### What changes were proposed in this pull request?
Add training summary for FMClassificationModel...
### Why are the changes needed?
so that user can get the training process status, such as loss value of each iteration and total iteration number.
### Does this PR introduce _any_ user-facing change?
Yes
FMClassificationModel.summary
FMClassificationModel.evaluate
### How was this patch tested?
new tests
Closes#28960 from huaxingao/fm_summary.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Huaxin Gao <huaxing@us.ibm.com>
### What changes were proposed in this pull request?
This PR aims to drop Python 2.7, 3.4 and 3.5.
Roughly speaking, it removes all the widely known Python 2 compatibility workarounds such as `sys.version` comparison, `__future__`. Also, it removes the Python 2 dedicated codes such as `ArrayConstructor` in Spark.
### Why are the changes needed?
1. Unsupport EOL Python versions
2. Reduce maintenance overhead and remove a bit of legacy codes and hacks for Python 2.
3. PyPy2 has a critical bug that causes a flaky test, SPARK-28358 given my testing and investigation.
4. Users can use Python type hints with Pandas UDFs without thinking about Python version
5. Users can leverage one latest cloudpickle, https://github.com/apache/spark/pull/28950. With Python 3.8+ it can also leverage C pickle.
### Does this PR introduce _any_ user-facing change?
Yes, users cannot use Python 2.7, 3.4 and 3.5 in the upcoming Spark version.
### How was this patch tested?
Manually tested and also tested in Jenkins.
Closes#28957 from HyukjinKwon/SPARK-32138.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
# What changes were proposed in this pull request?
current problems:
```
mlp = MultilayerPerceptronClassifier(layers=[2, 2, 2], seed=123)
model = mlp.fit(df)
path = tempfile.mkdtemp()
model_path = path + "/mlp"
model.save(model_path)
model2 = MultilayerPerceptronClassificationModel.load(model_path)
self.assertEqual(model2.getSolver(), "l-bfgs") # this fails because model2.getSolver() returns 'auto'
model2.transform(df)
# this fails with Exception pyspark.sql.utils.IllegalArgumentException: MultilayerPerceptronClassifier_dec859ed24ec parameter solver given invalid value auto.
```
FMClassifier/Regression and GeneralizedLinearRegression have the same problems.
Here are the root cause of the problems:
1. In HasSolver, both Scala and Python default solver to 'auto'
2. On Scala side, mlp overrides the default of solver to 'l-bfgs', FMClassifier/Regression overrides the default of solver to 'adamW', and glr overrides the default of solver to 'irls'
3. On Scala side, mlp overrides the default of solver in MultilayerPerceptronClassificationParams, so both MultilayerPerceptronClassification and MultilayerPerceptronClassificationModel have 'l-bfgs' as default
4. On Python side, mlp overrides the default of solver in MultilayerPerceptronClassification, so it has default as 'l-bfgs', but MultilayerPerceptronClassificationModel doesn't override the default so it gets the default from HasSolver which is 'auto'. In theory, we don't care about the solver value or any other params values for MultilayerPerceptronClassificationModel, because we have the fitted model already. That's why on Python side, we never set default values for any of the XXXModel.
5. when calling getSolver on the loaded mlp model, it calls this line of code underneath:
```
def _transfer_params_from_java(self):
"""
Transforms the embedded params from the companion Java object.
"""
......
# SPARK-14931: Only check set params back to avoid default params mismatch.
if self._java_obj.isSet(java_param):
value = _java2py(sc, self._java_obj.getOrDefault(java_param))
self._set(**{param.name: value})
......
```
that's why model2.getSolver() returns 'auto'. The code doesn't get the default Scala value (in this case 'l-bfgs') to set to Python param, so it takes the default value (in this case 'auto') on Python side.
6. when calling model2.transform(df), it calls this underneath:
```
def _transfer_params_to_java(self):
"""
Transforms the embedded params to the companion Java object.
"""
......
if self.hasDefault(param):
pair = self._make_java_param_pair(param, self._defaultParamMap[param])
pair_defaults.append(pair)
......
```
Again, it gets the Python default solver which is 'auto', and this caused the Exception
7. Currently, on Scala side, for some of the algorithms, we set default values in the XXXParam, so both estimator and transformer get the default value. However, for some of the algorithms, we only set default in estimators, and the XXXModel doesn't get the default value. On Python side, we never set defaults for the XXXModel. This causes the default value inconsistency.
8. My proposed solution: set default params in XXXParam for both Scala and Python, so both the estimator and transformer have the same default value for both Scala and Python. I currently only changed solver in this PR. If everyone is OK with the fix, I will change all the other params as well.
I hope my explanation makes sense to your folks :)
### Why are the changes needed?
Fix bug
### Does this PR introduce _any_ user-facing change?
No
### How was this patch tested?
existing and new tests
Closes#29060 from huaxingao/solver_parity.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
### What changes were proposed in this pull request?
Add summary to RandomForestClassificationModel...
### Why are the changes needed?
so user can get a summary of this classification model, and retrieve common metrics such as accuracy, weightedTruePositiveRate, roc (for binary), pr curves (for binary), etc.
### Does this PR introduce _any_ user-facing change?
Yes
```
RandomForestClassificationModel.summary
RandomForestClassificationModel.evaluate
```
### How was this patch tested?
Add new tests
Closes#28913 from huaxingao/rf_summary.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
### What changes were proposed in this pull request?
Add training summary for LinearSVCModel......
