Merge branch 'main' of github.com:VariantSync/DiffDetective into main

Author: pmbittner

.github/workflows/maven.yml

@@ -0,0 +1,26 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
+
+name: Java CI with Maven
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up JDK 17
+      uses: actions/setup-java@v3
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+        cache: maven
+    - name: Build with Maven
+      run: mvn -B package --file pom.xml

.run/GenAutomationResults.run.xml

@@ -1,6 +1,6 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="GenAutomationResults" type="Application" factoryName="Application">
-    <option name="MAIN_CLASS_NAME" value="org.variantsync.diffdetective.main.FindMedianCommitTime" />
+    <option name="MAIN_CLASS_NAME" value="org.variantsync.diffdetective.validation.FindMedianCommitTime" />
     <module name="DiffDetective" />
     <option name="PROGRAM_PARAMETERS" value="results/difftrees" />
     <extension name="coverage">

.run/Generate Javadoc.run.xml

@@ -0,0 +1,27 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="Generate Javadoc" type="MavenRunConfiguration" factoryName="Maven">
+    <MavenSettings>
+      <option name="myGeneralSettings" />
+      <option name="myRunnerSettings" />
+      <option name="myRunnerParameters">
+        <MavenRunnerParameters>
+          <option name="profiles">
+            <set />
+          </option>
+          <option name="goals">
+            <list>
+              <option value="javadoc:javadoc" />
+            </list>
+          </option>
+          <option name="pomFileName" />
+          <option name="profilesMap">
+            <map />
+          </option>
+          <option name="resolveToWorkspace" value="false" />
+          <option name="workingDirPath" value="$PROJECT_DIR$" />
+        </MavenRunnerParameters>
+      </option>
+    </MavenSettings>
+    <method v="2" />
+  </configuration>
+</component>

Dockerfile

@@ -49,7 +49,7 @@ WORKDIR /home/sherlock
 # Copy the compiled JAR file from the first stage into the second stage
 # Syntax: COPY --from=STAGE_ID SOURCE_PATH TARGET_PATH
 WORKDIR /home/sherlock/holmes
-COPY --from=0 /home/user/target/DiffDetectiveRunner.jar .
+COPY --from=0 /home/user/target/diffdetective-1.0.0-jar-with-dependencies.jar ./DiffDetective.jar
 WORKDIR /home/sherlock
 
 # Copy the setup

INSTALL.md

@@ -36,22 +36,22 @@ To build the Docker container you can run the build script corresponding to your
   ./build.sh
 ```
 
-## Validation & Expected Output
+## Verification & Expected Output
 
-### Running the Validation
-To run the validation you can run the script corresponding to your OS with `validation` as first argument. The validation should take about 10-20 minutes depending on your hardware.
+### Running the Verification
+To run the verification you can run the script corresponding to your OS with `verification` as first argument. The verification should take about 10-20 minutes depending on your hardware.
 ```
 # Windows: 
-  .\execute.bat validation
+  .\execute.bat verification
 # Linux/Mac (bash): 
-  ./execute.sh validation
+  ./execute.sh verification
 ```
-The results of the validation will be stored in the [results](results) directory.
+The results of the verification will be stored in the [results](results) directory.
 
-### Expected Output of the Validation
-The aggregated results of the validation can be found in the following files.
+### Expected Output of the Verification
+The aggregated results of the verification can be found in the following files.
 
-- The [speed statistics](results/difftrees/speedstatistics.txt) contain information about the total runtime, median runtime, mean runtime, and more:
+- The [speed statistics](results/validation/speedstatistics.txt) contain information about the total runtime, median runtime, mean runtime, and more:
   ```
   #Commits: 14527
   Total   commit process time is: 12.427866666666667min
@@ -60,7 +60,7 @@ The aggregated results of the validation can be found in the following files.
   Median  commit process time is: 6dc71f6b2c7ff49adb504426b4cd206e4745e1e3___xorg-server___19ms
   Average commit process time is: 51.330075032697735ms
   ```
-- The [classification results](results/difftrees/ultimateresult.metadata.txt) contain information about how often each pattern was found, and more.
+- The [classification results](results/validation/ultimateresult.metadata.txt) contain information about how often each pattern was found, and more.
   ```
   repository: <NONE>
   total commits: 18046
@@ -96,7 +96,7 @@ The aggregated results of the validation can be found in the following files.
   #Error[not all annotations closed]: 6
   ```
 
-(Note that the above links only have a target after running the validation.)
+(Note that the above links only have a target after running the verification.)
 The processing times might deviate.
 
 ## Troubleshooting
@@ -111,7 +111,7 @@ The processing times might deviate.
 
 `Fix:` Follow the instructions described above in the section `Build the Docker Container`.
 
-### No results after validation, or 'cannot create directory '../results/difftrees': Permission denied'
+### No results after verification, or 'cannot create directory '../results/difftrees': Permission denied'
 `Problem:` This problem can occur due to how permissions are managed inside the Docker container. More specifically, it will appear, if Docker is executed with elevated permissions (i.e., `sudo`) and if there is no [results](results) directory because it was deleted manually. In this case, Docker will create the directory with elevated permissions, and the Docker user has no permissions to access the directory.
 
 `Fix:` If there is a _results_ directory delete it with elevated permission (e.g., `sudo rm -r results`). 

LICENSE.LGPL3

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
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