Merge pull request #113 from VariantSync/develop

Release 2.1.0

.github/workflows/maven.yml

@@ -17,17 +17,17 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - name: Install Nix with cached packages
-      uses: rikhuijzer/cache-install@v1.1.1
+      uses: rikhuijzer/cache-install@v.1.1.3
       with:
-        key: nix-${{ hashFiles('.github/workflows/maven.yml', 'default.nix', 'nix/**') }}
+        key: nix-${{ hashFiles('.github/workflows/maven.yml', 'default.nix', 'nix/**', 'pom.xml', 'local-maven-repo') }}
         nix_file: nix/github-workflow-dependencies.nix
     - name: Build
       run: nix-build
     - name: Upload Javadoc artifact
       if: ${{ github.event_name == 'push' && github.event.ref == 'refs/heads/main' }}
       uses: actions/upload-pages-artifact@v1
       with:
-        path: result/share/doc/DiffDetective
+        path: result/share/github-pages
 
   # An additional job is recommened in the documentation of `actions/deploy-pages`
   deploy-javadoc:

.run/EditClassValidation.run.xml

@@ -1,7 +1,7 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="EditClassValidation" type="Application" factoryName="Application" nameIsGenerated="true">
     <option name="MAIN_CLASS_NAME" value="org.variantsync.diffdetective.validation.EditClassValidation" />
-    <module name="diffdetective" />
+    <module name="DiffDetective" />
     <method v="2">
       <option name="Make" enabled="true" />
     </method>

.run/GenAutomationResults.run.xml

@@ -1,9 +1,8 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="GenAutomationResults" type="Application" factoryName="Application">
     <option name="ALTERNATIVE_JRE_PATH" value="openjdk-16" />
-    <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="true" />
     <option name="MAIN_CLASS_NAME" value="org.variantsync.diffdetective.validation.FindMedianCommitTime" />
-    <module name="diffdetective" />
+    <module name="DiffDetective" />
     <option name="PROGRAM_PARAMETERS" value="results/validation/current" />
     <extension name="coverage">
       <pattern>

.run/GenUltimateResults.run.xml

@@ -1,9 +1,8 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="GenUltimateResults" type="Application" factoryName="Application">
     <option name="ALTERNATIVE_JRE_PATH" value="openjdk-16" />
-    <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="true" />
     <option name="MAIN_CLASS_NAME" value="org.variantsync.diffdetective.tablegen.MiningResultAccumulator" />
-    <module name="diffdetective" />
+    <module name="DiffDetective" />
     <option name="PROGRAM_PARAMETERS" value="results/validation/current results/validation/current" />
     <extension name="coverage">
       <pattern>

default.nix

@@ -8,17 +8,29 @@
       inherit system;
     },
   doCheck ? true,
-  buildJavadoc ? true,
+  buildGitHubPages ? true,
 }:
 pkgs.stdenv.mkDerivation rec {
   pname = "DiffDetective";
-  version = "2.0.0";
-  src = ./.;
+  version = "2.1.0";
+  src = with pkgs.lib.fileset;
+    toSource {
+      root = ./.;
+      # This should be `gitTracked ./.`. However, this currently doesn't accept
+      # shallow repositories as used in GitHub CI.
+      fileset =
+        (import (sources.nixpkgs + "/lib/fileset/internal.nix") {inherit (pkgs) lib;})._fromFetchGit
+        "gitTracked"
+        "argument"
+        ./.
+        {shallow = true;};
+    };
 
   nativeBuildInputs = with pkgs; [
     maven
     makeWrapper
     graphviz
+    (ruby.withPackages (pkgs: with pkgs; [github-pages jekyll-theme-cayman]))
   ];
 
   mavenRepo = pkgs.stdenv.mkDerivation {
@@ -45,17 +57,27 @@ pkgs.stdenv.mkDerivation rec {
     dontConfigure = true;
     outputHashAlgo = "sha256";
     outputHashMode = "recursive";
-    outputHash = "sha256-qIKFqNwooJ0iqzkv6TTS5GM4bA6iYkVa35zqE+q5izY=";
+    outputHash = "sha256-jQxZ6eSokwM6bP/vHkYczhE7xW/rHS/IH4pGy2SzzH0=";
   };
 
   buildPhase = ''
     runHook preBuild
 
-    mvn --offline -Dmaven.repo.local="$mavenRepo" -Dmaven.test.skip=true clean package ${
-      if buildJavadoc
-      then "javadoc:javadoc"
+    mvn() {
+      command mvn --offline -Dmaven.repo.local="$mavenRepo" "$@"
+    }
+
+    ${
+      # Build the documentation before the code because we don't want to include
+      # the generated files in the GitHub Pages
+      if buildGitHubPages
+      then ''
+        mvn javadoc:javadoc
+        PAGES_REPO_NWO=VariantSync/DiffDetective JEKYLL_BUILD_REVISION= github-pages build
+      ''
       else ""
     }
+    mvn -Dmaven.test.skip=true clean package
 
