Align directories closer to maven standard

:q!

.gitignore

@@ -5,21 +5,20 @@
 *hs_err_pid*
 *stdout.txt
 *~
+/AwsCredentials.properties
+TAGS
 bin/
-build
+build.local.conf
+dist/
 flatfile*
 h2o_work.xml
 ice
 lib/h2o_core.jar
+nbbuild.xml
+nbproject/
 po.*
+private/
 pytest_flatfile-*
 sandbox
-dist/
-build/
-nbproject/
-nbbuild.xml
-TAGS
-build.local.conf
-/AwsCredentials.properties
-private/
-syn_datasets
+syn_datasets
+target/

build.sh

@@ -22,8 +22,8 @@ set -o errexit   ## set -e : exit the script if any statement returns a non-true
 # basic build properties
 # ------------------------------------------------------------------------------
 # This is where the source files (java) are relative to the path of this file
-SRC=src
-TESTSRC=test-src
+    SRC=src/main/java
+TESTSRC=src/test/java
 # and this is where the jar contents is stored relative to this file again
 JAR_ROOT=lib
 
@@ -32,7 +32,7 @@ JAR_ROOT=lib
 DEPENDENCIES="${JAR_ROOT}/jama/*${SEP}${JAR_ROOT}/apache/*${SEP}${JAR_ROOT}/junit/*${SEP}${JAR_ROOT}/gson/*${SEP}${JAR_ROOT}/javassist.jar${SEP}${JAR_ROOT}/poi/*${SEP}${JAR_ROOT}/trove/*${SEP}${JAR_ROOT}/s3/*${SEP}${JAR_ROOT}/jets3t/*"
 
 DEFAULT_HADOOP_VERSION="1.0.0"
-OUTDIR="build"
+OUTDIR="target"
 
