[WIP] [GSOC22] Improve the external changes resolver dialog

.github/workflows/cleanup_pr.yml

@@ -27,7 +27,7 @@ jobs:
           echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
       - name: Delete folder on builds.jabref.org
         if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/[email protected].4
+        uses: appleboy/[email protected].5
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

CHANGELOG.md

@@ -16,6 +16,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
 - We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322)
+- We added a feature to drag selected entries and drop them to other opened inactive library tabs [koppor521](https://github.com/koppor/jabref/issues/521).
+- We added support for the [biblatex-apa](https://github.com/plk/biblatex-apa) legal entry types `Legislation`, `Legadminmaterial`, `Jurisdiction`, `Constitution` and `Legal` [#8931](https://github.com/JabRef/jabref/issues/8931)
 
 ### Changed
 
@@ -35,7 +37,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - When configured SSL certificates changed, JabRef warns the user to restart to apply the configuration.
 - We improved the appearances and logic of the "Manage field names & content" dialog, and renamed it to "Automatic field editor". [#6536](https://github.com/JabRef/jabref/issues/6536)
 - We improved the message explaining the options when modifying an automatic keyword group [#8911](https://github.com/JabRef/jabref/issues/8911)
-- We moved the preferences option "Warn about duplicates on import" option from the tab "File" to the tab "Import and Export". [kopper#570](https://github.com/koppor/jabref/issues/570)
+- We moved the preferences option "Warn about duplicates on import" option from the tab "File" to the tab "Import and Export". [koppor#570](https://github.com/koppor/jabref/issues/570)
+- When JabRef encounters `% Encoding: UTF-8` header, it is kept during writing (and not removed). [#8964](https://github.com/JabRef/jabref/pull/8964)
+- We replace characters which cannot be decoded using the specified encoding by a (probably another) valid character. This happens if JabRef detects the wrong charset (e.g., UTF-8 instead of Windows 1252). One can use the [Integrity Check](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity) to find those characters.
 
 ### Fixed
 
@@ -54,6 +58,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where removing several groups deletes only one of them. [#8390](https://github.com/JabRef/jabref/issues/8390)
 - We fixed an issue where the Sidepane (groups, web search and open office) width is not remembered after restarting JabRef. [#8907](https://github.com/JabRef/jabref/issues/8907)
 - We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939)
+- We fixed a bug where files that were deleted in the source bibtex file were kept in the index. [#8962](https://github.com/JabRef/jabref/pull/8962)
+- We fixed "Error while sending to JabRef" when the browser extension interacts with JabRef. [JabRef-Browser-Extension#479](https://github.com/JabRef/JabRef-Browser-Extension/issues/479)
+- We fixed a bug where updating group view mode (intersection or union) requires re-selecting groups to take effect. [#6998](https://github.com/JabRef/jabref/issues/6998)
+- We fixed a bug that prevented external group metadata changes from being merged. [#8873](https://github.com/JabRef/jabref/issues/8873)
+- We fixed the shared database opening dialog to remember autosave folder and tick. [#7516](https://github.com/JabRef/jabref/issues/7516)
 
 ### Removed
 

build.gradle

@@ -85,7 +85,6 @@ repositories {
 }
 
 configurations {
-    antlr3
     antlr4
     // TODO: Remove the following workaround for split error messages such as
     // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation
@@ -100,7 +99,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "18"
+    version = "18.0.1"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -116,33 +115,29 @@ dependencies {
     implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
     implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'
 
-    implementation 'org.apache.lucene:lucene-core:9.2.0'
-    implementation 'org.apache.lucene:lucene-queryparser:9.2.0'
-    implementation 'org.apache.lucene:lucene-queries:9.2.0'
-    implementation 'org.apache.lucene:lucene-analysis-common:9.2.0'
-    implementation 'org.apache.lucene:lucene-highlighter:9.2.0'
+    implementation 'org.apache.lucene:lucene-core:9.3.0'
+    implementation 'org.apache.lucene:lucene-queryparser:9.3.0'
+    implementation 'org.apache.lucene:lucene-queries:9.3.0'
+    implementation 'org.apache.lucene:lucene-analysis-common:9.3.0'
+    implementation 'org.apache.lucene:lucene-highlighter:9.3.0'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
     implementation 'com.h2database:h2-mvstore:2.1.214'
 
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
-    implementation 'com.ibm.icu:icu4j-charset:71.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.71'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.3.4'
-    implementation 'org.libreoffice:unoloader:7.3.4'
+    implementation 'org.libreoffice:libreoffice:7.3.5'
+    implementation 'org.libreoffice:unoloader:7.3.5'
 
-    implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
+    implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
     implementation 'info.debatty:java-string-similarity:2.0.0'
 