     runHook postBuild
   '';
@@ -74,15 +96,13 @@ pkgs.stdenv.mkDerivation rec {
 
     local jar="$out/share/java/DiffDetective/DiffDetective.jar"
     install -Dm644 "target/diffdetective-${version}-jar-with-dependencies.jar" "$jar"
-    makeWrapper "${pkgs.maven.jdk}/bin/java" "$out/bin/DiffDetective" --add-flags "-cp \"$jar\"" \
+    makeWrapper "${pkgs.jdk}/bin/java" "$out/bin/DiffDetective" --add-flags "-cp \"$jar\"" \
       --prefix PATH : "${pkgs.graphviz}"
 
     ${
-      if buildJavadoc
+      if buildGitHubPages
       then ''
-        local doc="$out/share/doc"
-        mkdir -p "$doc"
-        cp -r docs/javadoc "$doc/DiffDetective"
+        cp -r _site "$out/share/github-pages"
       ''
       else ""
     }

local-maven-repo/deploy-functjonal.sh

@@ -0,0 +1,4 @@
+# A simple script for deploying an update of the functjonal library to the local maven repository
+# The script takes a single argument, the path to the functjonal jar file to deploy
+mvn deploy:deploy-file -DgroupId=org.variantsync -DartifactId=functjonal -Dversion=1.0-SNAPSHOT -Durl=file:../local-maven-repo/ -DrepositoryId=local-maven-repo -DupdateReleaseInfo=true -Dfile=$1
+rm -rf ~/.m2/repository/org/variantsync/functjonal/

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20230616.172827-4.jar.md5

@@ -0,0 +1 @@
+9c298528d8baeeccd664e5c06f881265

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20230616.172827-4.jar.sha1

@@ -0,0 +1 @@
+98de1b4bfa2aa9f4e9eaa8c547922f41c59e6e4f

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20240126.150022-5.jar.md5

@@ -0,0 +1 @@
+166a8af340cb15efc13930c6badbec7a

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20240126.150022-5.jar.sha1

@@ -0,0 +1 @@
+96b2f9fb7d51eccafc7bb09eaf2a528a59e17236

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20240126.150022-5.pom

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.variantsync</groupId>
+  <artifactId>functjonal</artifactId>
+  <version>1.0-SNAPSHOT</version>
+</project>

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20240126.150022-5.pom.md5

@@ -0,0 +1 @@
+0db2dd0cd5161aebfc81133a2f27802e

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/functjonal-1.0-20240126.150022-5.pom.sha1

@@ -0,0 +1 @@
+976fd7d0111c674401618825decf315ec237cecb

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/maven-metadata.xml

@@ -5,20 +5,20 @@
   <version>1.0-SNAPSHOT</version>
   <versioning>
     <snapshot>
-      <timestamp>20230308.125347</timestamp>
-      <buildNumber>1</buildNumber>
+      <timestamp>20240126.150022</timestamp>
+      <buildNumber>5</buildNumber>
     </snapshot>
-    <lastUpdated>20230308125347</lastUpdated>
+    <lastUpdated>20240126150022</lastUpdated>
     <snapshotVersions>
       <snapshotVersion>
         <extension>jar</extension>
-        <value>1.0-20230308.125347-1</value>
-        <updated>20230308125347</updated>
+        <value>1.0-20240126.150022-5</value>
+        <updated>20240126150022</updated>
       </snapshotVersion>
       <snapshotVersion>
         <extension>pom</extension>
-        <value>1.0-20230308.125347-1</value>
-        <updated>20230308125347</updated>
+        <value>1.0-20240126.150022-5</value>
+        <updated>20240126150022</updated>
       </snapshotVersion>
     </snapshotVersions>
   </versioning>