 JAVAC=`which javac`
 

prj.el

@@ -2,14 +2,14 @@
 (jde-set-variables
  '(jde-javadoc-gen-destination-directory "./doc")
  '(jde-run-working-directory "$HOME/Desktop/hexbase")
- '(jde-run-option-classpath (quote ("./build/classes" "./lib/sigar/sigar.jar" "./lib/hadoop/cdh4/hadoop-common.jar" "./lib/hadoop/cdh4/hadoop-auth.jar" "./lib/hadoop/cdh4/slf4j-api-1.6.1.jar" "./lib/hadoop/cdh4/slf4j-nop-1.6.1.jar" "./lib/hadoop/cdh4/hadoop-hdfs.jar" "./lib/hadoop/cdh4/protobuf-java-2.4.0a.jar" "./lib/apache/commons-codec-1.3.jar" "./lib/apache/commons-configuration-1.6.jar" "./lib/apache/commons-lang-2.4.jar" "./lib/apache/commons-logging-1.1.1.jar" "./lib/apache/commons-logging-api-1.0.4.jar" "./lib/apache/httpclient-4.1.1.jar" "./lib/apache/httpcore-4.1.jar" "./lib/junit/junit-4.11.jar" "./lib/apache/guava-12.0.1.jar" "./lib/gson/gson-2.2.2.jar" "./lib/javassist.jar" "./lib/trove/trove-3.0.3.jar" "./lib/poi/poi-3.8-20120326.jar" "./lib/poi/poi-ooxml-3.8-20120326.jar " "./lib/poi/poi-ooxml-schemas-3.8-20120326.jar" "./lib/poi/dom4j-1.6.1.jar" "./lib/Jama/Jama.jar" "./lib/s3/aws-java-sdk-1.3.27.jar" "./lib/jsr166y")))
+ '(jde-run-option-classpath (quote ("./target/classes" "./lib/sigar/sigar.jar" "./lib/hadoop/cdh4/hadoop-common.jar" "./lib/hadoop/cdh4/hadoop-auth.jar" "./lib/hadoop/cdh4/slf4j-api-1.6.1.jar" "./lib/hadoop/cdh4/slf4j-nop-1.6.1.jar" "./lib/hadoop/cdh4/hadoop-hdfs.jar" "./lib/hadoop/cdh4/protobuf-java-2.4.0a.jar" "./lib/apache/commons-codec-1.3.jar" "./lib/apache/commons-configuration-1.6.jar" "./lib/apache/commons-lang-2.4.jar" "./lib/apache/commons-logging-1.1.1.jar" "./lib/apache/commons-logging-api-1.0.4.jar" "./lib/apache/httpclient-4.1.1.jar" "./lib/apache/httpcore-4.1.jar" "./lib/junit/junit-4.11.jar" "./lib/apache/guava-12.0.1.jar" "./lib/gson/gson-2.2.2.jar" "./lib/javassist.jar" "./lib/trove/trove-3.0.3.jar" "./lib/poi/poi-3.8-20120326.jar" "./lib/poi/poi-ooxml-3.8-20120326.jar " "./lib/poi/poi-ooxml-schemas-3.8-20120326.jar" "./lib/poi/dom4j-1.6.1.jar" "./lib/Jama/Jama.jar" "./lib/s3/aws-java-sdk-1.3.27.jar" "./lib/jsr166y")))
  '(jde-run-option-debug nil)
  '(jde-run-option-vm-args nil)
- '(jde-compile-option-directory "./build/classes")
- '(jde-run-option-application-args (quote ("-mainClass" "embedded.ScoreMain" "org.junit.runner.JUnitCore" "water.score.ScorePmmlTest")))
+ '(jde-compile-option-directory "./target/classes")
+ '(jde-run-option-application-args (quote ("-mainClass" "org.junit.runner.JUnitCore" "water.score.ScorePmmlTest")))
  '(jde-debugger (quote ("JDEbug")))
  '(jde-compile-option-source (quote ("1.6")))
- '(jde-compile-option-classpath (quote ("./build/classes" "./lib/sigar/sigar.jar" "./lib/hadoop/1.0.0/hadoop-core-1.0.0.jar" "./lib/apache/commons-codec-1.3.jar" "./lib/apache/commons-configuration-1.6.jar" "./lib/apache/commons-lang-2.4.jar" "./lib/apache/commons-logging-1.1.1.jar" "./lib/apache/commons-logging-api-1.0.4.jar" "./lib/apache/httpclient-4.1.1.jar" "./lib/apache/httpcore-4.1.jar" "./lib/junit/junit-4.11.jar" "./lib/apache/guava-12.0.1.jar" "./lib/gson/gson-2.2.2.jar" "./lib/javassist.jar" "./lib/trove/trove-3.0.3.jar" "./lib/poi/poi-3.8-20120326.jar" "./lib/poi/poi-ooxml-3.8-20120326.jar " "./lib/poi/poi-ooxml-schemas-3.8-20120326.jar" "./lib/jama/Jama.jar" "./lib/s3/aws-java-sdk-1.3.27.jar")))
+ '(jde-compile-option-classpath (quote ("./target/classes" "./lib/sigar/sigar.jar" "./lib/hadoop/1.0.0/hadoop-core-1.0.0.jar" "./lib/apache/commons-codec-1.3.jar" "./lib/apache/commons-configuration-1.6.jar" "./lib/apache/commons-lang-2.4.jar" "./lib/apache/commons-logging-1.1.1.jar" "./lib/apache/commons-logging-api-1.0.4.jar" "./lib/apache/httpclient-4.1.1.jar" "./lib/apache/httpcore-4.1.jar" "./lib/junit/junit-4.11.jar" "./lib/apache/guava-12.0.1.jar" "./lib/gson/gson-2.2.2.jar" "./lib/javassist.jar" "./lib/trove/trove-3.0.3.jar" "./lib/poi/poi-3.8-20120326.jar" "./lib/poi/poi-ooxml-3.8-20120326.jar " "./lib/poi/poi-ooxml-schemas-3.8-20120326.jar" "./lib/jama/Jama.jar" "./lib/s3/aws-java-sdk-1.3.27.jar")))
  '(jde-db-option-classpath (quote ("$HOME/Desktop/Dropbox/Sris and Cliff/H2O/classes")))
  '(jde-run-option-enable-assertions "Everywhere")
  '(jde-compile-option-sourcepath (quote ("./src")))

py/h2o.py

@@ -331,12 +331,12 @@ def prog(sofar, total):
 
     if not slow_connection:
         for h in hosts:
-            f = find_file('build/h2o.jar')
+            f = find_file('target/h2o.jar')
             h.upload_file(f, progress=prog)
             # skipping progress indicator for the flatfile
             h.upload_file(flatfile_name())
     else:
-        f = find_file('build/h2o.jar')
+        f = find_file('target/h2o.jar')
         hosts[0].upload_file(f, progress=prog)
         hosts[0].push_file_to_remotes(f, hosts[1:])
 
