the changes in flume-sink because
this module does not currently depend on Spark core, but the
tests require it. There is not an easy way to make this work
because mvn test dependencies are not transitive (MNG-1378).
For now, we will leave the one test suite in flume-sink out
until we figure out a better solution. This patch is mainly
intended to unbreak the maven build.
Author: Andrew Or <andrew@databricks.com>
Closes#6511 from andrewor14/fix-build-mvn and squashes the following commits:
3d53643 [Andrew Or] [HOT FIX#6441] Fix maven build failures
The sbt part of the build is hacky; it basically tricks sbt
into generating the zip by using a generator, but returns
an empty list for the generated files so that nothing is
actually added to the assembly.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#6022 from vanzin/SPARK-7485 and squashes the following commits:
22c1e04 [Marcelo Vanzin] Remove unneeded code.
4893622 [Marcelo Vanzin] [SPARK-7485] [build] Remove pyspark files from assembly.
See PDF attached to the JIRA issue 1406.
The contribution is my original work and I license the work to the project under the project's open source license.
Author: Vincenzo Selvaggio <vselvaggio@hotmail.it>
Author: Xiangrui Meng <meng@databricks.com>
Author: selvinsource <vselvaggio@hotmail.it>
Closes#3062 from selvinsource/mllib_pmml_model_export_SPARK-1406 and squashes the following commits:
852aac6 [Vincenzo Selvaggio] [SPARK-1406] Update JPMML version to 1.1.15 in LICENSE file
085cf42 [Vincenzo Selvaggio] [SPARK-1406] Added Double Min and Max Fixed scala style
30165c4 [Vincenzo Selvaggio] [SPARK-1406] Fixed extreme cases for logit
7a5e0ec [Vincenzo Selvaggio] [SPARK-1406] Binary classification for SVM and Logistic Regression
cfcb596 [Vincenzo Selvaggio] [SPARK-1406] Throw IllegalArgumentException when exporting a multinomial logistic regression
25dce33 [Vincenzo Selvaggio] [SPARK-1406] Update code to latest pmml model
dea98ca [Vincenzo Selvaggio] [SPARK-1406] Exclude transitive dependency for pmml model
66b7c12 [Vincenzo Selvaggio] [SPARK-1406] Updated pmml model lib to 1.1.15, latest Java 6 compatible
a0a55f7 [Vincenzo Selvaggio] Merge pull request #2 from mengxr/SPARK-1406
3c22f79 [Xiangrui Meng] more code style
e2313df [Vincenzo Selvaggio] Merge pull request #1 from mengxr/SPARK-1406
472d757 [Xiangrui Meng] fix code style
1676e15 [Vincenzo Selvaggio] fixed scala issue
e2ffae8 [Vincenzo Selvaggio] fixed scala style
b8823b0 [Vincenzo Selvaggio] Merge remote-tracking branch 'upstream/master' into mllib_pmml_model_export_SPARK-1406
b25bbf7 [Vincenzo Selvaggio] [SPARK-1406] Added export of pmml to distributed file system using the spark context
7a949d0 [Vincenzo Selvaggio] [SPARK-1406] Fixed scala style
f46c75c [Vincenzo Selvaggio] [SPARK-1406] Added PMMLExportable to supported models
7b33b4e [Vincenzo Selvaggio] [SPARK-1406] Added a PMMLExportable interface Restructured code in a new package mllib.pmml Supported models implements the new PMMLExportable interface: LogisticRegression, SVM, KMeansModel, LinearRegression, RidgeRegression, Lasso
d559ec5 [Vincenzo Selvaggio] Merge remote-tracking branch 'upstream/master' into mllib_pmml_model_export_SPARK-1406
8fe12bb [Vincenzo Selvaggio] [SPARK-1406] Adjusted logistic regression export description and target categories
03bc3a5 [Vincenzo Selvaggio] added logistic regression
da2ec11 [Vincenzo Selvaggio] [SPARK-1406] added linear SVM PMML export
82f2131 [Vincenzo Selvaggio] Merge remote-tracking branch 'upstream/master' into mllib_pmml_model_export_SPARK-1406
19adf29 [Vincenzo Selvaggio] [SPARK-1406] Fixed scala style