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/maven-metadata.xml.md5

@@ -1 +1 @@
-cc732baa0478a9c6f2d21fdeb08f6a82
+f3e7ddea4327266ea976de9d7c6859ef

local-maven-repo/org/variantsync/functjonal/1.0-SNAPSHOT/maven-metadata.xml.sha1

@@ -1 +1 @@
-feb03041c908b3f11611fb2380e6bb9424ff2e63
+c20031accaeaa3a71c39b2d9e405b7f4fd383540

local-maven-repo/org/variantsync/functjonal/maven-metadata.xml

@@ -6,6 +6,6 @@
     <versions>
       <version>1.0-SNAPSHOT</version>
     </versions>
-    <lastUpdated>20230308125347</lastUpdated>
+    <lastUpdated>20240126150022</lastUpdated>
   </versioning>
 </metadata>

local-maven-repo/org/variantsync/functjonal/maven-metadata.xml.md5

@@ -1 +1 @@
-a9a0be7eec34faf063b51a34b7fed4a7
+f5de7e3d6f46ff9f69c4973738b4e196

local-maven-repo/org/variantsync/functjonal/maven-metadata.xml.sha1

@@ -1 +1 @@
-d53c3d14023e9052bda58ce2fdcc5580efda1a0b
+6b562596b8cfded33bf0f56638e5b08fc049d037

nix/sources.json

@@ -1,14 +1,14 @@
 {
     "nixpkgs": {
-        "branch": "nixos-23.05",
+        "branch": "nixos-23.11",
         "description": "Nix Packages collection",
         "homepage": null,
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "ad157fe26e74211e7dde0456cb3fd9ab78b6e552",
-        "sha256": "0l5gimzlbzq1svw48p4h3wf24ry21icl9198jk5x4xqvs6k2gffx",
+        "rev": "a77ab169a83a4175169d78684ddd2e54486ac651",
+        "sha256": "0r9a87aqhqr7dkhfy5zrx2dgqq11ma2rfvkfwqhz1xqg7y6mcxxg",
         "type": "tarball",
-        "url": "https://github.com/NixOS/nixpkgs/archive/ad157fe26e74211e7dde0456cb3fd9ab78b6e552.tar.gz",
+        "url": "https://github.com/NixOS/nixpkgs/archive/a77ab169a83a4175169d78684ddd2e54486ac651.tar.gz",
         "url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
     }
 }

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>org.variantsync</groupId>
     <artifactId>diffdetective</artifactId>
-    <version>2.0.0</version>
+    <version>2.1.0</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -67,6 +67,22 @@
                     </descriptorRefs>
                 </configuration>
             </plugin>
+
+            <plugin>
+                <groupId>org.antlr</groupId>
+                <artifactId>antlr4-maven-plugin</artifactId>
+                <version>4.13.1</version>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>antlr4</goal>
+                        </goals>
+                        <configuration>
+                            <visitor>true</visitor>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 
@@ -192,5 +208,11 @@
             <artifactId>slf4j-simple</artifactId>
             <version>2.0.5</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.antlr</groupId>
+            <artifactId>antlr4</artifactId>
+            <version>4.13.1</version>
+        </dependency>
     </dependencies>
 </project>

replication/esecfse22/Dockerfile

@@ -32,7 +32,7 @@ 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/diffdetective-2.0.0-jar-with-dependencies.jar ./DiffDetective.jar
+COPY --from=0 /home/user/target/diffdetective-2.1.0-jar-with-dependencies.jar ./DiffDetective.jar
 WORKDIR /home/sherlock
 RUN mkdir results
 

replication/splc23-views/Dockerfile

@@ -38,7 +38,7 @@ 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/diffdetective-2.0.0-jar-with-dependencies.jar ./DiffDetective.jar
+COPY --from=0 /home/user/target/diffdetective-2.1.0-jar-with-dependencies.jar ./DiffDetective.jar
 WORKDIR /home/sherlock
 
 # Copy the setup

scripts/genUltimateResults.sh

@@ -1,4 +1,4 @@
 resultsdir=$1
 
-java -cp "target/diffdetective-2.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.tablegen.MiningResultAccumulator $resultsdir $resultsdir
+java -cp "target/diffdetective-2.1.0-jar-with-dependencies.jar" org.variantsync.diffdetective.tablegen.MiningResultAccumulator $resultsdir $resultsdir
 echo "genUltimateResults.sh DONE"

scripts/runValidation.sh

@@ -1,2 +1,2 @@
-java -cp "target/diffdetective-2.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.validation.EditClassValidation
+java -cp "target/diffdetective-2.1.0-jar-with-dependencies.jar" org.variantsync.diffdetective.validation.EditClassValidation
 echo "runValidation.sh DONE"

scripts/runViewFeasibilityStudy.sh

@@ -1,2 +1,2 @@
-java -cp "target/diffdetective-2.0.0-jar-with-dependencies.jar" org.variantsync.diffdetective.experiments.views.Main "docs/datasets/views.md"
+java -cp "target/diffdetective-2.1.0-jar-with-dependencies.jar" org.variantsync.diffdetective.experiments.views.Main "docs/datasets/views.md"
 echo "runValidation.sh DONE"