@@ -1093,7 +1093,7 @@ def __init__(self, *args, **kwargs):
         super(ExternalH2O, self).__init__(*args, **kwargs)
 
     def get_h2o_jar(self):
-        return find_file('build/h2o.jar') # just a likely guess
+        return find_file('target/h2o.jar') # just a likely guess
 
     def get_ice_dir(self):
         return '/tmp/ice%d' % self.port # just a likely guess
@@ -1129,7 +1129,7 @@ def __init__(self, *args, **kwargs):
         self.ps = spawn[0]
 
     def get_h2o_jar(self):
-        return find_file('build/h2o.jar')
+        return find_file('target/h2o.jar')
 
     def get_flatfile(self):
         return self.flatfile
@@ -1257,7 +1257,7 @@ class RemoteH2O(H2O):
     def __init__(self, host, *args, **kwargs):
         super(RemoteH2O, self).__init__(*args, **kwargs)
 
-        self.jar = host.upload_file('build/h2o.jar')
+        self.jar = host.upload_file('target/h2o.jar')
         # need to copy the flatfile. We don't always use it (depends on h2o args)
         self.flatfile = host.upload_file(flatfile_name())
 

py/junit.py

@@ -5,7 +5,7 @@ class JUnit(unittest.TestCase):
     def testScoring(self):
         (ps, stdout, stderr) = h2o.spawn_cmd('junit', [
                 'java',
-                '-ea', '-jar', h2o.find_file('build/h2o.jar'),
+                '-ea', '-jar', h2o.find_file('target/h2o.jar'),
                 '-mainClass', 'org.junit.runner.JUnitCore',
                 # The tests
                 'water.score.ScorePmmlTest',
@@ -33,22 +33,22 @@ def testAll(self):
                     '-Dh2o.arg.ice_root='+h2o.tmp_dir('ice.'),
                     '-Dh2o.arg.name='+h2o.cloud_name(),
                     '-Dh2o.arg.ip='+h2o.get_ip_address(),
-                    '-ea', '-jar', h2o.find_file('build/h2o.jar'),
+                    '-ea', '-jar', h2o.find_file('target/h2o.jar'),
                     '-mainClass', 'org.junit.runner.JUnitCore',
                     # The tests
-                    'test.KVTest',
-                    'test.AppendKeyTest',
-                    'test.RandomForestTest',
-                    'test.AutoSerialTest',
-                    'test.DatasetCornerCasesTest',
-                    'test.ExprTest',
-                    'test.KeyToString',
-                    'test.RStringTest',
-                    'test.ParserTest',
-                    'test.MinorityClassTest',
-                    'test.GLMTest',
-                    'test.RBigDataTest',
-                    'test.KMeansTest'
+                    'hex.GLMTest',
+                    'hex.KMeansTest',
+                    'hex.MinorityClassTest',
+                    'hex.rf.RandomForestTest',
+                    'water.AppendKeyTest',
+                    'water.AutoSerialTest',
+                    'water.KVTest',
+                    'water.KeyToString',
+                    'water.api.RStringTest',
+                    'water.exec.ExprTest',
+                    'water.exec.RBigDataTest',
+                    'water.parser.DatasetCornerCasesTest',
+                    'water.parser.ParserTest'
                     ])
 
