suppress reporting of coverage stats

Arcmutates advanced incremental processing includes the option to avoid
gathering coverage for tests which cannot kill an in scope mutant.
Although this speeds up processing the html report shows most lines
as uncovered when this feature is activated. Reporting of line coverage
it therefore disabled when this feature is activated.

pitest-aggregator/src/main/java/org/pitest/aggregate/ReportAggregator.java

@@ -8,7 +8,6 @@
 import org.pitest.coverage.analysis.LineMapper;
 import org.pitest.mutationtest.ClassMutationResults;
 import org.pitest.mutationtest.MutationMetaData;
-import org.pitest.mutationtest.MutationResult;
 import org.pitest.mutationtest.MutationResultListener;
 import org.pitest.mutationtest.SourceLocator;
 import org.pitest.mutationtest.build.CoverageTransformer;
@@ -21,17 +20,20 @@
 import org.pitest.util.ResultOutputStrategy;
 
 import java.io.File;
+import java.io.IOException;
+import java.io.UncheckedIOException;
 import java.nio.charset.Charset;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
-import java.util.function.Function;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import static java.util.Arrays.asList;
 
@@ -68,7 +70,9 @@ private ReportAggregator(SettingsFactory settings,
   public AggregationResult aggregateReport() throws ReportAggregationException {
     SmartSourceLocator sourceLocator = new SmartSourceLocator(asPaths(this.sourceCodeDirectories), inputCharset);
 
-    final MutationResultListener mutationResultListener = createResultListener(sourceLocator, Collections.emptySet());
+    boolean partialCoverage = scanForPartialCoverageFlag(mutationFiles);
+
+    final MutationResultListener mutationResultListener = createResultListener(sourceLocator, Collections.emptySet(), partialCoverage);
     final ReportAggregatorResultListener reportAggregatorResultListener = new ReportAggregatorResultListener();
 
     reportAggregatorResultListener.runStart();
@@ -93,11 +97,27 @@ public AggregationResult aggregateReport() throws ReportAggregationException {
     return reportAggregatorResultListener.result();
   }
 
-  private MutationResultListener createResultListener(SourceLocator sourceLocator, Collection<String> mutatorNames) throws ReportAggregationException {
+  private boolean scanForPartialCoverageFlag(Set<File> mutationFiles) {
+    // scan for the partial coverage flag. All files should have the same flag, so only really
+    // need to scan the first line of the first file, but expressing as a loop here just because.
+    for (File each : mutationFiles) {
+      try (Stream<String> lines = Files.lines(each.toPath())) {
+        // search for a false flag as this is the most likely case
+        if (lines.anyMatch(l -> l.contains("<mutations partial=\"false\"")) ) {
+          return false;
+        }
+      } catch (IOException e) {
+        throw new UncheckedIOException(e);
+      }
+    }
+    return true;
+  }
+
+  private MutationResultListener createResultListener(SourceLocator sourceLocator, Collection<String> mutatorNames, boolean partialCoverage) throws ReportAggregationException {
     final CodeSource codeSource = this.codeSourceAggregator.createCodeSource();
     final ReportCoverage coverageDatabase = calculateCoverage(codeSource);
 
-    return new MutationHtmlReportListener(outputCharset, coverageDatabase, this.resultOutputStrategy, mutatorNames, sourceLocator);
+    return new MutationHtmlReportListener(outputCharset, coverageDatabase, this.resultOutputStrategy, mutatorNames, partialCoverage, sourceLocator);
   }
 
   private Collection<Path> asPaths(Collection<File> files) {
@@ -106,17 +126,6 @@ private Collection<Path> asPaths(Collection<File> files) {
             .collect(Collectors.toList());
   }
 
