Rename DiffTree -> VariationDiff

Author: ibbem

INSTALL.md

@@ -98,7 +98,7 @@ The example file content shown below should match your results when running the
   slowestCommit: 9838b7032ea9792bec21af424c53c07078636d21___xorg-server___7996ms
   runtime in seconds: 853.9739999999999
   runtime with multithreading in seconds: 144.549
-  treeformat: org.variantsync.diffdetective.variation.diff.serialize.treeformat.CommitDiffDiffTreeLabelFormat
+  treeformat: org.variantsync.diffdetective.variation.diff.serialize.treeformat.CommitDiffVariationDiffLabelFormat
   nodeformat: org.variantsync.diffdetective.mining.formats.ReleaseMiningDiffNodeFormat
   edgeformat: org.variantsync.diffdetective.mining.formats.DirectedEdgeLabelFormat with org.variantsync.diffdetective.mining.formats.ReleaseMiningDiffNodeFormat
   analysis: org.variantsync.diffdetective.validation.PatternValidationTask

README.md

@@ -19,7 +19,7 @@ This replication package consists of four parts:
 4. **Dataset Overview**: We provide an overview of the 44 inspected datasets with updated links to their repositories in the file [docs/datasets/all.md][dataset].
 
 ## 1. DiffDetective
-DiffDetective is a java library and command-line tool to parse and classify edits to variability in git histories of preprocessor-based software product lines by creating [variation diffs][difftree_class] and operating on them.
+DiffDetective is a java library and command-line tool to parse and classify edits to variability in git histories of preprocessor-based software product lines by creating [variation diffs][variationdiff_class] and operating on them.
 
 We offer a [Docker](https://www.docker.com/) setup to easily __replicate__ the validation performed in our paper. 
 In the following, we provide a quickstart guide for running the replication.
@@ -69,7 +69,7 @@ Moreover, the results comprise the (LaTeX) tables that are part of our paper and
 ### Documentation
 
 DiffDetective is documented with javadoc. The documentation can be accessed on this [website][documentation]. Notable classes of our library are:
-- [DiffTree](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/diff/difftree/DiffTree.html) and [DiffNode](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/diff/difftree/DiffNode.html) implement variation diffs from our paper. A variation diff is represented by an instance of the `DiffTree` class. It stores the root node of the diff and offers various methods to parse, traverse, and analyze variation diffs. `DiffNode`s represent individual nodes within a variation diff.
+- [VariationDiff](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/variation/diff/VariationDiff.html) and [DiffNode](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/variation/diff/DiffNode.html) implement variation diffs from our paper. A variation diff is represented by an instance of the `VariationDiff` class. It stores the root node of the diff and offers various methods to parse, traverse, and analyze variation diffs. `DiffNode`s represent individual nodes within a variation diff.
 - [EditClassValidation](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/validation/EditClassValidation.html) contains the main method for our validation.
 - [ProposedEditClasses](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/editclass/proposed/ProposedEditClasses.html) holds the catalog of the nine edit classes we proposed in our paper. It implements the interface [EditClassCatalogue](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/editclass/EditClassCatalogue.html), which allows to define custom edit classifications.
 - [BooleanAbstraction](https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/feature/BooleanAbstraction.html) contains data and methods for boolean abstraction of higher-order logic formulas. We use this for macro parsing.
@@ -112,7 +112,7 @@ You can also run DiffDetective on other datasets by providing the path to the da
 
 The input file must have the same format as the other dataset files (i.e., repositories are listed in a Markdown table). You can find [dataset files](docs/datasets/all.md) in the [docs/datasets](docs/datasets) folder.
 
-[difftree_class]: https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/diff/difftree/DiffTree.html
+[variationdiff_class]: https://variantsync.github.io/DiffDetective/docs/javadoc/org/variantsync/diffdetective/variation/diff/VariationDiff.html
 [haskell]: https://www.haskell.org/
 [dataset]: docs/datasets/all.md
 [appendix]: appendix.pdf

linegraph/renderLinegraph.backup.py

@@ -333,9 +333,9 @@ def plot_graphs(S, exportDir):
 #     plt.figure(0, figsize=(FIG_WIDTH, FIG_HEIGHT))
     plt.figure(0)
     for i in range(len(S)):
-        difftree = S[i]
+        variation_diff = S[i]
 
-        # print("Render tree", difftree.name.replace("\n", JAVA_TREE_NAME_SEPARATOR))
+        # print("Render tree", variation_diff.name.replace("\n", JAVA_TREE_NAME_SEPARATOR))
 
         plt.clf()
         if WITH_TITLE:
@@ -344,7 +344,7 @@ def plot_graphs(S, exportDir):
         node_colors = []
         node_type_colors = []
         rootNode = None
-        for v, d in difftree.nodes(data=True):
+        for v, d in variation_diff.nodes(data=True):
             name = d['label']
             nodedata = NODE_PARSER(v, name)
 