1faf985 [Vincenzo Selvaggio] [SPARK-1406] Added target field to the regression model for completeness Adjusted unit test to deal with this change
3ae8ae5 [Vincenzo Selvaggio] [SPARK-1406] Adjusted imported order according to the guidelines
c67ce81 [Vincenzo Selvaggio] Merge remote-tracking branch 'upstream/master' into mllib_pmml_model_export_SPARK-1406
78515ec [Vincenzo Selvaggio] [SPARK-1406] added pmml export for LinearRegressionModel, RidgeRegressionModel and LassoModel
e29dfb9 [Vincenzo Selvaggio] removed version, by default is set to 4.2 (latest from jpmml) removed copyright
ae8b993 [Vincenzo Selvaggio] updated some commented tests to use the new ModelExporter object reordered the imports
df8a89e [Vincenzo Selvaggio] added pmml version to pmml model changed the copyright to spark
a1b4dc3 [Vincenzo Selvaggio] updated imports
834ca44 [Vincenzo Selvaggio] reordered the import accordingly to the guidelines
349a76b [Vincenzo Selvaggio] new helper object to serialize the models to pmml format
c3ef9b8 [Vincenzo Selvaggio] set it to private
6357b98 [Vincenzo Selvaggio] set it to private
e1eb251 [Vincenzo Selvaggio] removed serialization part, this will be part of the ModelExporter helper object
aba5ee1 [Vincenzo Selvaggio] fixed cluster export
cd6c07c [Vincenzo Selvaggio] fixed scala style to run tests
f75b988 [Vincenzo Selvaggio] Merge remote-tracking branch 'origin/master' into mllib_pmml_model_export_SPARK-1406
07a29bf [selvinsource] Update LICENSE
8841439 [Vincenzo Selvaggio] adjust scala style in order to compile
1433b11 [Vincenzo Selvaggio] complete suite tests
8e71b8d [Vincenzo Selvaggio] kmeans pmml export implementation
9bc494f [Vincenzo Selvaggio] added scala suite tests added saveLocalFile to ModelExport trait
226e184 [Vincenzo Selvaggio] added javadoc and export model type in case there is a need to support other types of export (not just PMML)
a0e3679 [Vincenzo Selvaggio] export and pmml export traits kmeans test implementation
There are any bugs of breeze's SparseVector at 0.11.1. You know, Spark 1.3 depends on breeze 0.11.1. So I think we should upgrade it to 0.11.2.
https://issues.apache.org/jira/browse/SPARK-6341
And thanks you for your great cooperation, David Hall(dlwh)
Author: Yu ISHIKAWA <yuu.ishikawa@gmail.com>
Closes#5222 from yu-iskw/upgrade-breeze and squashes the following commits:
ad8a688 [Yu ISHIKAWA] Upgrade breeze from 0.11.1 to 0.11.2 because of a bug of SparseVector. Thanks you for your great cooperation, David Hall(@dlwh)
The issue is discussed in https://issues.apache.org/jira/browse/SPARK-5669. Replacing all JBLAS usage by netlib-java gives us a simpler dependency tree and less license issues to worry about. I didn't touch the test scope in this PR. The user guide is not modified to avoid merge conflicts with branch-1.3. srowen ankurdave pwendell
Author: Xiangrui Meng <meng@databricks.com>
Closes#4699 from mengxr/SPARK-5814 and squashes the following commits:
48635c6 [Xiangrui Meng] move netlib-java version to parent pom
ca21c74 [Xiangrui Meng] remove jblas from ml-guide
5f7767a [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-5814
c5c4183 [Xiangrui Meng] merge master
0f20cad [Xiangrui Meng] add mima excludes
e53e9f4 [Xiangrui Meng] remove jblas from mllib runtime
ceaa14d [Xiangrui Meng] replace jblas by netlib-java in graphx
fa7c2ca [Xiangrui Meng] move jblas to test scope
Option 1 of 2: Convert spark-parent module name to spark-parent_2.10 / spark-parent_2.11
Author: Sean Owen <sowen@cloudera.com>
Closes#4912 from srowen/SPARK-6182.1 and squashes the following commits:
eff60de [Sean Owen] Convert spark-parent module name to spark-parent_2.10 / spark-parent_2.11
LBFGS and OWLQN in Breeze 0.10 has convergence check bug.
