Merge branch 'master' into java5

.gitignore

@@ -21,12 +21,6 @@ tmp/
 !/dist/java5/java6.jar
 !/dist/java5/ui.jar
 
-# subprojects from separate repos
-/Mathematica-Link/
-/extensions/
-/plugins/
-/models/
-
 # autogenerated sources
 /src/main/org/nlogo/agent/ImportLexer.java
 /src/main/org/nlogo/app/Events.java

.gitmodules

@@ -0,0 +1,42 @@
+[submodule "models"]
+	path = models
+	url = git://git.assembla.com/models.git
+[submodule "extensions/array"]
+	path = extensions/array
+	url = http://github.com/NetLogo/Array-Extension.git
+[submodule "extensions/bitmap"]
+	path = extensions/bitmap
+	url = http://github.com/NetLogo/Bitmap-Extension.git
+[submodule "extensions/gis"]
+	path = extensions/gis
+	url = http://github.com/NetLogo/GIS-Extension.git
+[submodule "extensions/gogo"]
+	path = extensions/gogo
+	url = http://github.com/NetLogo/GoGo-Extension.git
+[submodule "extensions/matrix"]
+	path = extensions/matrix
+	url = http://github.com/NetLogo/Matrix-Extension.git
+[submodule "extensions/network"]
+	path = extensions/network
+	url = http://github.com/NetLogo/Network-Extension.git
+[submodule "extensions/profiler"]
+	path = extensions/profiler
+	url = http://github.com/NetLogo/Profiler-Extension.git
+[submodule "extensions/qtj"]
+	path = extensions/qtj
+	url = http://github.com/NetLogo/QTJ-Extension.git
+[submodule "extensions/sample"]
+	path = extensions/sample
+	url = http://github.com/NetLogo/Sample-Extension.git
+[submodule "extensions/sample-scala"]
+	path = extensions/sample-scala
+	url = http://github.com/NetLogo/Sample-Scala-Extension.git
+[submodule "extensions/sound"]
+	path = extensions/sound
+	url = http://github.com/NetLogo/Sound-Extension.git
+[submodule "extensions/table"]
+	path = extensions/table
+	url = http://github.com/NetLogo/Table-Extension.git
+[submodule "Mathematica-Link"]
+	path = Mathematica-Link
+	url = http://github.com/NetLogo/Mathematica-Link.git

Makefile

@@ -87,56 +87,10 @@ extensions: $(EXTENSIONS)
 
 # most of them use NetLogoLite.jar, but the profiler extension uses NetLogo.jar - ST 5/11/11
 $(EXTENSIONS): | NetLogo.jar NetLogoLite.jar
-	mkdir -p models
-	if [ ! -d models/test ] ; then git clone git://git.assembla.com/models.git ; fi
-	mkdir -p extensions
-	if [ ! -d extensions/array/src ] ; then git clone http://github.com/NetLogo/Array-Extension.git extensions/array ; fi
-	if [ ! -d extensions/bitmap/src ] ; then git clone http://github.com/NetLogo/Bitmap-Extension.git extensions/bitmap ; fi
-	if [ ! -d extensions/gis/src ] ; then git clone http://github.com/NetLogo/GIS-Extension.git extensions/gis ; fi
-	if [ ! -d extensions/gogo/src ] ; then git clone http://github.com/NetLogo/GoGo-Extension.git extensions/gogo ; fi
-	if [ ! -d extensions/matrix/src ] ; then git clone http://github.com/NetLogo/Matrix-Extension.git extensions/matrix ; fi
-	if [ ! -d extensions/network/src ] ; then git clone http://github.com/NetLogo/Network-Extension.git extensions/network ; fi
-	if [ ! -d extensions/profiler/src ] ; then git clone http://github.com/NetLogo/Profiler-Extension.git extensions/profiler ; fi
-	if [ ! -d extensions/qtj/src ] ; then git clone http://github.com/NetLogo/QTJ-Extension.git extensions/qtj ; fi
-	if [ ! -d extensions/sample/src ] ; then git clone http://github.com/NetLogo/Sample-Extension.git extensions/sample ; fi
-	if [ ! -d extensions/sample-scala/src ] ; then git clone http://github.com/NetLogo/Sample-Scala-Extension.git extensions/sample-scala ; fi
-	if [ ! -d extensions/sound/src ] ; then git clone http://github.com/NetLogo/Sound-Extension.git extensions/sound ; fi
-	if [ ! -d extensions/table/src ] ; then git clone http://github.com/NetLogo/Table-Extension.git extensions/table ; fi
+	git submodule update --init
 	@echo "@@@ building" $(notdir $@)
 	cd $(dir $@); JAVA_HOME=$(JAVA_HOME) SCALA_JAR=../../$(SCALA_JAR) make -s $(notdir $@)
 
