replace tab indent with spaces within Updaters

.classpath

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src/main/scala"/>
+	<classpathentry kind="con" path="org.scala-ide.sdt.launching.SCALA_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/BIDMat"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jhdf5.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/ptplot.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/ptplotapplication.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcublas-0.5.0.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcuda-0.5.0.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcufft-0.5.0.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcurand-0.5.0.jar"/>
+	<classpathentry kind="lib" path="C:/code/BIDMat/lib/jcusparse-0.5.0.jar"/>
+	<classpathentry kind="output" path="target/scala-2.9.1/classes"/>
+</classpath>

.project

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>BIDMach</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.scala-ide.sdt.core.scalabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.scala-ide.sdt.core.scalanature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

Copyright.txt

@@ -0,0 +1,25 @@
+Copyright (c) 2012, Regents of the University of California
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of the <organization> nor the
+      names of its contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

bidmach

@@ -0,0 +1,37 @@
+#!/bin/bash
+export JAVA_OPTS="-Xmx12G -Xms128M" # Set as much memory as possible
+BIDMACH_ROOT="${BASH_SOURCE[0]}"
+if [ ! `uname` = "Darwin" ]; then
+  BIDMACH_ROOT=`readlink -f "${BIDMACH_ROOT}"`
+else 
+  BIDMACH_ROOT=`readlink "${BIDMACH_ROOT}"`
+fi
+BIDMACH_ROOT=`dirname "$BIDMACH_ROOT"`
+BIDMACH_ROOT="$( echo ${BIDMACH_ROOT} | sed s+/cygdrive/c+c:+ )" 
+BIDMAT_ROOT="${BIDMACH_ROOT}/../BIDMat" # Change if needed
+# export JAVA_HOME="" # Set here if not set in environment
+# Fix these if needed
+JCUDA_VERSION="0.5.0"
+JCUDA_LIBDIR="${BIDMAT_ROOT}/lib"
+BIDLIB="${BIDMAT_ROOT}/lib"
+LIBDIR=${BIDMACH_ROOT}/lib
+if [ `uname` = "Darwin" ]; then
+  export DYLD_LIBRARY_PATH="${BIDMAT_ROOT}/lib:/usr/local/cuda/lib:${LD_LIBRARY_PATH}" 
+else
+  export LD_LIBRARY_PATH="${BIDMAT_ROOT}/lib:/usr/local/cuda/lib64:${LD_LIBRARY_PATH}" 
+fi
+
+BIDMAT_LIBS="${BIDMAT_ROOT}/BIDMat.jar;${BIDLIB}/ptplot.jar;${BIDLIB}/ptplotapplication.jar;${BIDLIB}/jhdf5.jar;${BIDLIB}/commons-math3-3.1.1.jar;${BIDLIB}/lz4-1.1.2.jar"
+JCUDA_LIBS="${JCUDA_LIBDIR}/jcuda-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcublas-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcufft-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcurand-${JCUDA_VERSION}.jar;${JCUDA_LIBDIR}/jcusparse-${JCUDA_VERSION}.jar"
+
+export ALL_LIBS="${BIDMACH_ROOT}/BIDMach.jar;${BIDMAT_LIBS};${JCUDA_LIBS};${JAVA_HOME}/lib/tools.jar"
+
+if [ ! "$OS" = "Windows_NT" ]; then
+    export ALL_LIBS=`echo "${ALL_LIBS}" | sed 's/;/:/g'`
+else
+    NEWPATH=`${BIDMAT_ROOT}/shortpath.bat "${CUDA_BIN_PATH}"`
+    NEWPATH=`echo $NEWPATH | sed 's_\\\\_/_g'`
+    JAVA_OPTS="-Djava.library.path=${BIDMAT_ROOT}/lib;${NEWPATH} "$JAVA_OPTS
+fi
+
+scala -nobootcp -cp "${ALL_LIBS}" -Yrepl-sync -i ${LIBDIR}/bidmach_init.scala