This is fixed in 0.11, see the description in Breeze project for detail:
https://github.com/scalanlp/breeze/pull/373#issuecomment-76879760
Author: Xiangrui Meng <meng@databricks.com>
Author: DB Tsai <dbtsai@alpinenow.com>
Author: DB Tsai <dbtsai@dbtsai.com>
Closes#4879 from dbtsai/breeze and squashes the following commits:
d848f65 [DB Tsai] Merge pull request #1 from mengxr/AlpineNow-breeze
c2ca6ac [Xiangrui Meng] upgrade to breeze-0.11.1
35c2f26 [Xiangrui Meng] fix LRSuite
397a208 [DB Tsai] upgrade breeze
Add single pseudo-eigenvector PIC
Including documentations and updated pom.xml with the following codes:
mllib/src/main/scala/org/apache/spark/mllib/clustering/PIClustering.scala
mllib/src/test/scala/org/apache/spark/mllib/clustering/PIClusteringSuite.scala
Author: sboeschhuawei <stephen.boesch@huawei.com>
Author: Fan Jiang <fanjiang.sc@huawei.com>
Author: Jiang Fan <fjiang6@gmail.com>
Author: Stephen Boesch <stephen.boesch@huawei.com>
Author: Xiangrui Meng <meng@databricks.com>
Closes#4254 from fjiang6/PIC and squashes the following commits:
4550850 [sboeschhuawei] Removed pic test data
f292f31 [Stephen Boesch] Merge pull request #44 from mengxr/SPARK-4259
4b78aaf [Xiangrui Meng] refactor PIC
24fbf52 [sboeschhuawei] Updated API to be similar to KMeans plus other changes requested by Xiangrui on the PR
c12dfc8 [sboeschhuawei] Removed examples files and added pic_data.txt. Revamped testcases yet to come
92d4752 [sboeschhuawei] Move the Guassian/ Affinity matrix calcs out of PIC. Presently in the test suite
7ebd149 [sboeschhuawei] Incorporate Xiangrui's first set of PR comments except restructure PIC.run to take Graph but do not remove Gaussian
121e4d5 [sboeschhuawei] Remove unused testing data files
1c3a62e [sboeschhuawei] removed matplot.py and reordered all private methods to bottom of PIC
218a49d [sboeschhuawei] Applied Xiangrui's comments - especially removing RDD/PICLinalg classes and making noncritical methods private
43ab10b [sboeschhuawei] Change last two println's to log4j logger
88aacc8 [sboeschhuawei] Add assert to testcase on cluster sizes
24f438e [sboeschhuawei] fixed incorrect markdown in clustering doc
060e6bf [sboeschhuawei] Added link to PIC doc from the main clustering md doc
be659e3 [sboeschhuawei] Added mllib specific log4j
90e7fa4 [sboeschhuawei] Converted from custom Linalg routines to Breeze: added JavaDoc comments; added Markdown documentation
bea48ea [sboeschhuawei] Converted custom Linear Algebra datatypes/routines to use Breeze.
b29c0db [Fan Jiang] Update PIClustering.scala
ace9749 [Fan Jiang] Update PIClustering.scala
a112f38 [sboeschhuawei] Added graphx main and test jars as dependencies to mllib/pom.xml
f656c34 [sboeschhuawei] Added iris dataset
b7dbcbe [sboeschhuawei] Added axes and combined into single plot for matplotlib
a2b1e57 [sboeschhuawei] Revert inadvertent update to KMeans
9294263 [sboeschhuawei] Added visualization/plotting of input/output data
e5df2b8 [sboeschhuawei] First end to end working PIC
0700335 [sboeschhuawei] First end to end working version: but has bad performance issue
32a90dc [sboeschhuawei] Update circles test data values
0ef163f [sboeschhuawei] Added ConcentricCircles data generation and KMeans clustering
3fd5bc8 [sboeschhuawei] PIClustering is running in new branch (up to the pseudo-eigenvector convergence step)
d5aae20 [Jiang Fan] Adding Power Iteration Clustering and Suite test
a3c5fbe [Jiang Fan] Adding Power Iteration Clustering
There is only a single `stat.py` file for the `mllib.stat` package. We recently added `MultivariateGaussian` under `mllib.stat.distribution` in Scala/Java. It would be nice to refactor `stat.py` and make it easy to expand. Note that `ChiSqTestResult` is moved from `mllib.stat` to `mllib.stat.test`. The latter is used in Scala/Java. It is only used in the return value of `Statistics.chiSqTest`, so this should be an okay change.
davies
Author: Xiangrui Meng <meng@databricks.com>
Closes#4266 from mengxr/py-stat-refactor and squashes the following commits:
1a5e1db [Xiangrui Meng] refactor stat.py
This PR adds Python API for ML pipeline and parameters. The design doc can be found on the JIRA page. It includes transformers and an estimator to demo the simple text classification example code.