             rc = ps.wait(None)
@@ -67,9 +67,9 @@ def testAll(self):
     #def testMore(self):
     #        (ps, stdout, stderr) = h2o.spawn_cmd('junit', [
     #                'java',
-    #                '-ea', '-jar', h2o.find_file('build/h2o.jar'),
+    #                '-ea', '-jar', h2o.find_file('target/h2o.jar'),
     #                '-mainClass', 'org.junit.runner.JUnitCore',
-    #                'test.RFRunner',
+    #                'hex.rf.RFRunner',
     #                ])
     #
     #        rc = ps.wait(None)

py/peta_singletest.py

@@ -15,10 +15,10 @@ def testAll(self):
                     '-Dh2o.arg.ice_root='+h2o.tmp_dir('ice.'),
                     '-Dh2o.arg.name=pytest-'+getpass.getuser(),
                     '-Dh2o.arg.ip='+h2o.get_ip_address(),
-                    '-ea', '-jar', h2o.find_file('build/h2o.jar'),
+                    '-ea', '-jar', h2o.find_file('target/h2o.jar'),
                     '-mainClass', 'org.junit.runner.JUnitCore',
                     # The tests
-                    'test.ParserTest',
+                    'water.parser.ParserTest',
                     ])
 
             rc = ps.wait(None)

py/run_remote.py

@@ -11,7 +11,7 @@
 # to come up quickly and fight with each other
 for h in hosts:
     print 'Uploading jar to', h
-    h.upload_file(h2o.find_file('build/h2o.jar'))
+    h.upload_file(h2o.find_file('target/h2o.jar'))
 
 nodes = []
 for h in hosts:

src/hex/rf/RandomForest.java → src/main/java/hex/rf/RandomForest.java

@@ -1,14 +1,12 @@
 package hex.rf;
+
 import hex.rf.Tree.StatType;
 import hex.rng.H2ORandomRNG.RNGKind;
-
 import java.io.File;
 import java.util.*;
-
-import test.RandomForestTest;
-import test.TestUtil;
 import water.*;
 import water.Timer;
+import water.util.TestUtil;
 
 /**
  * A RandomForest can be used for growing or validation. The former starts with a known target number of trees,

test-src/test/GLMGridTest.java → src/test/java/hex/GLMGridTest.java

@@ -1,13 +1,10 @@
-package test;
+package hex;
 
-import hex.*;
 import hex.GLMSolver.GLMModel;
-
 import java.util.Arrays;
-
 import org.junit.Test;
-
 import water.*;
+import water.util.TestUtil;
 
 // Test grid-search over GLM args
 public class GLMGridTest extends TestUtil {

test-src/test/GLMTest.java → src/test/java/hex/GLMTest.java

@@ -1,19 +1,18 @@
-package test;
+package hex;
+
 import static org.junit.Assert.assertEquals;
 import com.google.gson.*;
 import hex.GLMSolver.GLMModel;
-import hex.GLMSolver;
-import hex.LSMSolver;
-import hex.LinearRegression;
 import java.util.Arrays;
 import java.util.Map;
 import java.util.Random;
 import org.junit.*;
 import water.*;
+import water.api.Constants;
 import water.exec.Exec;
 import water.exec.PositionedException;
 import water.parser.ParseDataset;
-import water.api.Constants;
+import water.util.TestUtil;
 
 // A series of tests designed to validate GLM's *statistical results* and not,
 // i.e. correct behavior when handed bad/broken/null arguments (although those
@@ -89,7 +88,7 @@ JsonObject computeGLM( GLMSolver.Family family, LSMSolver lsms, ValueArray va, b
     try {
       // Make some data to test with.  2 columns, all numbers from 0-9
       ValueArray va = va_maker(datakey,2,10, new DataExpr() {
-          double expr( byte[] x ) { return 1.0/(1.0+Math.exp(-(0.1*x[0]+0.3*x[1]-2.5))); } } );
+          public double expr( byte[] x ) { return 1.0/(1.0+Math.exp(-(0.1*x[0]+0.3*x[1]-2.5))); } } );
 
