Merge develop into main

.github/workflows/closeDevIssues.yml

@@ -0,0 +1,21 @@
+name: Close linked issue on PR merge
+
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  close_issues:
+    if: github.event.pull_request.merged == true && github.base_ref == 'develop'
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout 🛎️
+      uses: actions/checkout@v4
+
+    - name: Run script
+      working-directory: .github/workflows/scripts
+      run: |
+        pip install requests
+        python closeDevIssues.py ${{ secrets.GITHUB_TOKEN }} jplag JPlag ${{ github.event.pull_request.number }}

.github/workflows/complete-e2e.yml

@@ -0,0 +1,160 @@
+# Builds JPlag and then runs Datasets and Report Viewer e2e tests on multiple OS
+name: Complete e2e Test
+
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [opened, synchronize, reopened]
+    paths:
+      - ".github/workflows/complete-e2e.yml"
+      - "report-viewer/**"
+      - "**/pom.xml"
+      - "**.java"
+      - "**.g4"
+
+jobs:
+  pre_job:
+    runs-on: ubuntu-latest
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          concurrent_skipping: 'same_content_newer'
+          skip_after_successful_duplicate: 'true'
+
+  build_jar:
+    needs: pre_job
+    if: ${{ needs.pre_job.outputs.should_skip != 'true' }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21
+          distribution: 'temurin'
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "18"
+
+      - name: Build Assembly
+        run: mvn -Pwith-report-viewer -DskipTests clean package assembly:single
+
+      - name: Rename Jar
+        run: mv cli/target/jplag-*-jar-with-dependencies.jar cli/target/jplag.jar
+
+      - name: Upload Assembly
+        uses: actions/upload-artifact@v4
+        with:
+          name: "JPlag"
+          path: "cli/target/jplag.jar"
+          retention-days: 30
+
+  run_jplag:
+    needs: build_jar
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        dataset: [
+          {zip: "progpedia.zip", name: "progpedia", folder: "ACCEPTED", language: "java", cliArgs: "-bc base"},
+          {zip: "fileSingleRoot.zip", name: "fileSingleRoot", folder: "fileSingleRoot", language: "java", cliArgs: ""},
+          {zip: "folderSingleRoot.zip", name: "folderSingleRoot", folder: "folderSingleRoot", language: "java", cliArgs: ""},
+          {zip: "fileMultiRoot.zip", name: "fileMultiRoot", folder: "f0", language: "java", cliArgs: "--new f1"},
+          {zip: "folderMultiRoot.zip", name: "folderMultiRoot", folder: "f0", language: "java", cliArgs: "--new f1"},
+          {zip: "mixedMultiRoot.zip", name: "mixedBaseFile", folder: "f0", language: "java", cliArgs: "--new f1"},
+          {zip: "mixedMultiRoot.zip", name: "mixedBaseFolder", folder: "f1", language: "java", cliArgs: "--new f0"},
+          {zip: "cpp.zip", name: "cpp", folder: "./cpp", language: "cpp", cliArgs: ""},
+          {zip: "csharp.zip", name: "csharp", folder: "./csharp", language: "csharp", cliArgs: ""},
+          {zip: "python.zip", name: "python", folder: "./python", language: "python3", cliArgs: ""}
+          ]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21
+          distribution: 'temurin'
+
+      - name: Get JAR
+        uses: actions/download-artifact@v4
+        with:
+          name: JPlag
+
+      - name: Copy and unzip dataset windows
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: |
+          Expand-Archive -LiteralPath .github/workflows/files/${{ matrix.dataset.zip }} -DestinationPath ./
+
+      - name: Copy and unzip dataset macos and ubuntu
+        if: ${{ matrix.os == 'macos-latest' || matrix.os == 'ubuntu-latest'}}
+        run: |
+          unzip .github/workflows/files/${{ matrix.dataset.zip }}
+
+      - name: Run JPlag
+        run: |
+          java -jar jplag.jar ${{ matrix.dataset.folder }} -l ${{ matrix.dataset.language }} -r ${{ matrix.dataset.name }}-report ${{ matrix.dataset.cliArgs }}
+
+      - name: Upload result
+        uses: actions/upload-artifact@v4
+        with:
+          name: "${{ matrix.dataset.name }}-${{ matrix.os }}"
+          path: "${{ matrix.dataset.name }}-report.zip"
+          retention-days: 30
+
+  e2e_test:
+    needs: run_jplag
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "18"
+
+      - name: Install and Build
+        working-directory: report-viewer
+        run: |
+          npm install
+          npm run build
+
+      - name: Install playwright
+        working-directory: report-viewer
+        run: npx playwright install --with-deps
+
+      - name: Download JPlag Reports
+        uses: actions/download-artifact@v4
+        with:
+          pattern: "*-${{ matrix.os }}"
+          path: "report-viewer/tests/e2e/assets"
+          merge-multiple: true
+
+      - name: Run tests
+        working-directory: report-viewer
+        run: |
+          npm run test:e2e
+
+      - name: Upload test results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: "test-results-${{ matrix.os }}"
+          path: |
+            report-viewer/test-results
+            report-viewer/playwright-report
+          retention-days: 30