### Why are the changes needed?
so that user can get the training process status, such as loss value of each iteration and total iteration number.
### Does this PR introduce _any_ user-facing change?
Yes
```LinearSVCModel.summary```
```LinearSVCModel.evaluate```
### How was this patch tested?
new tests
Closes#28884 from huaxingao/svc_summary.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
### What changes were proposed in this pull request?
Adding support to Association Rules in Spark ml.fpm.
### Why are the changes needed?
Support is an indication of how frequently the itemset of an association rule appears in the database and suggests if the rules are generally applicable to the dateset. Refer to [wiki](https://en.wikipedia.org/wiki/Association_rule_learning#Support) for more details.
### Does this PR introduce _any_ user-facing change?
Yes. Associate Rules now have support measure
### How was this patch tested?
existing and new unit test
Closes#28903 from huaxingao/fpm.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
### What changes were proposed in this pull request?
This patch adds user-specified fold column support to `CrossValidator`. User can assign fold numbers to dataset instead of letting Spark do random splits.
### Why are the changes needed?
This gives `CrossValidator` users more flexibility in splitting folds.
### Does this PR introduce _any_ user-facing change?
Yes, a new `foldCol` param is added to `CrossValidator`. User can use it to specify custom fold splitting.
### How was this patch tested?
Added unit tests.
Closes#28704 from viirya/SPARK-31777.
Authored-by: Liang-Chi Hsieh <viirya@gmail.com>
Signed-off-by: Liang-Chi Hsieh <liangchi@uber.com>
### What changes were proposed in this pull request?
In LogisticRegression and LinearRegression, if set maxIter=n, the model.summary.totalIterations returns n+1 if the training procedure does not drop out. This is because we use ```objectiveHistory.length``` as totalIterations, but ```objectiveHistory``` contains init sate, thus ```objectiveHistory.length``` is 1 larger than number of training iterations.
### Why are the changes needed?
correctness
### Does this PR introduce _any_ user-facing change?
No
### How was this patch tested?
add new tests and also modify existing tests
Closes#28786 from huaxingao/summary_iter.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
### What changes were proposed in this pull request?
Return LogisticRegressionSummary for multiclass logistic regression evaluate in PySpark
### Why are the changes needed?
Currently we have
```
since("2.0.0")
def evaluate(self, dataset):
if not isinstance(dataset, DataFrame):
raise ValueError("dataset must be a DataFrame but got %s." % type(dataset))
java_blr_summary = self._call_java("evaluate", dataset)
return BinaryLogisticRegressionSummary(java_blr_summary)
```
we should return LogisticRegressionSummary for multiclass logistic regression
### Does this PR introduce _any_ user-facing change?
Yes
return LogisticRegressionSummary instead of BinaryLogisticRegressionSummary for multiclass logistic regression in Python
### How was this patch tested?
unit test
Closes#28503 from huaxingao/lr_summary.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
### What changes were proposed in this pull request?
Add ANOVASelector and FValueSelector to PySpark
### Why are the changes needed?
ANOVASelector and FValueSelector have been implemented in Scala. We need to implement these in Python as well.
### Does this PR introduce _any_ user-facing change?
Yes. Add Python version of ANOVASelector and FValueSelector
### How was this patch tested?
new doctest
Closes#28464 from huaxingao/selector_py.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
Fix Pyspark CrossValidator/TrainValidationSplit with pipeline estimator cannot save and load model.
Most pyspark estimators/transformers inherit `JavaParams`, but some estimators are special (in order to support pure python implemented nested estimators/transformers):
* Pipeline
* OneVsRest
* CrossValidator
* TrainValidationSplit
But note that, currently, in pyspark, estimators listed above, their model reader/writer do NOT support pure python implemented nested estimators/transformers. Because they use java reader/writer wrapper as python side reader/writer.
Pyspark CrossValidator/TrainValidationSplit model reader/writer require all estimators define the `_transfer_param_map_to_java` and `_transfer_param_map_from_java` (used in model read/write).
OneVsRest class already defines the two methods, but Pipeline do not, so it lead to this bug.
In this PR I add `_transfer_param_map_to_java` and `_transfer_param_map_from_java` into Pipeline class.
### Why are the changes needed?
Bug fix.
### Does this PR introduce any user-facing change?
No
### How was this patch tested?
Unit test.
Manually test in pyspark shell:
1) CrossValidator with Simple Pipeline estimator
```
from pyspark.ml import Pipeline
from pyspark.ml.classification import LogisticRegression
from pyspark.ml.evaluation import BinaryClassificationEvaluator
from pyspark.ml.feature import HashingTF, Tokenizer
from pyspark.ml.tuning import CrossValidator, CrossValidatorModel, ParamGridBuilder
training = spark.createDataFrame([
(0, "a b c d e spark", 1.0),
(1, "b d", 0.0),
(2, "spark f g h", 1.0),
(3, "hadoop mapreduce", 0.0),
(4, "b spark who", 1.0),
(5, "g d a y", 0.0),
(6, "spark fly", 1.0),
(7, "was mapreduce", 0.0),
], ["id", "text", "label"])