-  private static Function<MutationResult, List<String>> resultToMutatorName() {
-    return a -> {
-      try {
-        final String mutatorName = a.getDetails().getId().getMutator();//MutatorUtil.loadMutator(a.getDetails().getMutator()).getName();
-        return Collections.singletonList(mutatorName);
-      } catch (final Exception e) {
-        throw new RuntimeException("Cannot convert to mutator: " + a.getDetails().getMutator(), e);
-      }
-    };
-  }
-
   private ReportCoverage calculateCoverage(final CodeSource codeSource) throws ReportAggregationException {
     try {
       Collection<BlockLocation> coverageData = this.blockCoverageLoader.loadData().stream()

pitest-entry/src/main/java/org/pitest/mutationtest/config/ReportOptions.java

@@ -132,6 +132,8 @@ public class ReportOptions {
 
   private boolean                        includeLaunchClasspath         = true;
 
+  private boolean                        reportCoverage                 = true;
+
   private Properties                     properties;
 
   private int maxSurvivors;
@@ -647,6 +649,13 @@ public void setOutputEncoding(Charset outputEncoding) {
     this.outputEncoding = outputEncoding;
   }
 
+  public boolean shouldReportCoverage() {
+    return reportCoverage;
+  }
+
+  public void setReportCoverage(boolean reportCoverage) {
+    this.reportCoverage = reportCoverage;
+  }
 
   @Override
   public String toString() {
@@ -695,6 +704,7 @@ public String toString() {
             .add("projectBase=" + projectBase)
             .add("inputEncoding=" + inputEncoding)
             .add("outputEncoding=" + outputEncoding)
+            .add("reportCoverage=" + reportCoverage)
             .toString();
   }
 

pitest-entry/src/main/java/org/pitest/mutationtest/report/xml/XMLReportFactory.java

@@ -25,7 +25,7 @@ public class XMLReportFactory implements MutationResultListenerFactory {
   @Override
   public MutationResultListener getListener(Properties props,
       final ListenerArguments args) {
-    return new XMLReportListener(args.getOutputStrategy(), args.isFullMutationMatrix());
+    return new XMLReportListener(args.getOutputStrategy(), args.isFullMutationMatrix(), args.data().shouldReportCoverage());
   }
 
   @Override

pitest-entry/src/main/java/org/pitest/mutationtest/report/xml/XMLReportListener.java

@@ -55,13 +55,16 @@ public class XMLReportListener implements MutationResultListener {
   private final Writer out;
   private final boolean fullMutationMatrix;
 
-  public XMLReportListener(final ResultOutputStrategy outputStrategy, boolean fullMutationMatrix) {
-    this(outputStrategy.createWriterForFile("mutations.xml"), fullMutationMatrix);
+  private final boolean partialCoverage;
+
+  public XMLReportListener(final ResultOutputStrategy outputStrategy, boolean fullMutationMatrix, boolean partialCoverage) {
+    this(outputStrategy.createWriterForFile("mutations.xml"), fullMutationMatrix, partialCoverage);
   }
 
-  public XMLReportListener(final Writer out, boolean fullMutationMatrix) {
+  public XMLReportListener(final Writer out, boolean fullMutationMatrix, boolean partialCoverage) {
     this.out = out;
     this.fullMutationMatrix = fullMutationMatrix;
+    this.partialCoverage = partialCoverage;
   }
 
   private void writeResult(final ClassMutationResults metaData) {
@@ -176,7 +179,7 @@ private void write(final String value) {
   @Override
   public void runStart() {
     write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
-    write("<mutations>\n");
+    write("<mutations partial=\"" + this.partialCoverage + "\">\n");
   }
 
   @Override

pitest-entry/src/test/java/org/pitest/mutationtest/report/xml/XMLReportListenerTest.java

@@ -37,14 +37,14 @@ public class XMLReportListenerTest {
   @Before
   public void setup() {
     this.out = new StringWriter();
-    this.testee = new XMLReportListener(this.out, false);
+    this.testee = new XMLReportListener(this.out, false, false);
   }
 
   @Test
   public void shouldCreateAValidXmlDocumentWhenNoResults() {
     this.testee.runStart();
     this.testee.runEnd();
-    final String expected = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<mutations>\n</mutations>\n";
+    final String expected = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<mutations partial=\"false\">\n</mutations>\n";
     assertThat(expected).isEqualTo(this.out.toString());
   }
 