TODO:
- [x] handle parameters in LRModel
- [x] unit tests
- [x] missing some docs
CC: davies jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Author: Davies Liu <davies@databricks.com>
Closes#4151 from mengxr/SPARK-4586 and squashes the following commits:
415268e [Xiangrui Meng] remove inherit_doc from __init__
edbd6fe [Xiangrui Meng] move Identifiable to ml.util
44c2405 [Xiangrui Meng] Merge pull request #2 from davies/ml
dd1256b [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-4586
14ae7e2 [Davies Liu] fix docs
54ca7df [Davies Liu] fix tests
78638df [Davies Liu] Merge branch 'SPARK-4586' of github.com:mengxr/spark into ml
fc59a02 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-4586
1dca16a [Davies Liu] refactor
090b3a3 [Davies Liu] Merge branch 'master' of github.com:apache/spark into ml
0882513 [Xiangrui Meng] update doc style
a4f4dbf [Xiangrui Meng] add unit test for LR
7521d1c [Xiangrui Meng] add unit tests to HashingTF and Tokenizer
ba0ba1e [Xiangrui Meng] add unit tests for pipeline
0586c7b [Xiangrui Meng] add more comments to the example
5153cff [Xiangrui Meng] simplify java models
036ca04 [Xiangrui Meng] gen numFeatures
46fa147 [Xiangrui Meng] update mllib/pom.xml to include python files in the assembly
1dcc17e [Xiangrui Meng] update code gen and make param appear in the doc
f66ba0c [Xiangrui Meng] make params a property
d5efd34 [Xiangrui Meng] update doc conf and move embedded param map to instance attribute
f4d0fe6 [Xiangrui Meng] use LabeledDocument and Document in example
05e3e40 [Xiangrui Meng] update example
d3e8dbe [Xiangrui Meng] more docs optimize pipeline.fit impl
56de571 [Xiangrui Meng] fix style
d0c5bb8 [Xiangrui Meng] a working copy
bce72f4 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-4586
17ecfb9 [Xiangrui Meng] code gen for shared params
d9ea77c [Xiangrui Meng] update doc
c18dca1 [Xiangrui Meng] make the example working
dadd84e [Xiangrui Meng] add base classes and docs
a3015cf [Xiangrui Meng] add Estimator and Transformer
46eea43 [Xiangrui Meng] a pipeline in python
33b68e0 [Xiangrui Meng] a working LR
This change does a few things to make the hadoop-provided profile more useful:
- Create new profiles for other libraries / services that might be provided by the infrastructure
- Simplify and fix the poms so that the profiles are only activated while building assemblies.
- Fix tests so that they're able to run when the profiles are activated
- Add a new env variable to be used by distributions that use these profiles to provide the runtime
classpath for Spark jobs and daemons.
Author: Marcelo Vanzin <vanzin@cloudera.com>
Closes#2982 from vanzin/SPARK-4048 and squashes the following commits:
82eb688 [Marcelo Vanzin] Add a comment.
eb228c0 [Marcelo Vanzin] Fix borked merge.
4e38f4e [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
9ef79a3 [Marcelo Vanzin] Alternative way to propagate test classpath to child processes.
371ebee [Marcelo Vanzin] Review feedback.
52f366d [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
83099fc [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
7377e7b [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
322f882 [Marcelo Vanzin] Fix merge fail.
f24e9e7 [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
8b00b6a [Marcelo Vanzin] Merge branch 'master' into SPARK-4048
9640503 [Marcelo Vanzin] Cleanup child process log message.
115fde5 [Marcelo Vanzin] Simplify a comment (and make it consistent with another pom).
e3ab2da [Marcelo Vanzin] Fix hive-thriftserver profile.
7820d58 [Marcelo Vanzin] Fix CliSuite with provided profiles.
1be73d4 [Marcelo Vanzin] Restore flume-provided profile.
d1399ed [Marcelo Vanzin] Restore jetty dependency.
82a54b9 [Marcelo Vanzin] Remove unused profile.
5c54a25 [Marcelo Vanzin] Fix HiveThriftServer2Suite with *-provided profiles.
1fc4d0b [Marcelo Vanzin] Update dependencies for hive-thriftserver.
f7b3bbe [Marcelo Vanzin] Add snappy to hadoop-provided list.