# Configure an ML pipeline, which consists of tree stages: tokenizer, hashingTF, and lr.
tokenizer = Tokenizer(inputCol="text", outputCol="words")
hashingTF = HashingTF(inputCol=tokenizer.getOutputCol(), outputCol="features")
lr = LogisticRegression(maxIter=10)
pipeline = Pipeline(stages=[tokenizer, hashingTF, lr])
paramGrid = ParamGridBuilder() \
.addGrid(hashingTF.numFeatures, [10, 100, 1000]) \
.addGrid(lr.regParam, [0.1, 0.01]) \
.build()
crossval = CrossValidator(estimator=pipeline,
estimatorParamMaps=paramGrid,
evaluator=BinaryClassificationEvaluator(),
numFolds=2) # use 3+ folds in practice
# Run cross-validation, and choose the best set of parameters.
cvModel = crossval.fit(training)
cvModel.save('/tmp/cv_model001')
CrossValidatorModel.load('/tmp/cv_model001')
```
2) CrossValidator with Pipeline estimator which include a OneVsRest estimator stage, and OneVsRest estimator nest a LogisticRegression estimator.
```
from pyspark.ml.linalg import Vectors
from pyspark.ml import Estimator, Model
from pyspark.ml.classification import LogisticRegression, LogisticRegressionModel, OneVsRest
from pyspark.ml.evaluation import BinaryClassificationEvaluator, \
MulticlassClassificationEvaluator, RegressionEvaluator
from pyspark.ml.linalg import Vectors
from pyspark.ml.param import Param, Params
from pyspark.ml.tuning import CrossValidator, CrossValidatorModel, ParamGridBuilder, \
TrainValidationSplit, TrainValidationSplitModel
from pyspark.sql.functions import rand
from pyspark.testing.mlutils import SparkSessionTestCase
dataset = spark.createDataFrame(
[(Vectors.dense([0.0]), 0.0),
(Vectors.dense([0.4]), 1.0),
(Vectors.dense([0.5]), 0.0),
(Vectors.dense([0.6]), 1.0),
(Vectors.dense([1.0]), 1.0)] * 10,
["features", "label"])
ova = OneVsRest(classifier=LogisticRegression())
lr1 = LogisticRegression().setMaxIter(100)
lr2 = LogisticRegression().setMaxIter(150)
grid = ParamGridBuilder().addGrid(ova.classifier, [lr1, lr2]).build()
evaluator = MulticlassClassificationEvaluator()
pipeline = Pipeline(stages=[ova])
cv = CrossValidator(estimator=pipeline, estimatorParamMaps=grid, evaluator=evaluator)
cvModel = cv.fit(dataset)
cvModel.save('/tmp/model002')
cvModel2 = CrossValidatorModel.load('/tmp/model002')
```
TrainValidationSplit testing code are similar so I do not paste them.
Closes#28279 from WeichenXu123/fix_pipeline_tuning.
Authored-by: Weichen Xu <weichen.xu@databricks.com>
Signed-off-by: Xiangrui Meng <meng@databricks.com>
### What changes were proposed in this pull request?
Implement common base ML classes (`Predictor`, `PredictionModel`, `Classifier`, `ClasssificationModel` `ProbabilisticClassifier`, `ProbabilisticClasssificationModel`, `Regressor`, `RegrssionModel`) for non-Java backends.
Note
- `Predictor` and `JavaClassifier` should be abstract as `_fit` method is not implemented.
- `PredictionModel` should be abstract as `_transform` is not implemented.
### Why are the changes needed?
To provide extensions points for non-JVM algorithms, as well as a public (as opposed to `Java*` variants, which are commonly described in docstrings as private) hierarchy which can be used to distinguish between different classes of predictors.
For longer discussion see [SPARK-29212](https://issues.apache.org/jira/browse/SPARK-29212) and / or https://github.com/apache/spark/pull/25776.
### Does this PR introduce any user-facing change?
It adds new base classes as listed above, but effective interfaces (method resolution order notwithstanding) stay the same.
Additionally "private" `Java*` classes in`ml.regression` and `ml.classification` have been renamed to follow PEP-8 conventions (added leading underscore).
It is for discussion if the same should be done to equivalent classes from `ml.wrapper`.
If we take `JavaClassifier` as an example, type hierarchy will change from
to
Similarly the old model
will become
### How was this patch tested?
Existing unit tests.
Closes#27245 from zero323/SPARK-29212.
Authored-by: zero323 <mszymkiewicz@gmail.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
Change ```DecisionTreeClassifier``` to ```FMClassifier``` in ```OneVsRest``` setWeightCol test
### Why are the changes needed?
In ```OneVsRest```, if the classifier doesn't support instance weight, ```OneVsRest``` weightCol will be ignored, so unit test has tested one classifier(```LogisticRegression```) that support instance weight, and one classifier (```DecisionTreeClassifier```) that doesn't support instance weight. Since ```DecisionTreeClassifier``` now supports instance weight, we need to change it to the classifier that doesn't have weight support.
### Does this PR introduce any user-facing change?
No
### How was this patch tested?
Existing test
Closes#27204 from huaxingao/spark-ovr-minor.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
This PR adjusts `_to_java` and `_from_java` of `OneVsRest` and `OneVsRestModel` to preserve `weightCol`.