bidmach.cmd

@@ -0,0 +1,20 @@
+@ECHO OFF
+:: Set JAVA_HOME here if not set in environment
+:: SET JAVA_HOME= 
+:: Set as much memory as possible
+(SET JAVA_OPTS=-Xmx12G -Xms128M)
+:: Fix these if needed
+SET JCUDA_VERSION=0.5.0
+SET BIDLIB="%CD%\..\BIDMat\lib"
+SET LIBDIR="%CD%\lib"
+SET JCUDA_LIBDIR=%BIDLIB%
+SET PATH=%BIDLIB%;%PATH%
+
+SET BIDMACH_LIBS=%BIDLIB%\..\BIDMat.jar;%CD%\BIDMach.jar;%BIDLIB%\ptplot.jar;%BIDLIB%\ptplotapplication.jar;%BIDLIB%\jhdf5.jar;%BIDLIB%\commons-math3-3.1.1.jar;%BIDLIB%\lz4-1.1.2.jar
+
+SET JCUDA_LIBS=%JCUDA_LIBDIR%\jcuda-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcublas-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcufft-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcurand-%JCUDA_VERSION%.jar;%JCUDA_LIBDIR%\jcusparse-%JCUDA_VERSION%.jar
+
+SET ALL_LIBS=%BIDMACH_LIBS%;%JCUDA_LIBS%;%JAVA_HOME%\lib\tools.jar
+:: echo %ALL_LIBS%
+
+scala -nobootcp -cp "%ALL_LIBS%" -Yrepl-sync -i %LIBDIR%\bidmach_init.scala

build.sbt

@@ -0,0 +1,40 @@
+
+name := "BIDMach"
+
+version := "0.1.0"
+
+organization := "edu.berkeley.bid"
+
+scalaVersion := "2.9.2"
+
+resolvers ++= Seq(
+  "Scala Tools Snapshots" at "http://scala-tools.org/repo-snapshots/",
+  "Scala Mirror" at "https://oss.sonatype.org/content/repositories/releases/"
+)
+
+libraryDependencies <<= (scalaVersion, libraryDependencies) { (sv, deps) =>
+  deps :+ ("org.scala-lang" % "scala-compiler" % sv)
+}
+
+libraryDependencies += "org.scala-lang" % "jline" % "2.9.2"
+
+libraryDependencies += "org.scalatest" %% "scalatest" % "1.8" % "test"
+
+libraryDependencies += "org.scalacheck" %% "scalacheck" % "1.9" % "test"
+
+libraryDependencies += "junit" % "junit" % "4.5" % "test"
+
+credentials += Credentials(Path.userHome / ".ivy2" / ".credentials")
+
+javacOptions ++= Seq("-source", "1.5", "-target", "1.5")
+
+scalacOptions ++= Seq("-deprecation","-target:jvm-1.5")
+
+initialCommands := scala.io.Source.fromFile("lib/bidmach_init.scala").getLines.mkString("\n")
+
+javaOptions += "-Xmx12g"
+
+//seq(ProguardPlugin.proguardSettings :_*)
+
+
+

lib/bidmach_init.scala

@@ -0,0 +1,10 @@
+import BIDMat.{BMat,CMat,CSMat,DMat,Dict,IDict,FMat,GMat,GIMat,GSMat,HMat,IMat,Mat,SMat,SDMat}
+import BIDMat.MatFunctions._
+import BIDMat.SciFunctions._
+import BIDMat.Solvers._
+import BIDMat.Plotting._
+import BIDMach.{MatDataSource,FilesDataSource,SFilesDataSource,Learner,LDAModel,NMFModel}
+
+Mat.checkMKL
+Mat.checkCUDA
+

project/plugins.sbt

@@ -0,0 +1,7 @@
+
+libraryDependencies <+= sbtVersion(v => "com.github.siasia" %% "xsbt-proguard-plugin" % (v+"-0.1.1"))
+
+resolvers += "Proguard plugin repo" at "http://siasia.github.com/maven2"
+
+
+