@@ -61,7 +61,7 @@ public void shouldOutputKillingTestWhenOneFound() {
 
   @Test
   public void shouldOutputFullMutationMatrixWhenEnabled() {
-    this.testee = new XMLReportListener(this.out, true);
+    this.testee = new XMLReportListener(this.out, true, false);
     final MutationResult mr = new MutationResult(
             MutationTestResultMother.createDetails(),
             new MutationStatusTestPair(3, DetectionStatus.KILLED, Arrays.asList("foo", "foo2"), Arrays.asList("bar")));

pitest-html-report/src/main/java/org/pitest/mutationtest/report/html/AnnotatedLineFactory.java

@@ -32,19 +32,20 @@
 
 public class AnnotatedLineFactory {
 
-  private final Collection<MutationResult>         mutations;
-  private final ReportCoverage                     coverage;
-  private final Collection<ClassLines>             classesInFile;
-
-  private final Set<Integer>                       coveredLines;
+  private final Collection<MutationResult> mutations;
+  private final Collection<ClassLines> classesInFile;
+  private final Set<Integer>  coveredLines;
+  private final boolean reportCoverage;
 
   public AnnotatedLineFactory(
           final Collection<MutationResult> mutations,
-          final ReportCoverage coverage, final Collection<ClassLines> classes) {
+          final ReportCoverage coverage,
+          final Collection<ClassLines> classes,
+          boolean reportCoverage) {
     this.mutations = mutations;
-    this.coverage = coverage;
     this.classesInFile = classes;
     this.coveredLines = findCoveredLines(classes,coverage);
+    this.reportCoverage = reportCoverage;
   }
 
   private Set<Integer> findCoveredLines(Collection<ClassLines> classes, ReportCoverage coverage) {
@@ -93,7 +94,7 @@ private Predicate<MutationResult> isAtLineNumber(final int lineNumber) {
 
   private LineStatus lineCovered(final int line) {
 
-    if (!isCodeLine(line)) {
+    if (!isCodeLine(line) || !reportCoverage) {
       return LineStatus.NotApplicable;
     } else {
       if (isLineCovered(line)) {

pitest-html-report/src/main/java/org/pitest/mutationtest/report/html/HtmlReportFactory.java

@@ -27,7 +27,7 @@ public class HtmlReportFactory implements MutationResultListenerFactory {
   public MutationResultListener getListener(Properties props,
       ListenerArguments args) {
     return new MutationHtmlReportListener(args.data().getOutputEncoding(), args.getCoverage(),
-        args.getOutputStrategy(), args.getEngine().getMutatorNames(),
+        args.getOutputStrategy(), args.getEngine().getMutatorNames(), args.data().shouldReportCoverage(),
         args.getLocator());
   }
 

pitest-html-report/src/main/java/org/pitest/mutationtest/report/html/MutationHtmlReportListener.java

@@ -56,16 +56,21 @@ public class MutationHtmlReportListener implements MutationResultListener {
 
   private final String                    css;
   private final Charset                   outputCharset;
-
-  public MutationHtmlReportListener(Charset outputCharset, final ReportCoverage coverage,
-                                    final ResultOutputStrategy outputStrategy,
-                                    Collection<String> mutatorNames, final SourceLocator... locators) {
+  private final boolean reportCoverage;
+
+  public MutationHtmlReportListener(Charset outputCharset,
+                                    ReportCoverage coverage,
+                                    ResultOutputStrategy outputStrategy,
+                                    Collection<String> mutatorNames,
+                                    boolean reportCoverage,
+                                    SourceLocator... locators) {
     this.outputCharset = outputCharset;
     this.coverage = coverage;
     this.outputStrategy = outputStrategy;
     this.sourceRoots = new HashSet<>(asList(locators));
     this.mutatorNames = new HashSet<>(mutatorNames);
     this.css = loadCss();
+    this.reportCoverage = reportCoverage;
   }
 
   private String loadCss() {
@@ -101,7 +106,7 @@ private void generateAnnotatedSourceFile(
       st.setAttribute("sourceFile", sourceFile);
       st.setAttribute("mutatedClasses", mutationMetaData.getMutatedClasses());
       st.setAttribute("outputCharset", this.outputCharset);
-
+      st.setAttribute("showCoverage", this.reportCoverage);
       writer.write(st.toString());
 