9e4e001 [Marcelo Vanzin] Remove duplicate hive profile.
d928d62 [Marcelo Vanzin] Redirect child stderr to parent's log.
4d67469 [Marcelo Vanzin] Propagate SPARK_DIST_CLASSPATH on Yarn.
417d90e [Marcelo Vanzin] Introduce "SPARK_DIST_CLASSPATH".
2f95f0d [Marcelo Vanzin] Propagate classpath to child processes during testing.
1adf91c [Marcelo Vanzin] Re-enable maven-install-plugin for a few projects.
284dda6 [Marcelo Vanzin] Rework the "hadoop-provided" profile, add new ones.
This PR:
- Reenables `surefire`, and copies config from `scalatest` (which is itself an old fork of `surefire`, so similar)
- Tells `surefire` to test only Java tests
- Enables `surefire` and `scalatest` for all children, and in turn eliminates some duplication.
For me this causes the Scala and Java tests to be run once each, it seems, as desired. It doesn't affect the SBT build but works for Maven. I still need to verify that all of the Scala tests and Java tests are being run.
Author: Sean Owen <sowen@cloudera.com>
Closes#3651 from srowen/SPARK-4159 and squashes the following commits:
2e8a0af [Sean Owen] Remove specialized SPARK_HOME setting for REPL, YARN tests as it appears to be obsolete
12e4558 [Sean Owen] Append to unit-test.log instead of overwriting, so that both surefire and scalatest output is preserved. Also standardize/correct comments a bit.
e6f8601 [Sean Owen] Reenable Java tests by reenabling surefire with config cloned from scalatest; centralize test config in the parent
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.
This PR adds package "org.apache.spark.ml" with pipeline and parameters, as discussed on the JIRA. This is a joint work of jkbradley etrain shivaram and many others who helped on the design, also with help from marmbrus and liancheng on the Spark SQL side. The design doc can be found at:
https://docs.google.com/document/d/1rVwXRjWKfIb-7PI6b86ipytwbUH7irSNLF1_6dLmh8o/edit?usp=sharing
**org.apache.spark.ml**
This is a new package with new set of ML APIs that address practical machine learning pipelines. (Sorry for taking so long!) It will be an alpha component, so this is definitely not something set in stone. The new set of APIs, inspired by the MLI project from AMPLab and scikit-learn, takes leverage on Spark SQL's schema support and execution plan optimization. It introduces the following components that help build a practical pipeline:
1. Transformer, which transforms a dataset into another
2. Estimator, which fits models to data, where models are transformers
3. Evaluator, which evaluates model output and returns a scalar metric
4. Pipeline, a simple pipeline that consists of transformers and estimators
Parameters could be supplied at fit/transform or embedded with components.
1. Param: a strong-typed parameter key with self-contained doc
2. ParamMap: a param -> value map
3. Params: trait for components with parameters
For any component that implements `Params`, user can easily check the doc by calling `explainParams`:
~~~
> val lr = new LogisticRegression
> lr.explainParams
maxIter: max number of iterations (default: 100)
regParam: regularization constant (default: 0.1)
labelCol: label column name (default: label)
featuresCol: features column name (default: features)
~~~
or user can check individual param:
~~~
> lr.maxIter
maxIter: max number of iterations (default: 100)
~~~
**Please start with the example code in test suites and under `org.apache.spark.examples.ml`, where I put several examples:**
1. run a simple logistic regression job
~~~
val lr = new LogisticRegression()
.setMaxIter(10)
.setRegParam(1.0)
val model = lr.fit(dataset)
model.transform(dataset, model.threshold -> 0.8) // overwrite threshold
.select('label, 'score, 'prediction).collect()
.foreach(println)
~~~
2. run logistic regression with cross-validation and grid search using areaUnderROC (default) as the metric
~~~
val lr = new LogisticRegression
val lrParamMaps = new ParamGridBuilder()
.addGrid(lr.regParam, Array(0.1, 100.0))
.addGrid(lr.maxIter, Array(0, 5))
.build()
val eval = new BinaryClassificationEvaluator