-# pull down versions core devel has rights to push to - ST 5/12/11
-.PHONY: repos
-repos:
-	mkdir -p models
-	if [ ! -d models/test ] ; then git clone git@git.assembla.com:models.git ; fi
-	cd models; git pull; git status
-	mkdir -p extensions
-	if [ ! -d extensions/array/src ] ; then git clone git@github.com:/NetLogo/Array-Extension.git extensions/array ; fi
-	cd extensions/array; git pull; git status
-	if [ ! -d extensions/bitmap/src ] ; then git clone git@github.com:/NetLogo/Bitmap-Extension.git extensions/bitmap ; fi
-	cd extensions/bitmap; git pull; git status
-	if [ ! -d extensions/gis/src ] ; then git clone git@github.com:/NetLogo/GIS-Extension.git extensions/gis ; fi
-	cd extensions/gis; git pull; git status
-	if [ ! -d extensions/gogo/src ] ; then git clone git@github.com:/NetLogo/GoGo-Extension.git extensions/gogo ; fi
-	cd extensions/gogo; git pull; git status
-	if [ ! -d extensions/matrix/src ] ; then git clone git@github.com:/NetLogo/Matrix-Extension.git extensions/matrix ; fi
-	cd extensions/matrix; git pull; git status
-	if [ ! -d extensions/network/src ] ; then git clone git@github.com:/NetLogo/Network-Extension.git extensions/network ; fi
-	cd extensions/network; git pull; git status
-	if [ ! -d extensions/profiler/src ] ; then git clone git@github.com:/NetLogo/Profiler-Extension.git extensions/profiler ; fi
-	cd extensions/profiler; git pull; git status
-	if [ ! -d extensions/qtj/src ] ; then git clone git@github.com:/NetLogo/QTJ-Extension.git extensions/qtj ; fi
-	cd extensions/qtj; git pull; git status
-	if [ ! -d extensions/sample/src ] ; then git clone git@github.com:/NetLogo/Sample-Extension.git extensions/sample ; fi
-	cd extensions/sample; git pull; git status
-	if [ ! -d extensions/sample-scala/src ] ; then git clone git@github.com:/NetLogo/Sample-Scala-Extension.git extensions/sample-scala ; fi
-	cd extensions/sample-scala; git pull; git status
-	if [ ! -d extensions/sound/src ] ; then git clone git@github.com:/NetLogo/Sound-Extension.git extensions/sound ; fi
-	cd extensions/sound; git pull; git status
-	if [ ! -d extensions/table/src ] ; then git clone git@github.com:/NetLogo/Table-Extension.git extensions/table ; fi
-	cd extensions/table; git pull; git status
-
 ### Scaladoc
 
 # for internal devel team use
@@ -150,8 +104,11 @@ tmp/scaladoc: netlogo | tmp
 	  -doc-version `cat tmp/version.txt` \
 	  -classpath $(LIBS)$(CLASSES) \
 	  -sourcepath src/main \
+          -doc-source-url https://github.com/NetLogo/NetLogo/blob/`cat tmp/version.txt`/src/main€{FILE_PATH}.scala \
 	  -encoding us-ascii \
           `find src/main -name \*.scala -o -name \*.java`
+# compensate for issues.scala-lang.org/browse/SI-5388
+	perl -pi -e 's/\.java.scala/.java/g' `find tmp/scaladoc -name \*.html`
 