 
@@ -153,7 +158,7 @@ private List<Line> createAnnotatedSourceCodeLines(final String sourceFile,
         sourceFile);
     if (reader.isPresent()) {
       final AnnotatedLineFactory alf = new AnnotatedLineFactory(
-          mutationsForThisFile.list(), this.coverage, classes);
+          mutationsForThisFile.list(), this.coverage, classes, this.reportCoverage);
       return alf.convert(reader.get());
     }
     return Collections.emptyList();
@@ -215,6 +220,7 @@ private void createIndexPages() {
     st.setAttribute("totals", totals);
     st.setAttribute("packageSummaries", psd);
     st.setAttribute("outputCharset", this.outputCharset);
+    st.setAttribute("showCoverage", this.reportCoverage);
     try {
       writer.write(st.toString());
       writer.close();
@@ -233,6 +239,7 @@ private void createPackageIndexPage(final PackageSummaryData psData) {
         .getPackageDirectory() + File.separator + "index.html");
     st.setAttribute("packageData", psData);
     st.setAttribute("outputCharset", this.outputCharset);
+    st.setAttribute("showCoverage", this.reportCoverage);
     try {
       writer.write(st.toString());
       writer.close();

pitest-html-report/src/main/resources/templates/mutation/mutation_package_index.st

@@ -21,7 +21,9 @@
     <tbody>
         <tr>
             <td>$totals.numberOfFiles$</td>
-            <td>$totals.lineCoverage$% <div class="coverage_bar"><div class="coverage_complete width-$totals.lineCoverage$"></div><div class="coverage_legend">$totals.numberOfLinesCovered$/$totals.numberOfLines$</div></div></td>
+            $if(showCoverage)$ <td>$totals.lineCoverage$% <div class="coverage_bar"><div class="coverage_complete width-$totals.lineCoverage$"></div><div class="coverage_legend">$totals.numberOfLinesCovered$/$totals.numberOfLines$</div></div></td>
+            $else$<td><div class="coverage_bar"><div class="coverage_complete width-100"></div><div class="coverage_legend">n/a</div></div></td>
+            $endif$
             <td>$totals.mutationCoverage$% <div class="coverage_bar"><div class="coverage_complete width-$totals.mutationCoverage$"></div><div class="coverage_legend">$totals.numberOfMutationsDetected$/$totals.numberOfMutations$</div></div></td>
             <td>$totals.testStrength$% <div class="coverage_bar"><div class="coverage_complete width-$totals.testStrength$"></div><div class="coverage_legend">$totals.numberOfMutationsDetected$/$totals.numberOfMutationsWithCoverage$</div></div></td>
         </tr>
@@ -45,7 +47,9 @@ $packageSummaries:{ summary |
         <tr>
             <td><a href="./$summary.packageDirectory$/index.html">$summary.packageName$</a></td>
             <td>$summary.totals.numberOfFiles$</td>
-            <td><div class="coverage_percentage">$summary.totals.lineCoverage$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.lineCoverage$"></div><div class="coverage_legend">$summary.totals.numberOfLinesCovered$/$summary.totals.numberOfLines$</div></div></td>
+            $if(showCoverage)$ <td><div class="coverage_percentage">$summary.totals.lineCoverage$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.lineCoverage$"></div><div class="coverage_legend">$summary.totals.numberOfLinesCovered$/$summary.totals.numberOfLines$</div></div></td>
+            $else$<td><div class="coverage_bar"><div class="coverage_complete width-100"></div><div class="coverage_legend">n/a</div></div></td>
+            $endif$
             <td><div class="coverage_percentage">$summary.totals.mutationCoverage$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.mutationCoverage$"></div><div class="coverage_legend">$summary.totals.numberOfMutationsDetected$/$summary.totals.numberOfMutations$</div></div></td>
             <td><div class="coverage_percentage">$summary.totals.testStrength$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.testStrength$"></div><div class="coverage_legend">$summary.totals.numberOfMutationsDetected$/$summary.totals.numberOfMutationsWithCoverage$</div></div></td>
         </tr>