       LSMSolver lsms = LSMSolver.makeSolver(); // Default normalization of NONE
       JsonObject glm = computeGLMlog(lsms,va,false); // Solve it!
@@ -110,7 +109,7 @@ public static class DataExpr_Dirty extends DataExpr {
     final Random _R;
     final double _coefs[];
     DataExpr_Dirty( Random R, double[] coefs ) { _R = R; _coefs = coefs; }
-    double expr( byte[] cols ) {
+    public double expr( byte[] cols ) {
       double sum = _coefs[_coefs.length-1]+
         (_R.nextDouble()-0.5)/1000.0; // Add some noise
       for( int i = 0; i< cols.length; i++ )
@@ -146,7 +145,7 @@ public static class DataExpr_Dirty extends DataExpr {
     try {
       // Make some data to test with.  2 columns, all numbers from 0-9
       ValueArray va = va_maker(datakey,2,10, new DataExpr() {
-          double expr( byte[] x ) { return 1.0/(1.0+Math.exp(-(0.1*x[0]+0.3*x[1]-2.5))); } } );
+          public double expr( byte[] x ) { return 1.0/(1.0+Math.exp(-(0.1*x[0]+0.3*x[1]-2.5))); } } );
 
       // No penalty
       LSMSolver lsms0 = LSMSolver.makeSolver();

test-src/test/KMeansTest.java → src/test/java/hex/KMeansTest.java

@@ -1,10 +1,10 @@
-package test;
+package hex;
 
-import hex.KMeans;
 import java.util.Arrays;
 import java.util.Random;
 import org.junit.*;
 import water.*;
+import water.util.TestUtil;
 
 public class KMeansTest extends TestUtil {
 

test-src/test/MinorityClassTest.java → src/test/java/hex/MinorityClassTest.java

@@ -1,21 +1,19 @@
-package test;
+package hex;
 
 import static org.junit.Assert.assertTrue;
-import hex.rf.MinorityClasses;
 import hex.rf.MinorityClasses.UnbalancedClass;
-
+import hex.rf.MinorityClasses;
 import java.io.FileInputStream;
 import java.util.Arrays;
-
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.runner.JUnitCore;
 import org.junit.runner.Result;
 import org.junit.runner.notification.Failure;
-
 import water.*;
 import water.parser.ParseDataset;
+import water.util.TestUtil;
 
 public class MinorityClassTest extends TestUtil {
   static final int _classIdx = 10;

test-src/test/RFRunner.java → src/test/java/hex/rf/RFRunner.java

@@ -1,14 +1,12 @@
-package test;
-
-import hex.rf.Utils;
+package hex.rf;
 
 import java.io.*;
 import java.text.SimpleDateFormat;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-
 import water.Arguments;
+import water.util.TestUtil;
 
 /** Launch RF in a new vm and records  results.
  */

test-src/test/RandomForestTest.java → src/test/java/hex/rf/RandomForestTest.java

@@ -1,12 +1,11 @@
-package test;
+package hex.rf;
+
 import static org.junit.Assert.assertEquals;
-import hex.rf.*;
 import hex.rf.Tree.StatType;
-
 import org.junit.BeforeClass;
-
 import water.*;
 import water.parser.ParseDataset;
+import water.util.TestUtil;
 
 public class RandomForestTest extends TestUtil {
 

test-src/test/AppendKeyTest.java → src/test/java/water/AppendKeyTest.java

@@ -1,10 +1,10 @@
-package test;
+package water;
+
 import java.util.Arrays;
 import java.util.Random;
-
 import org.junit.*;
-
 import water.*;
+import water.util.TestUtil;
 
 public class AppendKeyTest extends TestUtil {
 

test-src/test/AutoSerialTest.java → src/test/java/water/AutoSerialTest.java

@@ -1,10 +1,9 @@
-package test;
+package water;
 
 import java.io.*;
 import java.util.Arrays;
 import org.junit.Assert;
 import org.junit.Test;
-import water.*;
 
 public class AutoSerialTest extends Iced {
   byte _byte, _bytes[];

test-src/test/ConcurrentKeyTest.java → src/test/java/water/ConcurrentKeyTest.java

@@ -1,10 +1,11 @@
-package test;
+package water;
 
 import hex.KMeans;
 import java.util.Arrays;
 import java.util.Random;
 import org.junit.*;
 import water.*;
+import water.util.TestUtil;
 
 public class ConcurrentKeyTest extends TestUtil {