@@ -366,7 +366,7 @@ def plot_graphs(S, exportDir):
             d['label'] = nodedata.label
 
         edge_colors = []
-        for _, _, d in difftree.edges.data():
+        for _, _, d in variation_diff.edges.data():
             typeName = str(d['label'])
             if typeName == "a":
                 edge_colors.append('#bbeb37')
@@ -380,7 +380,7 @@ def plot_graphs(S, exportDir):
 
         # We have to do this to circumvent a bug:
         # https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pydot.pydot_layout.html
-        H = nx.convert_node_labels_to_integers(difftree, label_attribute='label')
+        H = nx.convert_node_labels_to_integers(variation_diff, label_attribute='label')
         H_layout = nx.drawing.nx_pydot.pydot_layout(H, prog=NODE_POSITION_LAYOUT, root=rootNode)
         pos = {H.nodes[n]['label']: p for n, p in H_layout.items()}
 
@@ -390,14 +390,14 @@ def plot_graphs(S, exportDir):
         pos = new_pos
 
         # draw type borders
-        nx.draw_networkx_nodes(difftree, pos,
+        nx.draw_networkx_nodes(variation_diff, pos,
                 node_size=int(NODE_SIZE * TYPE_BORDER_SIZE),
                 node_color=node_type_colors)
 
         # draw nodes
         if SHOW_LABELS:
-            node_labels = dict([(v, d['label']) for v, d in difftree.nodes(data=True)])
-            nx.draw(difftree, pos,
+            node_labels = dict([(v, d['label']) for v, d in variation_diff.nodes(data=True)])
+            nx.draw(variation_diff, pos,
                     node_size=NODE_SIZE,
                     node_color=node_colors,
                     width=EDGE_SIZE,
@@ -407,15 +407,15 @@ def plot_graphs(S, exportDir):
                     labels=node_labels,
                     bbox=dict(facecolor="white", edgecolor='black', linewidth=0.3, boxstyle='round,pad=0.2', linestyle='solid'))
         else:
-            nx.draw(difftree, pos,
+            nx.draw(variation_diff, pos,
                     node_size=NODE_SIZE,
                     node_color=node_colors,
                     width=EDGE_SIZE,
                     arrowsize=ARROW_SIZE,
                     edge_color=edge_colors,
                     font_size=FONT_SIZE)
 
-        save_path = os.path.join(exportDir, difftree.graph['outfilename'] + OUTPUT_FORMAT)
+        save_path = os.path.join(exportDir, variation_diff.graph['outfilename'] + OUTPUT_FORMAT)
 
         # Save
         print("Exporting", save_path)
@@ -436,7 +436,7 @@ def getAllFilesInDirectoryRecusivelyThat(dirname, condition):
     return listOfFiles
 
 if __name__ == "__main__":
-    argparser = argparse.ArgumentParser(description="Render DiffTrees specified in linegraph files (.lg).")
+    argparser = argparse.ArgumentParser(description="Render VariationDiffs specified in linegraph files (.lg).")
     argparser.add_argument('infile')
     argparser.add_argument('--nodesize', nargs='?', default=700, type=int)
     argparser.add_argument('--edgesize', nargs='?', default=1.0, type=float)

linegraph/renderLinegraph.py

@@ -129,9 +129,9 @@ def plot_graphs(S, exportDir):
 #     plt.figure(0, figsize=(FIG_WIDTH, FIG_HEIGHT))
     fig = plt.figure(0)
     for i in range(len(S)):
-        difftree = S[i]
+        variation_diff = S[i]
 
-        # print("Render tree", difftree.name.replace("\n", JAVA_TREE_NAME_SEPARATOR))
+        # print("Render tree", variation_diff.name.replace("\n", JAVA_TREE_NAME_SEPARATOR))
 
         plt.clf()
         if WITH_TITLE:
@@ -140,7 +140,7 @@ def plot_graphs(S, exportDir):
         node_colors = []
         node_type_colors = []
         rootNode = None
-        for v, d in difftree.nodes(data=True):
+        for v, d in variation_diff.nodes(data=True):
             name = d['label']
             nodedata = NODE_PARSER(v, name)
 
@@ -164,7 +164,7 @@ def plot_graphs(S, exportDir):
             d['label'] = nodedata.label
 
         edge_colors = []
-        for _, _, d in difftree.edges.data():
+        for _, _, d in variation_diff.edges.data():
             typeName = str(d['label'])
             edge_colors.append(g.edgeColour(typeName))
 
@@ -173,7 +173,7 @@ def plot_graphs(S, exportDir):
 