### Why are the changes needed?
Currently both `Params` don't preserve `weightCol` `Params` when data is saved / loaded:
```python
from pyspark.ml.classification import LogisticRegression, OneVsRest, OneVsRestModel
from pyspark.ml.linalg import DenseVector
df = spark.createDataFrame([(0, 1, DenseVector([1.0, 0.0])), (0, 1, DenseVector([1.0, 0.0]))], ("label", "w", "features"))
ovr = OneVsRest(classifier=LogisticRegression()).setWeightCol("w")
ovrm = ovr.fit(df)
ovr.getWeightCol()
## 'w'
ovrm.getWeightCol()
## 'w'
ovr.write().overwrite().save("/tmp/ovr")
ovr_ = OneVsRest.load("/tmp/ovr")
ovr_.getWeightCol()
## KeyError
## ...
## KeyError: Param(parent='OneVsRest_5145d56b6bd1', name='weightCol', doc='weight column name. ...)
ovrm.write().overwrite().save("/tmp/ovrm")
ovrm_ = OneVsRestModel.load("/tmp/ovrm")
ovrm_ .getWeightCol()
## KeyError
## ...
## KeyError: Param(parent='OneVsRestModel_598c6d900fad', name='weightCol', doc='weight column name ...
```
### Does this PR introduce any user-facing change?
After this PR is merged, loaded objects will have `weightCol` `Param` set.
### How was this patch tested?
- Manual testing.
- Extension of existing persistence tests.
Closes#27190 from zero323/SPARK-30504.
Authored-by: zero323 <mszymkiewicz@gmail.com>
Signed-off-by: Sean Owen <srowen@gmail.com>
modify Param._copyValues to check valid Param objects supplied as extra
### What changes were proposed in this pull request?
Estimator.fit() and Model.transform() accept a dictionary of extra parameters whose values are used to overwrite those supplied at initialization or by default. Additionally, the ParamGridBuilder.addGrid accepts a parameter and list of values. The keys are presumed to be valid Param objects. This change adds a check that only Param objects are supplied as keys.
### Why are the changes needed?
Param objects are created by and bound to an instance of Params (Estimator, Model, or Transformer). They may be obtained from their parent as attributes, or by name through getParam.
The documentation does not state that keys must be valid Param objects, nor describe how one may be obtained. The current behavior is to silently ignore keys which are not valid Param objects.
### Does this PR introduce any user-facing change?
If the user does not pass in a Param object as required for keys in `extra` for Estimator.fit() and Model.transform(), and `param` for ParamGridBuilder.addGrid, an error will be raised indicating it is an invalid object.
### How was this patch tested?
Added method test_copy_param_extras_check to test_param.py. Tested with Python 3.7
Closes#26527 from JohnHBauer/paramExtra.
Authored-by: John Bauer <john.h.bauer@gmail.com>
Signed-off-by: Bryan Cutler <cutlerb@gmail.com>
## What changes were proposed in this pull request?
This PR proposes to add **Single threading model design (pinned thread model)** mode which is an experimental mode to sync threads on PVM and JVM. See https://www.py4j.org/advanced_topics.html#using-single-threading-model-pinned-thread
### Multi threading model
Currently, PySpark uses this model. Threads on PVM and JVM are independent. For instance, in a different Python thread, callbacks are received and relevant Python codes are executed. JVM threads are reused when possible.
Py4J will create a new thread every time a command is received and there is no thread available. See the current model we're using - https://www.py4j.org/advanced_topics.html#the-multi-threading-model
One problem in this model is that we can't sync threads on PVM and JVM out of the box. This leads to some problems in particular at some codes related to threading in JVM side. See:
7056e004ee/core/src/main/scala/org/apache/spark/SparkContext.scala (L334)
Due to reusing JVM threads, seems the job groups in Python threads cannot be set in each thread as described in the JIRA.
### Single threading model design (pinned thread model)
This mode pins and syncs the threads on PVM and JVM to work around the problem above. For instance, in the same Python thread, callbacks are received and relevant Python codes are executed. See https://www.py4j.org/advanced_topics.html#the-single-threading-model
Even though this mode can sync threads on PVM and JVM for other thread related code paths,
this might cause another problem: seems unable to inherit properties as below (assuming multi-thread mode still creates new threads when existing threads are busy, I suspect this issue already exists when multiple jobs are submitted in multi-thread mode; however, it can be always seen in single threading mode):
```bash
$ PYSPARK_PIN_THREAD=true ./bin/pyspark
```
```python
import threading
spark.sparkContext.setLocalProperty("a", "hi")
def print_prop():
print(spark.sparkContext.getLocalProperty("a"))
threading.Thread(target=print_prop).start()
```
```
None
```
Unlike Scala side:
```scala
spark.sparkContext.setLocalProperty("a", "hi")
new Thread(new Runnable {
def run() = println(spark.sparkContext.getLocalProperty("a"))
}).start()
```
```
hi
```
This behaviour potentially could cause weird issues but this PR currently does not target this fix this for now since this mode is experimental.
### How does this PR fix?
Basically there are two types of Py4J servers `GatewayServer` and `ClientServer`. The former is for multi threading and the latter is for single threading. This PR adds a switch to use the latter.
In Scala side:
The logic to select a server is encapsulated in `Py4JServer` and use `Py4JServer` at `PythonRunner` for Spark summit and `PythonGatewayServer` for Spark shell. Each uses `ClientServer` when `PYSPARK_PIN_THREAD` is `true` and `GatewayServer` otherwise.
