Merge branch 'heads/v2.1'

Author: nmacedo

build.xml

@@ -37,7 +37,7 @@
 
 		<taskdef name="jarbundler" classpath="./lib/jarbundler-2.4.0.jar" classname="net.sourceforge.jarbundler.JarBundler" />
 
-		<jarbundler dir="dist" name="Alloy${env.VERSION}" mainclass="edu.mit.csail.sdg.alloy4whole.SimpleGUI" jar="dist/${env.jarName}" jvmversion="1.6+" vmoptions="-Xmx1024m -Xdock:name=Alloy${env.VERSION}" signature="AA42" build="${env.VERSION}" bundleid="edu.mit.csail.sdg.alloy4whole.SimpleGUI" stubfile="OSX-JavaStub/JavaApplicationStub" icon="OSX-icons/AlloyLogo.icns" copyright="Alloy Analyzer by SDG group, MIT" shortname="Alloy">
+		<jarbundler dir="dist" name="Alloy${env.VERSION}" mainclass="edu.mit.csail.sdg.alloy4whole.SimpleMain" jar="dist/${env.jarName}" jvmversion="1.6+" vmoptions="-Xmx1024m -Xdock:name=Alloy${env.VERSION}" signature="AA42" build="${env.VERSION}" bundleid="edu.mit.csail.sdg.alloy4whole.SimpleMain" stubfile="OSX-JavaStub/JavaApplicationStub" icon="OSX-icons/AlloyLogo.icns" copyright="Alloy Analyzer by SDG group, MIT" shortname="Alloy">
 
 			<javaproperty name="apple.laf.useScreenMenuBar" value="true" />
 			<javaproperty name="apple.awt.antialiasing" value="true" />

cnf/central.xml

@@ -60,6 +60,11 @@
 			<artifactId>slf4j-simple</artifactId>
 			<version>1.7.5</version>
 		</dependency>
+		<dependency>
+			<groupId>commons-cli</groupId>
+			<artifactId>commons-cli</artifactId>
+			<version>1.4</version>
+		</dependency>
 	</dependencies>
 
 </project>

org.alloytools.alloy.application/.settings/org.eclipse.jdt.core.prefs

@@ -133,12 +133,16 @@ org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
 org.eclipse.jdt.core.compiler.problem.unusedWarningToken=ignore
 org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
 org.eclipse.jdt.core.compiler.processAnnotations=disabled
+org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.8
 org.eclipse.jdt.core.compiler.taskCaseSensitive=enabled
 org.eclipse.jdt.core.compiler.taskPriorities=NORMAL,NORMAL
 org.eclipse.jdt.core.compiler.taskTags=TODO,FIXME
+org.eclipse.jdt.core.formatter.align_assignment_statements_on_columns=false
 org.eclipse.jdt.core.formatter.align_fields_grouping_blank_lines=4
 org.eclipse.jdt.core.formatter.align_type_members_on_columns=true
+org.eclipse.jdt.core.formatter.align_variable_declarations_on_columns=false
+org.eclipse.jdt.core.formatter.align_with_spaces=false
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression=2
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation=51
 org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant=50
@@ -148,6 +152,7 @@ org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_e
 org.eclipse.jdt.core.formatter.alignment_for_assignment=2
 org.eclipse.jdt.core.formatter.alignment_for_binary_expression=2
 org.eclipse.jdt.core.formatter.alignment_for_compact_if=2
+org.eclipse.jdt.core.formatter.alignment_for_compact_loops=16
 org.eclipse.jdt.core.formatter.alignment_for_conditional_expression=2
 org.eclipse.jdt.core.formatter.alignment_for_enum_constants=51
 org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer=2
@@ -191,6 +196,8 @@ org.eclipse.jdt.core.formatter.brace_position_for_lambda_body=end_of_line
 org.eclipse.jdt.core.formatter.brace_position_for_method_declaration=end_of_line
 org.eclipse.jdt.core.formatter.brace_position_for_switch=end_of_line
 org.eclipse.jdt.core.formatter.brace_position_for_type_declaration=end_of_line
+org.eclipse.jdt.core.formatter.comment.align_tags_descriptions_grouped=false
+org.eclipse.jdt.core.formatter.comment.align_tags_names_descriptions=false
 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment=true
 org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment=false
 org.eclipse.jdt.core.formatter.comment.count_line_length_from_starting_position=true
@@ -242,13 +249,13 @@ org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_ini
 org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement=do not insert
 org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement=do not insert
 org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement=insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=do not insert
-org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=do not insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_constant=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_enum_declaration=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_method_body=insert
+org.eclipse.jdt.core.formatter.insert_new_line_in_empty_type_declaration=insert
 org.eclipse.jdt.core.formatter.insert_space_after_and_in_type_parameter=insert
 org.eclipse.jdt.core.formatter.insert_space_after_assignment_operator=insert
 org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation=do not insert
@@ -415,6 +422,9 @@ org.eclipse.jdt.core.formatter.join_wrapped_lines=false
 org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_empty_array_initializer_on_one_line=false
 org.eclipse.jdt.core.formatter.keep_imple_if_on_one_line=false
+org.eclipse.jdt.core.formatter.keep_simple_do_while_body_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_simple_for_body_on_same_line=false
+org.eclipse.jdt.core.formatter.keep_simple_while_body_on_same_line=false
 org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line=false
 org.eclipse.jdt.core.formatter.lineSplit=140
 org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column=false