val cv = new CrossValidator()
.setEstimator(lr)
.setEstimatorParamMaps(lrParamMaps)
.setEvaluator(eval)
.setNumFolds(3)
val bestModel = cv.fit(dataset)
~~~
3. run a pipeline that consists of a standard scaler and a logistic regression component
~~~
val scaler = new StandardScaler()
.setInputCol("features")
.setOutputCol("scaledFeatures")
val lr = new LogisticRegression()
.setFeaturesCol(scaler.getOutputCol)
val pipeline = new Pipeline()
.setStages(Array(scaler, lr))
val model = pipeline.fit(dataset)
val predictions = model.transform(dataset)
.select('label, 'score, 'prediction)
.collect()
.foreach(println)
~~~
4. a simple text classification pipeline, which recognizes "spark":
~~~
val training = sparkContext.parallelize(Seq(
LabeledDocument(0L, "a b c d e spark", 1.0),
LabeledDocument(1L, "b d", 0.0),
LabeledDocument(2L, "spark f g h", 1.0),
LabeledDocument(3L, "hadoop mapreduce", 0.0)))
val tokenizer = new Tokenizer()
.setInputCol("text")
.setOutputCol("words")
val hashingTF = new HashingTF()
.setInputCol(tokenizer.getOutputCol)
.setOutputCol("features")
val lr = new LogisticRegression()
.setMaxIter(10)
val pipeline = new Pipeline()
.setStages(Array(tokenizer, hashingTF, lr))
val model = pipeline.fit(training)
val test = sparkContext.parallelize(Seq(
Document(4L, "spark i j k"),
Document(5L, "l m"),
Document(6L, "mapreduce spark"),
Document(7L, "apache hadoop")))
model.transform(test)
.select('id, 'text, 'prediction, 'score)
.collect()
.foreach(println)
~~~
Java examples are very similar. I put example code that creates a simple text classification pipeline in Scala and Java, where a simple tokenizer is defined as a transformer outside `org.apache.spark.ml`.
**What are missing now and will be added soon:**
1. ~~Runtime check of schemas. So before we touch the data, we will go through the schema and make sure column names and types match the input parameters.~~
2. ~~Java examples.~~
3. ~~Store training parameters in trained models.~~
4. (later) Serialization and Python API.
Author: Xiangrui Meng <meng@databricks.com>
Closes#3099 from mengxr/SPARK-3530 and squashes the following commits:
2cc93fd [Xiangrui Meng] hide APIs as much as I can
34319ba [Xiangrui Meng] use local instead local[2] for unit tests
2524251 [Xiangrui Meng] rename PipelineStage.transform to transformSchema
c9daab4 [Xiangrui Meng] remove mockito version
1397ab5 [Xiangrui Meng] use sqlContext from LocalSparkContext instead of TestSQLContext
6ffc389 [Xiangrui Meng] try to fix unit test
a59d8b7 [Xiangrui Meng] doc updates
977fd9d [Xiangrui Meng] add scala ml package object
6d97fe6 [Xiangrui Meng] add AlphaComponent annotation
731f0e4 [Xiangrui Meng] update package doc
0435076 [Xiangrui Meng] remove ;this from setters
fa21d9b [Xiangrui Meng] update extends indentation
f1091b3 [Xiangrui Meng] typo
228a9f4 [Xiangrui Meng] do not persist before calling binary classification metrics
f51cd27 [Xiangrui Meng] rename default to defaultValue
b3be094 [Xiangrui Meng] refactor schema transform in lr
8791e8e [Xiangrui Meng] rename copyValues to inheritValues and make it do the right thing
51f1c06 [Xiangrui Meng] remove leftover code in Transformer
494b632 [Xiangrui Meng] compure score once
ad678e9 [Xiangrui Meng] more doc for Transformer
4306ed4 [Xiangrui Meng] org imports in text pipeline
6e7c1c7 [Xiangrui Meng] update pipeline
4f9e34f [Xiangrui Meng] more doc for pipeline
aa5dbd4 [Xiangrui Meng] fix typo
11be383 [Xiangrui Meng] fix unit tests
3df7952 [Xiangrui Meng] clean up
986593e [Xiangrui Meng] re-org java test suites
2b11211 [Xiangrui Meng] remove external data deps
9fd4933 [Xiangrui Meng] add unit test for pipeline
2a0df46 [Xiangrui Meng] update tests
2d52e4d [Xiangrui Meng] add @AlphaComponent to package-info
27582a4 [Xiangrui Meng] doc changes
73a000b [Xiangrui Meng] add schema transformation layer
6736e87 [Xiangrui Meng] more doc / remove HasMetricName trait
80a8b5e [Xiangrui Meng] rename SimpleTransformer to UnaryTransformer
62ca2bb [Xiangrui Meng] check param parent in set/get
1622349 [Xiangrui Meng] add getModel to PipelineModel