         # We have to do this to circumvent a bug:
         # https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pydot.pydot_layout.html
-        H = nx.convert_node_labels_to_integers(difftree, label_attribute='label')
+        H = nx.convert_node_labels_to_integers(variation_diff, label_attribute='label')
         H_layout = nx.drawing.nx_pydot.pydot_layout(H, prog=NODE_POSITION_LAYOUT, root=rootNode)
         pos = {H.nodes[n]['label']: p for n, p in H_layout.items()}
 
@@ -209,14 +209,14 @@ def plot_graphs(S, exportDir):
         axes.set_ylim([-yhalf, +yhalf])
 
         # draw type borders
-        nx.draw_networkx_nodes(difftree, pos,
+        nx.draw_networkx_nodes(variation_diff, pos,
                 node_size=int(NODE_SIZE * g.TYPE_BORDER_SIZE),
                 node_color=node_type_colors)
 
         # draw nodes
         if SHOW_LABELS:
-            node_labels = dict([(v, d['label']) for v, d in difftree.nodes(data=True)])
-            nx.draw(difftree,
+            node_labels = dict([(v, d['label']) for v, d in variation_diff.nodes(data=True)])
+            nx.draw(variation_diff,
                     pos,
                     node_size=NODE_SIZE,
                     node_color=node_colors,
@@ -227,15 +227,15 @@ def plot_graphs(S, exportDir):
                     labels=node_labels,
                     bbox=dict(facecolor="white", edgecolor='black', linewidth=0.3, boxstyle='round,pad=0.2', linestyle='solid'))
         else:
-            nx.draw(difftree, pos,
+            nx.draw(variation_diff, pos,
                     node_size=NODE_SIZE,
                     node_color=node_colors,
                     width=EDGE_SIZE,
                     arrowsize=ARROW_SIZE,
                     edge_color=edge_colors,
                     font_size=FONT_SIZE)
 
-        save_path = os.path.join(exportDir, difftree.graph['outfilename'] + OUTPUT_FORMAT)
+        save_path = os.path.join(exportDir, variation_diff.graph['outfilename'] + OUTPUT_FORMAT)
 
         # Save
         print("Exporting", save_path)
@@ -257,7 +257,7 @@ def getAllFilesInDirectoryRecusivelyThat(dirname, condition):
     return listOfFiles
 
 if __name__ == "__main__":
-    argparser = argparse.ArgumentParser(description="Render DiffTrees specified in linegraph files (.lg).")
+    argparser = argparse.ArgumentParser(description="Render VariationDiffs specified in linegraph files (.lg).")
     argparser.add_argument('infile')
     argparser.add_argument('--nodesize', nargs='?', default=700, type=int)
     argparser.add_argument('--edgesize', nargs='?', default=1.0, type=float)

linegraph/renderMinedTrees.sh

@@ -1,2 +1,2 @@
 # Run in project root
-.venv/bin/python3 linegraph/renderLinegraph.py "linegraph/data/difftrees.lg"
+.venv/bin/python3 linegraph/renderLinegraph.py "linegraph/data/variationdiffs.lg"

scripts/runPostprocessing.sh

@@ -1,2 +1,2 @@
-java -cp "target/diffdetective-1.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.mining.postprocessing.MiningPostprocessing "results/fsg/difftrees_pilot/all_results" "results/compositeCandidates"
+java -cp "target/diffdetective-1.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.mining.postprocessing.MiningPostprocessing "results/fsg/variationdiffs_pilot/all_results" "results/compositeCandidates"
 echo "runPostprocessing.sh DONE"

scripts/runPreprocessing.sh

@@ -1,2 +1,2 @@
-java -cp "target/diffdetective-1.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.mining.DiffTreeMiner
+java -cp "target/diffdetective-1.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.mining.VariationDiffMiner
 echo "runPreprocessing.sh DONE"

src/main/java/org/variantsync/diffdetective/analysis/Analysis.java

@@ -26,13 +26,13 @@
 import org.variantsync.diffdetective.util.Diagnostics;
 import org.variantsync.diffdetective.util.InvocationCounter;
 import org.variantsync.diffdetective.variation.DiffLinesLabel;
-import org.variantsync.diffdetective.variation.diff.DiffTree;
+import org.variantsync.diffdetective.variation.diff.VariationDiff;
 import org.variantsync.functjonal.iteration.ClusteredIterator;
 import org.variantsync.functjonal.iteration.MappedIterator;
 
 /**
  * Encapsulates the state and control flow during an analysis of the commit history of multiple
- * repositories using {@link DiffTree}s. Each repository is processed sequentially but the commits
+ * repositories using {@link VariationDiff}s. Each repository is processed sequentially but the commits
  * of each repository can be processed in parallel.
  *
  * <p>For thread safety, each thread receives its own instance of {@code Analysis}. The getters
@@ -65,7 +65,7 @@ public class Analysis {
     protected RevCommit currentCommit;
     protected CommitDiff currentCommitDiff;
     protected PatchDiff currentPatch;
-    protected DiffTree<DiffLinesLabel> currentDiffTree;
+    protected VariationDiff<DiffLinesLabel> currentVariationDiff;
 
     protected final Path outputDir;
     protected Path outputFile;
@@ -105,10 +105,10 @@ public PatchDiff getCurrentPatch() {
 