pitest-html-report/src/main/resources/templates/mutation/package_index.st

@@ -21,7 +21,9 @@
     <tbody>
         <tr>
             <td>$packageData.totals.numberOfFiles$</td>
-            <td>$packageData.totals.lineCoverage$% <div class="coverage_bar"><div class="coverage_complete width-$packageData.totals.lineCoverage$"></div><div class="coverage_legend">$packageData.totals.numberOfLinesCovered$/$packageData.totals.numberOfLines$</div></div></td>
+            $if(showCoverage)$<td>$packageData.totals.lineCoverage$% <div class="coverage_bar"><div class="coverage_complete width-$packageData.totals.lineCoverage$"></div><div class="coverage_legend">$packageData.totals.numberOfLinesCovered$/$packageData.totals.numberOfLines$</div></div></td>
+            $else$<td><div class="coverage_bar"><div class="coverage_complete width-100"></div><div class="coverage_legend">n/a</div></div></td>
+            $endif$
             <td>$packageData.totals.mutationCoverage$% <div class="coverage_bar"><div class="coverage_complete width-$packageData.totals.mutationCoverage$"></div><div class="coverage_legend">$packageData.totals.numberOfMutationsDetected$/$packageData.totals.numberOfMutations$</div></div></td>
             <td>$packageData.totals.testStrength$% <div class="coverage_bar"><div class="coverage_complete width-$packageData.totals.testStrength$"></div><div class="coverage_legend">$packageData.totals.numberOfMutationsDetected$/$packageData.totals.numberOfMutationsWithCoverage$</div></div></td>
         </tr>
@@ -43,7 +45,9 @@
 $packageData.summaryData:{ summary | 
         <tr>
             <td><a href="./$summary.fileName$.html">$summary.fileName$</a></td>
-            <td><div class="coverage_percentage">$summary.totals.lineCoverage$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.lineCoverage$"></div><div class="coverage_legend">$summary.totals.numberOfLinesCovered$/$summary.totals.numberOfLines$</div></div></td>
+            $if(showCoverage)$<td><div class="coverage_percentage">$summary.totals.lineCoverage$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.lineCoverage$"></div><div class="coverage_legend">$summary.totals.numberOfLinesCovered$/$summary.totals.numberOfLines$</div></div></td>
+            $else$<td><div class="coverage_bar"><div class="coverage_complete width-100"></div><div class="coverage_legend">n/a</div></div></td>
+            $endif$
             <td><div class="coverage_percentage">$summary.totals.mutationCoverage$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.mutationCoverage$"></div><div class="coverage_legend">$summary.totals.numberOfMutationsDetected$/$summary.totals.numberOfMutations$</div></div></td>
             <td><div class="coverage_percentage">$summary.totals.testStrength$% </div><div class="coverage_bar"><div class="coverage_complete width-$summary.totals.testStrength$"></div><div class="coverage_legend">$summary.totals.numberOfMutationsDetected$/$summary.totals.numberOfMutationsWithCoverage$</div></div></td>
         </tr>

pitest-html-report/src/test/java/org/pitest/mutationtest/report/html/MutationHtmlReportListenerTest.java

@@ -69,7 +69,7 @@ public void setUp() {
         this.classInfo);
 
     this.testee = new MutationHtmlReportListener(StandardCharsets.UTF_8, this.coverageDb,
-        this.outputStrategy, Collections.<String>emptyList(), this.sourceLocator);
+        this.outputStrategy, Collections.<String>emptyList(), true, this.sourceLocator);
   }
 
   @Test

pitest-maven/src/main/java/org/pitest/maven/report/AbstractPitAggregationReportMojo.java

@@ -157,8 +157,7 @@ private List<File> getProjectFilesByFilter(final File projectBaseDir,
   }
 
   @SuppressWarnings("unchecked")
-  private List<File> getCompiledDirs(final MavenProject project)
-      throws Exception {
+  private List<File> getCompiledDirs(final MavenProject project) {
     final List<String> sourceRoots = new ArrayList<>();
     for (final Object artifactObj : FCollection
         .filter(project.getPluginArtifactMap().values(), new DependencyFilter(