org.alloytools.alloy.application/.settings/org.eclipse.jdt.ui.prefs

@@ -31,7 +31,9 @@ cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=tru
 cleanup.qualify_static_member_accesses_with_declaring_class=true
 cleanup.qualify_static_method_accesses_with_declaring_class=false
 cleanup.remove_private_constructors=true
-cleanup.remove_redundant_type_arguments=true
+cleanup.remove_redundant_modifiers=false
+cleanup.remove_redundant_semicolons=false
+cleanup.remove_redundant_type_arguments=false
 cleanup.remove_trailing_whitespaces=false
 cleanup.remove_trailing_whitespaces_all=true
 cleanup.remove_trailing_whitespaces_ignore_empty=false
@@ -60,7 +62,7 @@ cleanup_settings_version=2
 eclipse.preferences.version=1
 editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
 formatter_profile=_Alloy
-formatter_settings_version=13
+formatter_settings_version=14
 org.eclipse.jdt.ui.exception.name=e
 org.eclipse.jdt.ui.gettersetter.use.is=true
 org.eclipse.jdt.ui.ignorelowercasenames=true
@@ -88,7 +90,7 @@ sp_cleanup.convert_functional_interfaces=false
 sp_cleanup.convert_to_enhanced_for_loop=false
 sp_cleanup.correct_indentation=false
 sp_cleanup.format_source_code=true
-sp_cleanup.format_source_code_changes_only=false
+sp_cleanup.format_source_code_changes_only=true
 sp_cleanup.insert_inferred_type_arguments=false
 sp_cleanup.make_local_variable_final=false
 sp_cleanup.make_parameters_final=false
@@ -105,6 +107,8 @@ sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=
 sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
 sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
 sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_modifiers=false
+sp_cleanup.remove_redundant_semicolons=false
 sp_cleanup.remove_redundant_type_arguments=false
 sp_cleanup.remove_trailing_whitespaces=true
 sp_cleanup.remove_trailing_whitespaces_all=true

org.alloytools.alloy.application/bnd.bnd

@@ -1,10 +1,14 @@
 -includeresource: \
-	src/main/resources
+	src/main/resources,\
+    @${repo;slf4j.api},\
 
 -buildpath: \
 	lib/apple-osx-ui.jar;version=file,\
 	org.alloytools.pardinus;version=latest,\
 	org.alloytools.alloy.core;version=latest,\
+	org.apache.commons.cli;version=1.4,\
+    slf4j.api, \
+	
 
 -testpath: \
 	osgi.enroute.junit.wrapper, \
@@ -19,4 +23,4 @@
 Private-Package: \
 	edu.mit.csail.sdg.alloy4graph,\
 	edu.mit.csail.sdg.alloy4viz,\
-	edu.mit.csail.sdg.alloy4whole,\
+	edu.mit.csail.sdg.alloy4whole

org.alloytools.alloy.application/src/main/java/edu/mit/csail/sdg/alloy4graph/Graph.java

@@ -316,7 +316,7 @@ private void layout_assignOrder() {
                 grOUT.get(n.pos()).remove(x);
             for (GraphNode n : grOUT.get(x.pos()))
                 grIN.get(n.pos()).remove(x);
-            // [HASLab] hack to get nodes sorted lexicographically in each layer
+            // [HASLab] hack to get nodes sorted lexicographically within each layer
             // can't fast join since read-only
             //          Iterable<GraphNode> aux = Util.fastJoin(grIN.get(x.pos()), );
             List<GraphNode> aux = new ArrayList<GraphNode>(grIN.get(x.pos()));
@@ -336,7 +336,6 @@ public int compare(GraphNode o1, GraphNode o2) {
                     bins.get(b).add(n);
                 }
             }
-
         }
         sortNodes(Util.fastJoin(s1, s2));
     }

org.alloytools.alloy.application/src/main/java/edu/mit/csail/sdg/alloy4viz/StaticInstanceReader.java

@@ -235,7 +235,13 @@ private void atoms(A4Solution sol, PrimSig s, int state) throws Err {
             sum = sum.plus(c);
             atoms(sol, c, state); // [HASLab]
         }
-        A4TupleSet ts = (A4TupleSet) (sol.eval(s.minus(sum), state)); // [HASLab] // This ensures that atoms will be associated with the most specific sig
+        A4TupleSet ts = (A4TupleSet) (sol.eval(s.minus(sum), state)); // [HASLab]
+                                                              // This ensures
+                                                              // that atoms
+                                                              // will be
+                                                              // associated
+                                                              // with the most
+                                                              // specific sig
         for (A4Tuple z : ts) {
             String atom = z.atom(0);
             int i, dollar = atom.lastIndexOf('$');
@@ -416,7 +422,7 @@ private StaticInstanceReader(XMLNode root, int state) throws Err {
     }
 
     /** Parse the file into an AlloyInstance if possible. */
-    // [HASLab]
+    // [HASLab] particular state
     public static AlloyInstance parseInstance(File file, int state) throws Err {
         try {
             return (new StaticInstanceReader(new XMLNode(file), state)).ans; // [HASLab]
@@ -429,7 +435,7 @@ public static AlloyInstance parseInstance(File file, int state) throws Err {
      * Parse the file into an AlloyInstance if possible, then close the Reader
      * afterwards.
      */
-    // [HASLab]
+    // [HASLab] particular state
     public static AlloyInstance parseInstance(Reader reader, int state) throws Err {
         try {
             return (new StaticInstanceReader(new XMLNode(reader), state)).ans; // [HASLab]