Merge branch 'develop'

# Conflicts:
#	src/main/java/de/tlc4b/TLC4B.java

.gitignore

@@ -14,3 +14,7 @@ src/test/resources/testing
 src/test/resources/todo
 TLC4B.jar
 temp
+out/
+src/test/**/*.tla
+src/test/**/*.cfg
+public_examples

.travis.yml

 language: java
-sudo: true
-script: gradle build
+script: ./gradlew --no-daemon --console verbose --stacktrace build
 before_install:
 - openssl aes-256-cbc -pass pass:$ENCRYPTION_PASSWORD -in secring.gpg.enc -out secring.gpg
   -d
@@ -8,10 +7,7 @@ before_install:
   -d
 - openssl aes-256-cbc -pass pass:$ENCRYPTION_PASSWORD -in gradle.properties.enc -out
   gradle.properties -d
-after_success: "[ $TRAVIS_BRANCH = 'master' ] && gradle uploadArchives"
+after_success: "[ $TRAVIS_BRANCH = 'master' ] && ./gradlew --no-daemon uploadArchives"
 env:
   global:
   - secure: EnIo0zaQsHATGH8S5L1W0EHtqgV2kx6bfSgxyhz7XU+xw5y2JLDn+Y3ZaX7EcMK25RkgM8nld5Se72QmpienkP7tQlb5KHdwC10KgwbHDq+IP9q+ZMD2V1MsMRdTilW/eTZ0SUohlV5g4t3KqIe8l3Hs1dzNL0YmCMtXwYHdfwk=
-notifications:
-  slack:
-    secure: VWTQE6Z6o9Xz4gZ1SOUKroz5g+exD//+FUdd6wM0tLESFhqqrfwR1dyZHIbQJpcC8KROQD5Bip6vihhACBmr+NU6nPwoNN7fJ9Dvgqt4xG4NEk3+VpVCQVfRDJF4IhHqRFx4K+9fV5I2Kr93G39U/N92lMLk/RkyoaUyju85uwM=

build.gradle

-apply plugin: 'java'
-apply plugin: 'eclipse'
-apply plugin: 'maven'
-apply plugin: 'jacoco'
-apply plugin: 'findbugs'
+plugins {
+    id 'java'
+    id 'eclipse'
+    id 'maven'
+    id 'jacoco'
+    id 'findbugs'
+    id "de.undercouch.download" version "3.4.3"
+}
 
-project.version = '1.0.3'
+project.version = '1.0.4'
 project.group = 'de.hhu.stups'
 
 project.sourceCompatibility = '1.7'
@@ -46,11 +49,12 @@ jacoco {
     reportsDir = file("$buildDir/JacocoReports")
 }
 
+
 jacocoTestReport {
     reports {
         xml.enabled false
         csv.enabled false
-        html.destination "${buildDir}/jacocoHtml"
+        html.destination file("${buildDir}/jacocoHtml")
     }
 }
 
@@ -61,13 +65,28 @@ test {
 	//exclude('de/tlc4b/tlc/integration')
 }
 
+task downloadPublicExamples(type: Download) {
+  src 'https://www3.hhu.de/stups/downloads/prob/source/ProB_public_examples.tgz'
+  dest buildDir
+  onlyIfModified true
+}
+
+task extractPublicExamples(dependsOn: downloadPublicExamples, type: Copy) {
+  from tarTree(resources.gzip("${buildDir}/ProB_public_examples.tgz"))
+  into projectDir
+}
+
+clean {
+  delete "${projectDir}/public_examples"
+}
 
-task regressionTests(type: Test){
+task regressionTests(dependsOn: extractPublicExamples, type: Test){
 	doFirst{ println("Running integration tests") }
 	scanForTestClasses = true
 	//include('de/tlc4b/tlc/integration/probprivate/**')
 	include('de/tlc4b/**')
 }
+check.dependsOn(regressionTests)
 
 // type 'gradle integrationTests jacocoIntegrationTestReport' in order to run the jacoco code coverage analysis
 task jacocoIntegrationTestReport(type: JacocoReport) {

gradle/wrapper/gradle-wrapper.properties

+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.10.2-bin.zip
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists

gradlew

+#!/usr/bin/env sh
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn () {
+    echo "$*"
+}
+
+die () {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
+
+exec "$JAVACMD" "$@"

gradlew.bat

+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

src/main/java/de/tlc4b/TLC4B.java

@@ -376,7 +376,7 @@ public class TLC4B {
 		// the following lines fix incorrect file names
 		filename = filename.replace("\\", File.separator);
 		filename = filename.replace("/", File.separator);
-		if (!filename.toLowerCase().endsWith(".mch") ||
+		if (!filename.toLowerCase().endsWith(".mch") &&
 		    !filename.toLowerCase().endsWith(".sys")) {
 			filename = filename + ".mch";
 		}

src/test/java/de/tlc4b/coverage/CoverageTest.java

@@ -32,7 +32,7 @@ public class CoverageTest extends AbstractParseMachineTest {
 	public static Configuration getConfig() {
 		final ArrayList<String> list = new ArrayList<String>();
 		final ArrayList<String> ignoreList = new ArrayList<String>();
-		list.add("../prob_examples/public_examples/TLC/");
+		list.add("public_examples/TLC/");
 
 		list.add("./src/test/resources/");
 		ignoreList.add("./src/test/resources/compound/");