.github/workflows/maven.yml

@@ -57,7 +57,7 @@ jobs:
     - name: Upload Assembly
       uses: actions/upload-artifact@v4
       with:
-        name: "JPlag"
-        path: "jplag.cli/target/jplag-*-jar-with-dependencies.jar"
+        name: "JPlag Jar"
+        path: "cli/target/jplag-*-jar-with-dependencies.jar"
 
 

.github/workflows/publish.yml

@@ -2,7 +2,7 @@ name: Deploy to Maven Central & GitHub
 on:
   workflow_dispatch:
   release:
-    types: [created]
+    types: [created, published]
 jobs:
   publish-maven-central:
     runs-on: ubuntu-latest
@@ -42,7 +42,7 @@ jobs:
         run: mvn -Pwith-report-viewer -U -B clean package assembly:single
 
       - name: Attach CLI to Release on GitHub
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         if: startsWith(github.ref, 'refs/tags/')
         with:
           files: cli/target/jplag-*-jar-with-dependencies.jar

.github/workflows/report-viewer-demo.yml

@@ -102,7 +102,7 @@ jobs:
           npm run build-demo
 
       - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4.6.1
         with:
           branch: gh-pages
           folder: report-viewer/dist

.github/workflows/report-viewer-dev.yml

@@ -27,7 +27,7 @@ jobs:
           npm run build-dev
 
       - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4.6.1
         with:
           branch: gh-pages
           folder: report-viewer/dist

.github/workflows/report-viewer.yml

@@ -37,7 +37,7 @@ jobs:
           npm run build-prod
 
       - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@v4.6.1
         with:
           branch: gh-pages
           folder: report-viewer/dist