In Python side:
Simply do an if-else to switch the server to talk. It uses `ClientServer` when `PYSPARK_PIN_THREAD` is `true` and `GatewayServer` otherwise.
This is disabled by default for now.
## How was this patch tested?
Manually tested. This can be tested via:
```python
PYSPARK_PIN_THREAD=true ./bin/pyspark
```
and/or
```bash
cd python
./run-tests --python-executables=python --testnames "pyspark.tests.test_pin_thread"
```
Also, ran the Jenkins tests with `PYSPARK_PIN_THREAD` enabled.
Closes#24898 from HyukjinKwon/pinned-thread.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
### What changes were proposed in this pull request?
Remove automatically generated param setters in _shared_params_code_gen.py
### Why are the changes needed?
To keep parity between scala and python
### Does this PR introduce any user-facing change?
Yes
Add some setters in Python ML XXXModels
### How was this patch tested?
unit tests
Closes#26232 from huaxingao/spark-29093.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
change PySpark ml ```Params._clear``` to ```Params.clear```
### Why are the changes needed?
PySpark ML currently has a private _clear() method that will unset a param. This should be made public to match the Scala API and give users a way to unset a user supplied param.
### Does this PR introduce any user-facing change?
Yes. PySpark ml ```Params._clear``` ---> ```Params.clear```
### How was this patch tested?
Add test.
Closes#26130 from huaxingao/spark-29464.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Bryan Cutler <cutlerb@gmail.com>
### What changes were proposed in this pull request?
Binarizer support multi-column by extending `HasInputCols`/`HasOutputCols`/`HasThreshold`/`HasThresholds`
### Why are the changes needed?
similar algs in `ml.feature` already support multi-column, like `Bucketizer`/`StringIndexer`/`QuantileDiscretizer`
### Does this PR introduce any user-facing change?
yes, add setter/getter of `thresholds`/`inputCols`/`outputCols`
### How was this patch tested?
added suites
Closes#26064 from zhengruifeng/binarizer_multicols.
Authored-by: zhengruifeng <ruifengz@foxmail.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
add column setters/getters support in Pyspark feature models
### Why are the changes needed?
keep parity between Pyspark and Scala
### Does this PR introduce any user-facing change?
Yes.
After the change, Pyspark feature models have column setters/getters support.
### How was this patch tested?
Add some doctests
Closes#25908 from huaxingao/spark-29143.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
### What changes were proposed in this pull request?
Add some common classes in Python to make it have the same structure as Scala
1. Scala has ClassifierParams/Classifier/ClassificationModel:
```
trait ClassifierParams
extends PredictorParams with HasRawPredictionCol
abstract class Classifier
extends Predictor with ClassifierParams {
def setRawPredictionCol
}
abstract class ClassificationModel
extends PredictionModel with ClassifierParams {
def setRawPredictionCol
}
```
This PR makes Python has the following:
```
class JavaClassifierParams(HasRawPredictionCol, JavaPredictorParams):
pass
class JavaClassifier(JavaPredictor, JavaClassifierParams):
def setRawPredictionCol
class JavaClassificationModel(JavaPredictionModel, JavaClassifierParams):
def setRawPredictionCol
```
2. Scala has ProbabilisticClassifierParams/ProbabilisticClassifier/ProbabilisticClassificationModel:
```
trait ProbabilisticClassifierParams
extends ClassifierParams with HasProbabilityCol with HasThresholds
abstract class ProbabilisticClassifier
extends Classifier with ProbabilisticClassifierParams {
def setProbabilityCol
def setThresholds
}
abstract class ProbabilisticClassificationModel
extends ClassificationModel with ProbabilisticClassifierParams {
def setProbabilityCol
def setThresholds
}
```
This PR makes Python have the following:
```
class JavaProbabilisticClassifierParams(HasProbabilityCol, HasThresholds, JavaClassifierParams):
pass
class JavaProbabilisticClassifier(JavaClassifier, JavaProbabilisticClassifierParams):
def setProbabilityCol
def setThresholds
class JavaProbabilisticClassificationModel(JavaClassificationModel, JavaProbabilisticClassifierParams):
def setProbabilityCol
def setThresholds
```
3. Scala has PredictorParams/Predictor/PredictionModel:
```
trait PredictorParams extends Params
with HasLabelCol with HasFeaturesCol with HasPredictionCol
abstract class Predictor
extends Estimator with PredictorParams {
def setLabelCol
def setFeaturesCol
def setPredictionCol
}
abstract class PredictionModel
extends Model with PredictorParams {
def setFeaturesCol
def setPredictionCol
def numFeatures
def predict
}
```
This PR makes Python have the following:
```
class JavaPredictorParams(HasLabelCol, HasFeaturesCol, HasPredictionCol):
pass
class JavaPredictor(JavaEstimator, JavaPredictorParams):
def setLabelCol
def setFeaturesCol
def setPredictionCol
class JavaPredictionModel(JavaModel, JavaPredictorParams):
def setFeaturesCol
def setPredictionCol
def numFeatures
def predict
```
### Why are the changes needed?
Have parity between Python and Scala ML
### Does this PR introduce any user-facing change?
Yes. Add the following changes:
```
LinearSVCModel
- get/setFeatureCol
- get/setPredictionCol
- get/setLabelCol
- get/setRawPredictionCol
- predict
```
```
LogisticRegressionModel
DecisionTreeClassificationModel
RandomForestClassificationModel
GBTClassificationModel
NaiveBayesModel
MultilayerPerceptronClassificationModel
- get/setFeatureCol
- get/setPredictionCol
- get/setLabelCol
- get/setRawPredictionCol
- get/setProbabilityCol
- predict
```
```
LinearRegressionModel
IsotonicRegressionModel
DecisionTreeRegressionModel
RandomForestRegressionModel
GBTRegressionModel
AFTSurvivalRegressionModel
GeneralizedLinearRegressionModel
- get/setFeatureCol
- get/setPredictionCol
- get/setLabelCol
- predict
```
### How was this patch tested?
Add a few doc tests.