src/test/java/de/tlc4b/tlc/integration/probprivate/AssertionErrorTest.java

@@ -37,7 +37,7 @@ public class AssertionErrorTest extends AbstractParseMachineTest {
 	@Config
 	public static Configuration getConfig() {
 		final ArrayList<TestPair> list = new ArrayList<TestPair>();
-		list.add(new TestPair(AssertionError, "../prob_examples/public_examples/TLC/AssertionError"));
+		list.add(new TestPair(AssertionError, "public_examples/TLC/AssertionError"));
 		return getConfiguration(list);
 	}
 }

src/test/java/de/tlc4b/tlc/integration/probprivate/DeadlockTest.java

@@ -38,7 +38,7 @@ public class DeadlockTest extends AbstractParseMachineTest {
 	public static Configuration getConfig() {
 		final ArrayList<TestPair> list = new ArrayList<TestPair>();
 		list.add(new TestPair(Deadlock,
-				"../prob_examples/public_examples/TLC/Deadlock"));
+				"public_examples/TLC/Deadlock"));
 		return getConfiguration(list);
 	}
 }

src/test/java/de/tlc4b/tlc/integration/probprivate/GoalTest.java

@@ -38,7 +38,7 @@ public class GoalTest extends AbstractParseMachineTest {
 	public static Configuration getConfig() {
 		final ArrayList<TestPair> list = new ArrayList<TestPair>();
 		list.add(new TestPair(Goal,
-				"../prob_examples/public_examples/TLC/GOAL"));
+				"public_examples/TLC/GOAL"));
 		return getConfiguration(list);
 	}
 }

src/test/java/de/tlc4b/tlc/integration/probprivate/InvariantViolationTest.java

@@ -38,7 +38,7 @@ public class InvariantViolationTest extends AbstractParseMachineTest {
 	public static Configuration getConfig() {
 		final ArrayList<TestPair> list = new ArrayList<TestPair>();
 		list.add(new TestPair(InvariantViolation,
-				"../prob_examples/public_examples/TLC/InvariantViolation"));
+				"public_examples/TLC/InvariantViolation"));
 		return getConfiguration(list);
 	}
 }

src/test/java/de/tlc4b/tlc/integration/probprivate/LawsTest.java

@@ -17,70 +17,70 @@ public class LawsTest {
 	@Test
 	public void BoolLaws() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/BoolLaws.mch"};
+		String[] a = new String[] { "public_examples/TLC/Laws/BoolLaws.mch"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void BoolWithArithLaws() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/BoolWithArithLaws.mch", "-nodead"};
+		String[] a = new String[] { "public_examples/TLC/Laws/BoolWithArithLaws.mch", "-nodead"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void FunLaws() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/FunLaws.mch"};
+		String[] a = new String[] { "public_examples/TLC/Laws/FunLaws.mch"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void FunLawsWithLambda() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/FunLawsWithLambda.mch"};
+		String[] a = new String[] { "public_examples/TLC/Laws/FunLawsWithLambda.mch"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void RelLaws_TLC() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/RelLaws_TLC.mch"};
+		String[] a = new String[] { "public_examples/TLC/Laws/RelLaws_TLC.mch"};
 		assertEquals(Goal, test(a));
 	}
 	
 	@Test
 	public void BoolLaws_SetCompr() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/BoolLaws_SetCompr.mch"};
+		String[] a = new String[] { "public_examples/TLC/Laws/BoolLaws_SetCompr.mch"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void BoolLaws_SetComprCLPFD() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/BoolLaws_SetComprCLPFD.mch"};
+		String[] a = new String[] { "public_examples/TLC/Laws/BoolLaws_SetComprCLPFD.mch"};
 		assertEquals(NoError, test(a));
 	}
 
 	@Test
 	public void CardinalityLaws_TLC() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/CardinalityLaws_TLC.mch", "-nodead"};
+		String[] a = new String[] { "public_examples/TLC/Laws/CardinalityLaws_TLC.mch", "-nodead"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void EqualityLaws() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/EqualityLaws.mch", "-nodead"};
+		String[] a = new String[] { "public_examples/TLC/Laws/EqualityLaws.mch", "-nodead"};
 		assertEquals(NoError, test(a));
 	}
 	
 	@Test
 	public void SubsetLaws() throws Exception {
 		TLC4BGlobals.setDeleteOnExit(true);
-		String[] a = new String[] { "../prob_examples/public_examples/TLC/Laws/SubsetLaws.mch", "-nodead"};
+		String[] a = new String[] { "public_examples/TLC/Laws/SubsetLaws.mch", "-nodead"};
 		assertEquals(NoError, test(a));
 	}
 }

src/test/java/de/tlc4b/tlc/integration/probprivate/NoErrorTest.java

@@ -38,7 +38,7 @@ public class NoErrorTest extends AbstractParseMachineTest {
 	public static Configuration getConfig() {
 		final ArrayList<TestPair> list = new ArrayList<TestPair>();
 		list.add(new TestPair(NoError,
-				"../prob_examples/public_examples/TLC/NoError"));
+				"public_examples/TLC/NoError"));
 		return getConfiguration(list);
 	}
 

src/test/java/de/tlc4b/tlc/integration/probprivate/WellDefinednessTest.java

@@ -37,7 +37,7 @@ public class WellDefinednessTest extends AbstractParseMachineTest  {
 		@Config
 		public static Configuration getConfig() {
 			final ArrayList<TestPair> list = new ArrayList<TestPair>();
-			list.add(new TestPair(WellDefinednessError, "../prob_examples/public_examples/TLC/WellDefinednessError"));
+			list.add(new TestPair(WellDefinednessError, "public_examples/TLC/WellDefinednessError"));
 			return getConfiguration(list);
 		}
 }