.github/workflows/scripts/closeDevIssues.py

@@ -0,0 +1,76 @@
+import requests
+import re
+import sys
+
+headers = {"Authorization": f"Bearer {sys.argv[1]}"}
+
+owner = sys.argv[2]
+repo = sys.argv[3]
+pr_number = int(sys.argv[4])
+
+query = f"""
+{{
+  repository(owner: "{owner}", name: "{repo}") {{
+    pullRequest(number: {pr_number}) {{
+      merged
+      baseRefName
+      body
+      closingIssuesReferences (first: 50) {{
+        nodes {{
+          number
+        }}
+      }}
+    }}
+  }}
+}}
+"""
+
+def run_query(query):
+    request = requests.post('https://api.github.com/graphql', json={'query': query}, headers=headers)
+    if request.status_code == 200:
+        return request.json()
+    else:
+        raise Exception("Query failed to run by returning code of {}. {}".format(request.status_code, query))
+
+
+closing_keywords = [
+    'closes', 'close', 'closed', 'fix', 'fixes', 'fixed', 'resolves', 'resolve', 'resolved'
+]
+
+# checks all subsequeces of the pr body for closing keywords and extracts the coresponidng issue numbers
+def subsequences_matching_regex(input_string, regex):
+    matches = []
+    for i in range(len(input_string)):
+        for j in range(i+1, len(input_string)+1):
+            subsequence = input_string[i:j]
+            match = re.fullmatch(regex, subsequence)
+            if match:
+                matches.append(int(match.group(1)))
+    return matches
+
+# gets all issues linked to pr either via the closing keywords or the sidebar
+def get_linked_issues(result):
+    issue_body = result['body'].lower() + "." # we append a dot to the end of the body to make sure the last word is checked with the regex
+    closing_issues = []
+    for keyword in closing_keywords:
+        closing_issues.extend(subsequences_matching_regex(issue_body, f'{keyword} #([0-9]+)[^0-9]'))
+    for k in result['closingIssuesReferences']['nodes']:
+        closing_issues.append(k['number'])
+    return list(set(closing_issues))
+
+result = run_query(query)['data']['repository']['pullRequest']
+issues = get_linked_issues(result)
+
+def close_issue(issue_number):
+    requests.post(f"https://api.github.com/repos/{owner}/{repo}/issues/{issue_number}/comments", json={"body": f"Closed by #{pr_number}."}, headers=headers)
+    requests.patch(f"https://api.github.com/repos/{owner}/{repo}/issues/{issue_number}", json={"state": "closed"}, headers=headers)
+
+if result['baseRefName'] != "develop":
+    print("PR not merged to develop, not closing issues")
+elif result['merged']:
+    print(f"Closing issues: {issues}")
+    for issue in issues:
+        close_issue(issue)
+        print(f"Closed issue {issue}")
+else:
+  print("PR not merged, not closing issues")

README.md

@@ -8,7 +8,7 @@
 [![Maven Central](https://maven-badges.herokuapp.com/maven-central/de.jplag/jplag/badge.svg)](https://maven-badges.herokuapp.com/maven-central/de.jplag/jplag)
 [![License](https://img.shields.io/github/license/jplag/jplag.svg)](https://github.com/jplag/jplag/blob/main/LICENSE)
 [![GitHub commit activity](https://img.shields.io/github/commit-activity/y/jplag/JPlag)](https://github.com/jplag/JPlag/pulse)
-[![SonarCloud Coverage](https://sonarcloud.io/api/project_badges/measure?project=jplag_JPlag&metric=coverage)](https://sonarcloud.io/component_measures/metric/coverage/list?id=jplag_JPlag)
+[![SonarCloud Coverage](https://sonarcloud.io/api/project_badges/measure?project=jplag_JPlag&metric=coverage)](https://sonarcloud.io/component_measures?metric=Coverage&view=list&id=jplag_JPlag)
 [![Report Viewer](https://img.shields.io/badge/report%20viewer-online-b80025)](https://jplag.github.io/JPlag/)
 [![Java Version](https://img.shields.io/badge/java-SE%2021-yellowgreen)](#download-and-installation)
 
@@ -32,7 +32,7 @@ All supported languages and their supported versions are listed below.
 | [C](https://isocpp.org)                                |                                                                                     11 | c                 |                               legacy                                |  JavaCC   |
 | [C++](https://isocpp.org)                              |                                                                                     14 | cpp               |                                beta                                 |  ANTLR 4  |
 | [C#](https://docs.microsoft.com/en-us/dotnet/csharp/)  |                                                                                      6 | csharp            |                               mature                                |  ANTLR 4  |
-| [Python](https://www.python.org)                       |                                                                                    3.6 | python3           |                               legacy                                |  ANTLR 4  |
+| [Python](https://www.python.org)                       |                                                                                    3.6 | python3           |                                beta                                 |  ANTLR 4  |
 | [JavaScript](https://www.javascript.com/)              |                                                                                    ES6 | javascript        |                                beta                                 |  ANTLR 4  |
 | [TypeScript](https://www.typescriptlang.org/)          | [~5](https://github.com/antlr/grammars-v4/tree/master/javascript/typescript/README.md) | typescript        |                                beta                                 |  ANTLR 4  |
 | [Go](https://go.dev)                                   |                                                                                   1.17 | golang            |                                beta                                 |  ANTLR 4  |