a0e0054 [Xiangrui Meng] update StandardScaler to use SimpleTransformer
d0faa04 [Xiangrui Meng] remove implicit mapping from ParamMap
c7f6921 [Xiangrui Meng] move ParamGridBuilder test to ParamGridBuilderSuite
e246f29 [Xiangrui Meng] re-org:
7772430 [Xiangrui Meng] remove modelParams add a simple text classification pipeline
b95c408 [Xiangrui Meng] remove implicits add unit tests to params
bab3e5b [Xiangrui Meng] update params
fe0ee92 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-3530
6e86d98 [Xiangrui Meng] some code clean-up
2d040b3 [Xiangrui Meng] implement setters inside each class, add Params.copyValues [ci skip]
fd751fc [Xiangrui Meng] add java-friendly versions of fit and tranform
3f810cd [Xiangrui Meng] use multi-model training api in cv
5b8f413 [Xiangrui Meng] rename model to modelParams
9d2d35d [Xiangrui Meng] test varargs and chain model params
f46e927 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into SPARK-3530
1ef26e0 [Xiangrui Meng] specialize methods/types for Java
df293ed [Xiangrui Meng] switch to setter/getter
376db0a [Xiangrui Meng] pipeline and parameters
Register MLlib's Vector as a SQL user-defined type (UDT) in both Scala and Python. With this PR, we can easily map a RDD[LabeledPoint] to a SchemaRDD, and then select columns or save to a Parquet file. Examples in Scala/Python are attached. The Scala code was copied from jkbradley.
~~This PR contains the changes from #3068 . I will rebase after #3068 is merged.~~
marmbrus jkbradley
Author: Xiangrui Meng <meng@databricks.com>
Closes#3070 from mengxr/SPARK-3573 and squashes the following commits:
3a0b6e5 [Xiangrui Meng] organize imports
236f0a0 [Xiangrui Meng] register vector as UDT and provide dataset examples
In #2928 , we shade commons-math3 to prevent future conflicts with hadoop. It caused problems with our Jenkins master build with maven. Some tests used local-cluster mode, where the assembly jar contains relocated math3 classes, while mllib test code still compiles with core and the untouched math3 classes.
This PR sets commons-math3 version based on hadoop profiles.
pwendell JoshRosen srowen
Author: Xiangrui Meng <meng@databricks.com>
Closes#3023 from mengxr/SPARK-4121-alt and squashes the following commits:
580f6d9 [Xiangrui Meng] replace tab by spaces
7f71f08 [Xiangrui Meng] revert changes to PoissonSampler to avoid conflicts
d3353d9 [Xiangrui Meng] do not shade commons-math3
b4180dc [Xiangrui Meng] temp work
This change replaces usages of colt with commons-math3 equivalents, and makes some minor necessary adjustments to related code and tests to match.
Author: Sean Owen <sowen@cloudera.com>
Closes#2928 from srowen/SPARK-4022 and squashes the following commits:
61a232f [Sean Owen] Fix failure due to different sampling in JavaAPISuite.sample()
16d66b8 [Sean Owen] Simplify seeding with call to reseedRandomGenerator
a1a78e0 [Sean Owen] Use Well19937c
31c7641 [Sean Owen] Fix Python Poisson test by choosing a different seed; about 88% of seeds should work but 1 didn't, it seems
5c9c67f [Sean Owen] Additional test fixes from review
d8f88e0 [Sean Owen] Replace colt with commons-math3. Some tests do not pass yet.
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.
2570911026
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. 2570911026
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
Refactored tests for streaming linear regression to use existing streaming test utilities. Summary of changes:
- Made ``mllib`` depend on tests from ``streaming``
- Rewrote accuracy and convergence tests to use ``setupStreams`` and ``runStreams``
- Added new test for the accuracy of predictions generated by ``predictOnValue``
These tests should run faster, be easier to extend/maintain, and provide a reference for new tests.
mengxr tdas
Author: freeman <the.freeman.lab@gmail.com>
Closes#2037 from freeman-lab/streamingLR-predict-tests and squashes the following commits:
e851ca7 [freeman] Fixed long lines
50eb0bf [freeman] Refactored tests to use streaming test tools
32c43c2 [freeman] Added test for prediction