Closes#25776 from huaxingao/spark-28985.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
### What changes were proposed in this pull request?
Bucketizer support multi-column in the python side
### Why are the changes needed?
Bucketizer should support multi-column like the scala side.
### Does this PR introduce any user-facing change?
yes, this PR add new Python API
### How was this patch tested?
added testsuites
Closes#25801 from zhengruifeng/20542_py.
Authored-by: zhengruifeng <ruifengz@foxmail.com>
Signed-off-by: zhengruifeng <ruifengz@foxmail.com>
### What changes were proposed in this pull request?
- Remove SQLContext.createExternalTable and Catalog.createExternalTable, deprecated in favor of createTable since 2.2.0, plus tests of deprecated methods
- Remove HiveContext, deprecated in 2.0.0, in favor of `SparkSession.builder.enableHiveSupport`
- Remove deprecated KinesisUtils.createStream methods, plus tests of deprecated methods, deprecate in 2.2.0
- Remove deprecated MLlib (not Spark ML) linear method support, mostly utility constructors and 'train' methods, and associated docs. This includes methods in LinearRegression, LogisticRegression, Lasso, RidgeRegression. These have been deprecated since 2.0.0
- Remove deprecated Pyspark MLlib linear method support, including LogisticRegressionWithSGD, LinearRegressionWithSGD, LassoWithSGD
- Remove 'runs' argument in KMeans.train() method, which has been a no-op since 2.0.0
- Remove deprecated ChiSqSelector isSorted protected method
- Remove deprecated 'yarn-cluster' and 'yarn-client' master argument in favor of 'yarn' and deploy mode 'cluster', etc
Notes:
- I was not able to remove deprecated DataFrameReader.json(RDD) in favor of DataFrameReader.json(Dataset); the former was deprecated in 2.2.0, but, it is still needed to support Pyspark's .json() method, which can't use a Dataset.
- Looks like SQLContext.createExternalTable was not actually deprecated in Pyspark, but, almost certainly was meant to be? Catalog.createExternalTable was.
- I afterwards noted that the toDegrees, toRadians functions were almost removed fully in SPARK-25908, but Felix suggested keeping just the R version as they hadn't been technically deprecated. I'd like to revisit that. Do we really want the inconsistency? I'm not against reverting it again, but then that implies leaving SQLContext.createExternalTable just in Pyspark too, which seems weird.
- I *kept* LogisticRegressionWithSGD, LinearRegressionWithSGD, LassoWithSGD, RidgeRegressionWithSGD in Pyspark, though deprecated, as it is hard to remove them (still used by StreamingLogisticRegressionWithSGD?) and they are not fully removed in Scala. Maybe should not have been deprecated.
### Why are the changes needed?
Deprecated items are easiest to remove in a major release, so we should do so as much as possible for Spark 3. This does not target items deprecated 'recently' as of Spark 2.3, which is still 18 months old.
### Does this PR introduce any user-facing change?
Yes, in that deprecated items are removed from some public APIs.
### How was this patch tested?
Existing tests.
Closes#25684 from srowen/SPARK-28980.
Lead-authored-by: Sean Owen <sean.owen@databricks.com>
Co-authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
<!--
Thanks for sending a pull request! Here are some tips for you:
1. If this is your first time, please read our contributor guidelines: https://spark.apache.org/contributing.html
2. Ensure you have added or run the appropriate tests for your PR: https://spark.apache.org/developer-tools.html
3. If the PR is unfinished, add '[WIP]' in your PR title, e.g., '[WIP][SPARK-XXXX] Your PR title ...'.
4. Be sure to keep the PR description updated to reflect all changes.
5. Please write your PR title to summarize what this PR proposes.
6. If possible, provide a concise example to reproduce the issue for a faster review.
-->
### What changes were proposed in this pull request?
<!--
Please clarify what changes you are proposing. The purpose of this section is to outline the changes and how this PR fixes the issue.
If possible, please consider writing useful notes for better and faster reviews in your PR. See the examples below.
1. If you refactor some codes with changing classes, showing the class hierarchy will help reviewers.
2. If you fix some SQL features, you can provide some references of other DBMSes.
3. If there is design documentation, please add the link.
4. If there is a discussion in the mailing list, please add the link.
-->
This PR proposes to fix both tests below:
```
======================================================================
FAIL: test_raw_and_probability_prediction (pyspark.ml.tests.test_algorithms.MultilayerPerceptronClassifierTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/dongjoon/APACHE/spark-master/python/pyspark/ml/tests/test_algorithms.py", line 89, in test_raw_and_probability_prediction
self.assertTrue(np.allclose(result.rawPrediction, expected_rawPrediction, atol=1E-4))
AssertionError: False is not true
```
```
File "/Users/dongjoon/APACHE/spark-master/python/pyspark/mllib/clustering.py", line 386, in __main__.GaussianMixtureModel
Failed example:
abs(softPredicted[0] - 1.0) < 0.001
Expected:
True
Got:
False
**********************************************************************
File "/Users/dongjoon/APACHE/spark-master/python/pyspark/mllib/clustering.py", line 388, in __main__.GaussianMixtureModel
Failed example:
abs(softPredicted[1] - 0.0) < 0.001
Expected:
True
Got:
False
```
to pass in JDK 11.