 # these are the docs we include with the User Manual
 docs/scaladoc: netlogo
@@ -164,6 +121,7 @@ docs/scaladoc: netlogo
 	  -doc-version `cat tmp/version.txt` \
 	  -classpath $(LIBS)$(CLASSES) \
 	  -sourcepath src/main \
+          -doc-source-url https://github.com/NetLogo/NetLogo/blob/`cat tmp/version.txt`/src/main€{FILE_PATH}.scala \
 	  -encoding us-ascii \
 	  src/main/org/nlogo/app/App.scala \
 	  src/main/org/nlogo/lite/InterfaceComponent.scala \
@@ -174,6 +132,8 @@ docs/scaladoc: netlogo
           src/main/org/nlogo/agent/*.*a \
           src/main/org/nlogo/workspace/*.*a \
           src/main/org/nlogo/nvm/*.*a
+# compensate for issues.scala-lang.org/browse/SI-5388
+	perl -pi -e 's/\.java.scala/.java/g' `find docs/scaladoc -name \*.html`
 
 ### misc targets
 

README.md

@@ -2,7 +2,7 @@
 
 This page is for open source developers interested in the source code for NetLogo.
 
-Other users should visit the NetLogo home page at [http://ccl.northwestern.edu/netlogo/](http://ccl.northwestern.edu/netlogo/).
+Other users should visit the [NetLogo home page](http://ccl.northwestern.edu/netlogo/) at Northwestern and the [NetLogo users group](http://groups.yahoo.com/group/netlogo-users/) on Yahoo.
 
 ## Issues
 

bin/release.sh

@@ -9,7 +9,6 @@ CHMOD=chmod
 CP=cp
 DU=du
 FIND=find
-GIT=git
 GREP=grep
 HDIUTIL=hdiutil
 IJ=bin/install4jc
@@ -45,11 +44,6 @@ then
   exit 1
 fi
 
-# maybe we should be using the "submodules" feature of git for this? - ST 5/7/11
-if [ ! -d "Mathematica-Link" ]; then
-  $GIT clone git@github.com:NetLogo/Mathematica-Link.git
-fi
-
 if [ ! -f "Mathematica-Link/JLink.jar" ]; then
   echo "Mathematica-Link/JLink.jar missing. copy it from a Mathematica installation (or the 4.1 branch, if you're a CCL'er)"
   echo "(it's needed to compile the link, but we don't have a license to distribute it)"

bin/submodules.sh

@@ -0,0 +1,22 @@
+#!/bin/sh -ev
+
+# Normally "git submodule update --init", invoked by the Makefile, clones
+# our submodules from read-only URLs.  But if you are a NetLogo committer,
+# you want to clone from URLs that you have push access to.  Running this
+# script after cloning the main repo will override the URLs in .git/config
+# so you can push to all repos.
+
+git config submodule.models.url git@git.assembla.com:models.git
+git config submodule.Mathematica-Link.url git@github.com:NetLogo/Mathematica-Link.git
+git config submodule.extensions/array.url git@github.com:/NetLogo/Array-Extension.git
+git config submodule.extensions/bitmap.url git@github.com:/NetLogo/Bitmap-Extension.git
+git config submodule.extensions/gis.url git@github.com:/NetLogo/GIS-Extension.git
+git config submodule.extensions/gogo.url git@github.com:/NetLogo/GoGo-Extension.git
+git config submodule.extensions/matrix.url git@github.com:/NetLogo/Matrix-Extension.git
+git config submodule.extensions/network.url git@github.com:/NetLogo/Network-Extension.git
+git config submodule.extensions/profiler.url git@github.com:/NetLogo/Profiler-Extension.git
+git config submodule.extensions/qtj.url git@github.com:/NetLogo/QTJ-Extension.git
+git config submodule.extensions/sample.url git@github.com:/NetLogo/Sample-Extension.git
+git config submodule.extensions/sample-scala.url git@github.com:/NetLogo/Sample-Scala-Extension.git
+git config submodule.extensions/sound.url git@github.com:/NetLogo/Sound-Extension.git
+git config submodule.extensions/table.url git@github.com:/NetLogo/Table-Extension.git

src/test/org/nlogo/headless/TestCompiler.scala

@@ -168,7 +168,6 @@ class TestCompiler extends FunSuite with OneInstancePerTest with BeforeAndAfterE
   test("isReporter on user-defined procedures") {
     workspace.initForTesting(5, "to foo end to-report bar [] report 5 end")
     import collection.JavaConverters._
-    println(workspace.getProcedures.asScala.toMap)
     expect(false) { workspace.isReporter("foo") }
     expect(true) { workspace.isReporter("bar") }
   }