     /**
      * The currently processed patch.
-     * Valid only during {@link Hooks#analyzeDiffTree}.
+     * Valid only during {@link Hooks#analyzeVariationDiff}.
      */
-    public DiffTree<DiffLinesLabel> getCurrentDiffTree() {
-        return currentDiffTree;
+    public VariationDiff<DiffLinesLabel> getCurrentVariationDiff() {
+        return currentVariationDiff;
     }
 
     /**
@@ -154,7 +154,7 @@ public <T extends Metadata<T>> void append(ResultKey<T> resultKey, T value) {
     }
 
     /**
-     * Hooks for analyzing commits using {@link DiffTree}s.
+     * Hooks for analyzing commits using {@link VariationDiff}s.
      *
      * <p>In general the hooks of different {@code Hook} instances are called in sequence according
      * to the order specified in {@link Analysis#Analysis} (except end hooks). Hooks are separated
@@ -218,7 +218,7 @@ default void onFailedCommit(Analysis analysis) throws Exception {}
          * The main hook for analyzing non-empty diff trees.
          * Called at most once during the patch phase.
          */
-        default boolean analyzeDiffTree(Analysis analysis) throws Exception { return true; }
+        default boolean analyzeVariationDiff(Analysis analysis) throws Exception { return true; }
         default void endPatch(Analysis analysis) throws Exception {}
         default void endCommit(Analysis analysis) throws Exception {}
         default void endBatch(Analysis analysis) throws Exception {}
@@ -280,7 +280,7 @@ public static AnalysisResult forEachCommit(Supplier<Analysis> analysis) {
      * history is processed in batches of {@code commitsToProcessPerThread} on {@code nThreads} in
      * parallel. {@link Hooks} passed to {@link Analysis#Analysis} are the main customization point
      * for executing different analyses. By default only the total number of commits and the total
-     * runtime with multithreading of the {@link DiffTree} parsing is recorded.
+     * runtime with multithreading of the {@link VariationDiff} parsing is recorded.
      *
      * @param analysisFactory creates independent (at least thread safe) instances the analysis
      * state
@@ -426,7 +426,7 @@ protected void processCommit() throws Exception {
         // parse the commit
         final CommitDiffResult commitDiffResult = differ.createCommitDiff(currentCommit);
 
-        // report any errors that occurred and exit in case no DiffTree could be parsed.
+        // report any errors that occurred and exit in case no VariationDiff could be parsed.
         getResult().reportDiffErrors(commitDiffResult.errors());
         if (commitDiffResult.diff().isEmpty()) {
             Logger.debug("found commit that failed entirely because:\n{}", commitDiffResult.errors());
@@ -463,10 +463,10 @@ protected void processCommit() throws Exception {
     protected void processPatch() throws Exception {
         if (currentPatch.isValid()) {
             // generate TreeDiff
-            currentDiffTree = currentPatch.getDiffTree();
-            currentDiffTree.assertConsistency();
+            currentVariationDiff = currentPatch.getVariationDiff();
+            currentVariationDiff.assertConsistency();
 
-            runFilterHook(hooks.listIterator(), Hooks::analyzeDiffTree);
+            runFilterHook(hooks.listIterator(), Hooks::analyzeVariationDiff);
         }
     }
 

src/main/java/org/variantsync/diffdetective/analysis/AnalysisResult.java

@@ -128,7 +128,7 @@ public AnalysisResult(final String repoName) {
     }
 
     /**
-     * Report errors (that for example occurred when parsing DiffTrees).
+     * Report errors (that for example occurred when parsing VariationDiffs).
      * @param errors A list of errors to report.
      */
     public void reportDiffErrors(final List<DiffError> errors) {

src/main/java/org/variantsync/diffdetective/analysis/EditClassOccurenceAnalysis.java

@@ -45,11 +45,11 @@ public boolean beginCommit(Analysis analysis) {
     }
 
     @Override
-    public boolean analyzeDiffTree(Analysis analysis) throws IOException {
+    public boolean analyzeVariationDiff(Analysis analysis) throws IOException {
         var editClassCounts = new LinkedHashMap<EditClass, Integer>();
         ProposedEditClasses.Instance.all().forEach(e -> editClassCounts.put(e, 0));
 
-        analysis.getCurrentDiffTree().forAll(node -> {
+        analysis.getCurrentVariationDiff().forAll(node -> {
             if (node.isArtifact()) {
                 final EditClass editClass = ProposedEditClasses.Instance.match(node);