The root cause seems to be different float values being understood via Py4J. This issue also was found in https://github.com/apache/spark/pull/25132 before.
When floats are transferred from Python to JVM, the values are sent as are. Python floats are not "precise" due to its own limitation - https://docs.python.org/3/tutorial/floatingpoint.html.
For some reasons, the floats from Python on JDK 8 and JDK 11 are different, which is already explicitly not guaranteed.
This seems why only some tests in PySpark with floats are being failed.
So, this PR fixes it by increasing tolerance in identified test cases in PySpark.
### Why are the changes needed?
<!--
Please clarify why the changes are needed. For instance,
1. If you propose a new API, clarify the use case for a new API.
2. If you fix a bug, you can clarify why it is a bug.
-->
To fully support JDK 11. See, for instance, https://github.com/apache/spark/pull/25443 and https://github.com/apache/spark/pull/25423 for ongoing efforts.
### Does this PR introduce any user-facing change?
<!--
If yes, please clarify the previous behavior and the change this PR proposes - provide the console output, description and/or an example to show the behavior difference if possible.
If no, write 'No'.
-->
No.
### How was this patch tested?
<!--
If tests were added, say they were added here. Please make sure to add some test cases that check the changes thoroughly including negative and positive cases if possible.
If it was tested in a way different from regular unit tests, please clarify how you tested step by step, ideally copy and paste-able, so that other reviewers can test and check, and descendants can verify in the future.
If tests were not added, please describe why they were not added and/or why it was difficult to add.
-->
Manually tested as described in JIRAs:
```
$ build/sbt -Phadoop-3.2 test:package
$ python/run-tests --testnames 'pyspark.ml.tests.test_algorithms' --python-executables python
```
```
$ build/sbt -Phadoop-3.2 test:package
$ python/run-tests --testnames 'pyspark.mllib.clustering' --python-executables python
```
Closes#25475 from HyukjinKwon/SPARK-28735.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
Update HashingTF to use new implementation of MurmurHash3
Make HashingTF use the old MurmurHash3 when a model from pre 3.0 is loaded
## How was this patch tested?
Change existing unit tests. Also add one unit test to make sure HashingTF use the old MurmurHash3 when a model from pre 3.0 is loaded
Closes#25303 from huaxingao/spark-23469.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
I remove the deprecate `ImageSchema.readImages`.
Move some useful methods from class `ImageSchema` into class `ImageFileFormat`.
In pyspark, I rename `ImageSchema` class to be `ImageUtils`, and keep some useful python methods in it.
## How was this patch tested?
UT.
Please review https://spark.apache.org/contributing.html before opening a pull request.
Closes#25245 from WeichenXu123/remove_image_schema.
Authored-by: WeichenXu <weichen.xu@databricks.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
Currently, pretty skipped message added by f7435bec6a mechanism seems not working when xmlrunner is installed apparently.
This PR fixes two things:
1. When `xmlrunner` is installed, seems `xmlrunner` does not respect `vervosity` level in unittests (default is level 1).
So the output looks as below
```
Running tests...
----------------------------------------------------------------------
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
----------------------------------------------------------------------
```
So it is not caught by our message detection mechanism.
2. If we manually set the `vervocity` level to `xmlrunner`, it prints messages as below:
```
test_mixed_udf (pyspark.sql.tests.test_pandas_udf_scalar.ScalarPandasUDFTests) ... SKIP (0.000s)
test_mixed_udf_and_sql (pyspark.sql.tests.test_pandas_udf_scalar.ScalarPandasUDFTests) ... SKIP (0.000s)
...
```
This is different in our Jenkins machine:
```
test_createDataFrame_column_name_encoding (pyspark.sql.tests.test_arrow.ArrowTests) ... skipped 'Pandas >= 0.23.2 must be installed; however, it was not found.'
test_createDataFrame_does_not_modify_input (pyspark.sql.tests.test_arrow.ArrowTests) ... skipped 'Pandas >= 0.23.2 must be installed; however, it was not found.'
...
```
Note that last `SKIP` is different. This PR fixes the regular expression to catch `SKIP` case as well.
## How was this patch tested?
Manually tested.
**Before:**
```
Starting test(python2.7): pyspark....
Finished test(python2.7): pyspark.... (0s)
...
Tests passed in 562 seconds
========================================================================
...
```
**After:**
```
Starting test(python2.7): pyspark....
Finished test(python2.7): pyspark.... (48s) ... 93 tests were skipped
...
Tests passed in 560 seconds
Skipped tests pyspark.... with python2.7:
pyspark...(...) ... SKIP (0.000s)
...
========================================================================
...
```
Closes#24927 from HyukjinKwon/SPARK-28130.
