Catalyst: change package name to org.shemshak.alloy.catalyst

As well as a few minor enhancements to SSR.java

org.aminb.alloy.catalyst.dist/.project → org.shemshak.alloy.catalyst.dist/.project

 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>org.aminb.alloy.catalyst.dist</name>
+	<name>org.shemshak.alloy.catalyst.dist</name>
 	<comment></comment>
 	<projects>
 	</projects>

org.aminb.alloy.catalyst.dist/bnd.bnd → org.shemshak.alloy.catalyst.dist/bnd.bnd

 
-Main-Class: org.aminb.alloy.catalyst.MainCLI
+Main-Class: org.shemshak.alloy.catalyst.MainCLI
 
 -buildpath: \
-	org.aminb.alloy.catalyst,\
+	org.shemshak.alloy.catalyst,\
     org.alloytools.alloy.core,\
 	org.alloytools.kodkod.core;version=latest,\
 	org.alloytools.kodkod.nativesat.x86-windows;version=latest,\
@@ -14,7 +14,7 @@ Main-Class: org.aminb.alloy.catalyst.MainCLI
 -sources: false
 
 -includeresource: \
-	@${repo;org.aminb.alloy.catalyst}, \
+	@${repo;org.shemshak.alloy.catalyst}, \
     @${repo;org.alloytools.alloy.core}, \
 	@${repo;org.alloytools.kodkod.core}, \
 	@${repo;org.alloytools.kodkod.nativesat.util}, \

org.aminb.alloy.catalyst/.project → org.shemshak.alloy.catalyst/.project

 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>org.aminb.alloy.catalyst</name>
+	<name>org.shemshak.alloy.catalyst</name>
 	<comment></comment>
 	<projects>
 	</projects>

org.aminb.alloy.catalyst/bnd.bnd → org.shemshak.alloy.catalyst/bnd.bnd

-Main-Class: org.aminb.alloy.catalyst.MainCLI
+Main-Class: org.shemshak.alloy.catalyst.MainCLI
 
 -buildpath: \
 	org.alloytools.alloy.core;version=latest,\
@@ -15,5 +15,5 @@ Main-Class: org.aminb.alloy.catalyst.MainCLI
 	com.google.gson
 
 Private-Package: \
-	org.aminb.alloy.catalyst,\
+	org.shemshak.alloy.catalyst,\
 	kodkod.engine.satlab;-split-package:=merge-first

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/CatalystCommand.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/CatalystCommand.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import java.io.BufferedWriter;
 import java.io.FileNotFoundException;

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/GitHubAlloyCLI.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/GitHubAlloyCLI.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import org.apache.commons.codec.digest.DigestUtils;
 import org.kohsuke.github.GHRepository;

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/Item.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/Item.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import edu.mit.csail.sdg.ast.Expr;
 import edu.mit.csail.sdg.ast.Func;

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/MainCLI.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/MainCLI.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import picocli.CommandLine;
 import picocli.CommandLine.Command;
@@ -13,7 +13,7 @@ import picocli.CommandLine.Command;
              "Catalyst is free software: you are free to change and redistribute it.",
              "There is NO WARRANTY, to the extent permitted by law.",
              "",
-             "Written by Amin Bandali."
+             "Written by Amin Bandali <https://shemshak.org/~amin>."
          },
          description = "A framework for analysis/optimization of performance of Alloy models.",
          customSynopsis = "@|bold catalyst|@ [OPTION] COMMAND",

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/Mut.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/Mut.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import java.io.IOException;
 import java.io.Writer;

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/Result.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/Result.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import java.util.List;
 

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/SSR.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/SSR.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import java.io.File;
 import java.io.IOException;
@@ -10,8 +10,6 @@ import java.time.Duration;
 import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
-import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
@@ -71,9 +69,6 @@ public final class SSR extends CatalystCommand implements Runnable {
     protected final CorpusResult analyzeCorpus(String corpus) {
         CorpusResult cr = new CorpusResult();
         cr.corpus_name = corpus;
-        cr.file_results = parallel ?
-            Collections.synchronizedList(new ArrayList<FileResult>()) :
-            new ArrayList<FileResult>();
 
         pln();
 
@@ -81,15 +76,17 @@ public final class SSR extends CatalystCommand implements Runnable {
         try {
             List<Path> files = Files.walk(Paths.get(modelsDir, corpus))
                 .filter(Files::isRegularFile)
+                .filter(p -> p.getFileName().toString().endsWith(".als"))
+                .filter(p -> !Arrays.asList(ignoredFiles).contains(p.getFileName().toString()))
                 .collect(Collectors.toList());
             cr.file_count = files.size();
             pln("number of " + corpus + " models: " + cr.file_count);
             r.total_file_count += cr.file_count;
             AtomicInteger i = new AtomicInteger(1);
             Stream<Path> fs = parallel ? files.parallelStream() : files.stream();
-            fs.filter(p -> p.getFileName().toString().endsWith(".als"))
-                .filter(p -> !Arrays.asList(ignoredFiles).contains(p.getFileName().toString()))
-                .forEach(p -> cr.file_results.add(analyzeFile(corpus, p, i.getAndIncrement(), cr.file_count)));
+            cr.file_results =
+                fs.map(p -> analyzeFile(corpus, p, i.getAndIncrement(), cr.file_count))
+                .collect(Collectors.toList());
         } catch (Exception e) {
             String msg = "Failed while trying to iterate through and analyze " + corpus + " models.";
             cr.error = String.format("%s%n%s", msg, Utils.toString(e));
@@ -125,7 +122,6 @@ public final class SSR extends CatalystCommand implements Runnable {
     protected final FileResult analyzeFile(String corpus, Path p, int index, int total) {
         FileResult fr = new FileResult();
         fr.file_name = p.toString();
-        fr.mutation_results = new ArrayList<MutationResult>();
         fr.errors = new ArrayList<ParseOrTypeError>();
 
         String progress = String.format("[%d/%d]: ", index, total);

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/SSRVisitor.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/SSRVisitor.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import java.util.Arrays;
 import java.util.HashSet;

org.aminb.alloy.catalyst/src/main/java/org/aminb/alloy/catalyst/Utils.java → org.shemshak.alloy.catalyst/src/main/java/org/shemshak/alloy/catalyst/Utils.java

-package org.aminb.alloy.catalyst;
+package org.shemshak.alloy.catalyst;
 
 import java.io.File;
 import java.nio.file.Path;