Authored-by: HyukjinKwon <gurwls223@apache.org>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>
Before, you could have this code
```
A = SparseMatrix(2, 2, [0, 2, 3], [0], [2])
B = DenseMatrix(2, 2, [2, 0, 0, 0])
B == A # False
A == B # True
```
The second would be `True` as `SparseMatrix` already checks for semantic
equality. This commit changes `DenseMatrix` so that equality is
semantical as well.
## What changes were proposed in this pull request?
Better semantic equality for DenseMatrix
## How was this patch tested?
Unit tests were added, plus manual testing. Note that the code falls back to the old behavior when `other` is not a SparseMatrix.
Closes#17968 from gglanzani/SPARK-9792.
Authored-by: Giovanni Lanzani <giovanni@lanzani.nl>
Signed-off-by: Holden Karau <holden@pigscanfly.ca>
## What changes were proposed in this pull request?
The hashSeed method allocates 64 bytes instead of 8. Other bytes are always zeros (thanks to default behavior of ByteBuffer). And they could be excluded from hash calculation because they don't differentiate inputs.
## How was this patch tested?
By running the existing tests - XORShiftRandomSuite
Closes#20793 from MaxGekk/hash-buff-size.
Lead-authored-by: Maxim Gekk <maxim.gekk@databricks.com>
Co-authored-by: Maxim Gekk <max.gekk@gmail.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
Add RawPrediction to OneVsRest in PySpark to make it consistent with scala implementation
## How was this patch tested?
Add doctest
Closes#23910 from huaxingao/spark-27007.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
Add multiple column support to PySpark StringIndexer
## How was this patch tested?
Add doctest
Closes#23741 from huaxingao/spark-22798.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
Add PMML export support for ML KMeans to PySpark.
## How was this patch tested?
Add tests in ml.tests.PersistenceTest.
Closes#23592 from huaxingao/spark-16838.
Authored-by: Huaxin Gao <huaxing@us.ibm.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
This change exposes the `df` (document frequency) as a public val along with the number of documents (`m`) as part of the IDF model.
* The document frequency is returned as an `Array[Long]`
* If the minimum document frequency is set, this is considered in the df calculation. If the count is less than minDocFreq, the df is 0 for such terms
* numDocs is not very required. But it can be useful, if we plan to provide a provision in future for user to give their own idf function, instead of using a default (log((1+m)/(1+df))). In such cases, the user can provide a function taking input of `m` and `df` and returning the idf value
* Pyspark changes
## How was this patch tested?
The existing test case was edited to also check for the document frequency values.
I am not very good with python or pyspark. I have committed and run tests based on my understanding. Kindly let me know if I have missed anything
Reviewer request: mengxr zjffdu yinxusen
Closes#23549 from purijatin/master.
Authored-by: Jatin Puri <purijatin@gmail.com>
Signed-off-by: Sean Owen <sean.owen@databricks.com>
## What changes were proposed in this pull request?
This PR is a small follow up that puts some logic and functions into smaller scope and make it localized, and deduplicate.
## How was this patch tested?
Manually tested. Jenkins tests as well.
Closes#23200 from HyukjinKwon/followup-SPARK-26034-SPARK-26033.
Authored-by: Hyukjin Kwon <gurwls223@apache.org>
Signed-off-by: Bryan Cutler <cutlerb@gmail.com>
## What changes were proposed in this pull request?
Currently, some of PySpark tests sill assume the tests could be ran in Python 2.6 by importing `unittest2`. For instance:
```python
if sys.version_info[:2] <= (2, 6):
try:
import unittest2 as unittest
except ImportError:
sys.stderr.write('Please install unittest2 to test with Python 2.6 or earlier')
sys.exit(1)
else:
import unittest
```
While I am here, I removed some of unused imports and reordered imports per PEP 8.
We officially dropped Python 2.6 support a while ago and started to discuss about Python 2 drop. It's better to remove them out.
## How was this patch tested?
Manually tests, and existing tests via Jenkins.
Closes#23077 from HyukjinKwon/SPARK-26105.
Lead-authored-by: hyukjinkwon <gurwls223@apache.org>
Co-authored-by: Bryan Cutler <cutlerb@gmail.com>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
## What changes were proposed in this pull request?
This PR breaks down the large ml/tests.py file that contains all Python ML unit tests into several smaller test files to be easier to read and maintain.
The tests are broken down as follows:
```
pyspark
├── __init__.py
...
├── ml
│ ├── __init__.py
...
│ ├── tests
│ │ ├── __init__.py
│ │ ├── test_algorithms.py
│ │ ├── test_base.py
│ │ ├── test_evaluation.py
│ │ ├── test_feature.py
│ │ ├── test_image.py
│ │ ├── test_linalg.py
│ │ ├── test_param.py
│ │ ├── test_persistence.py
│ │ ├── test_pipeline.py
│ │ ├── test_stat.py
│ │ ├── test_training_summary.py
│ │ ├── test_tuning.py
│ │ └── test_wrapper.py
...
├── testing
...
│ ├── mlutils.py
...
```
## How was this patch tested?
Ran tests manually by module to ensure test count was the same, and ran `python/run-tests --modules=pyspark-ml` to verify all passing with Python 2.7 and Python 3.6.
Closes#23063 from BryanCutler/python-test-breakup-ml-SPARK-26033.
Authored-by: Bryan Cutler <cutlerb@gmail.com>
Signed-off-by: hyukjinkwon <gurwls223@apache.org>