-    antlr3 'org.antlr:antlr:3.5.3'
-    implementation 'org.antlr:antlr-runtime:3.5.3'
-
     antlr4 'org.antlr:antlr4:4.9.3'
     implementation 'org.antlr:antlr4-runtime:4.9.3'
 
@@ -208,9 +203,9 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.147'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
+    testImplementation 'io.github.classgraph:classgraph:4.8.149'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.0'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.9.0'
 
     testImplementation 'org.mockito:mockito-core:4.6.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
@@ -221,7 +216,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.2'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
@@ -274,14 +269,14 @@ task generateSource(dependsOn: ["generateBstGrammarSource",
 }
 
 tasks.register("generateBstGrammarSource", JavaExec) {
-    main = "org.antlr.Tool"
-    classpath = configurations.antlr3
+    main = "org.antlr.v4.Tool"
+    classpath = configurations.antlr4
     group = "JabRef"
-    description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.'
+    description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr4.'
 
-    inputs.dir('src/main/antlr3/org/jabref/bst/')
+    inputs.dir('src/main/antlr4/org/jabref/bst/')
     outputs.dir("src-gen/main/java/org/jabref/logic/bst/")
-    args = ["-o", "src-gen/main/java/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ]
+    args = ["-o", "src-gen/main/java/org/jabref/logic/bst/", "-visitor", "-no-listener", "-package", "org.jabref.logic.bst", "$projectDir/src/main/antlr4/org/jabref/bst/Bst.g4"]
 }
 
 tasks.register("generateSearchGrammarSource", JavaExec) {

buildres/csl/csl-locales/.github/workflows/merge.yaml

@@ -48,6 +48,10 @@ jobs:
             - deleted: [ '*.csl', 'dependent/*.csl', '*.xml' ]
           workflows:
             - added|modified: .github/workflows/*.yaml
+          updated_composer:
+            - added|modified: composer.json
+          deleted_composer:
+            - deleted: composer.json
 
     - name: Changed files
       if: github.event_name == 'push'
@@ -87,11 +91,24 @@ jobs:
       run: cd release && git rm ${{ steps.update.outputs.deleted_files }}
       if: github.event_name == 'push' && steps.update.outputs.deleted == 'true'
 
+    - name: Update composer.json
+      if: steps.update.outputs.updated_composer == 'true'
+      run: |
+        cp composer.json release/composer.json
+        cd release
+        git add composer.json
+
+    - name: Delete composer.json
+      if: steps.update.outputs.deleted_composer == 'true'
+      run: |
+        cd release
+        git rm composer.json
+
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         repository: 'release'
-        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }}
-      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true' || steps.update.outputs.updated_composer == 'true' || steps.update.outputs.deleted_composer == 'true')
 
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
@@ -116,3 +133,21 @@ jobs:
         git-user: "csl-bot"
         git-user-email: [email protected]
         git-commit-message: copied ${{ steps.update.outputs.workflows_files }} from styles
+
+    - name: Bump version and push tag
+      id: tag_version
+      uses: mathieudutour/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        default_bump: patch
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+
+    - name: Create a GitHub release
+      uses: softprops/[email protected]
+      env:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.tag_version.outputs.new_tag }}
+        name: Release ${{ steps.tag_version.outputs.new_tag }}
+        body: Released ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')

buildres/csl/csl-styles/.github/workflows/merge.yaml

@@ -48,6 +48,10 @@ jobs:
             - deleted: [ '*.csl', 'dependent/*.csl', '*.xml' ]
           workflows:
             - added|modified: .github/workflows/*.yaml
+          updated_composer:
+            - added|modified: composer.json
+          deleted_composer:
+            - deleted: composer.json
 
     - name: Changed files
       if: github.event_name == 'push'
@@ -87,11 +91,24 @@ jobs:
       run: cd release && git rm ${{ steps.update.outputs.deleted_files }}
       if: github.event_name == 'push' && steps.update.outputs.deleted == 'true'
 
+    - name: Update composer.json
+      if: steps.update.outputs.updated_composer == 'true'
+      run: |
+        cp composer.json release/composer.json
+        cd release
+        git add composer.json
+
+    - name: Delete composer.json
+      if: steps.update.outputs.deleted_composer == 'true'
+      run: |
+        cd release
+        git rm composer.json
+
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         repository: 'release'
-        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }}
-      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true' || steps.update.outputs.updated_composer == 'true' || steps.update.outputs.deleted_composer == 'true')
 
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
@@ -116,3 +133,21 @@ jobs:
         git-user: "csl-bot"
         git-user-email: [email protected]
         git-commit-message: copied ${{ steps.update.outputs.workflows_files }} from styles
+
+    - name: Bump version and push tag
+      id: tag_version
+      uses: mathieudutour/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        default_bump: patch
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+
+    - name: Create a GitHub release
+      uses: softprops/[email protected]
+      env:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.tag_version.outputs.new_tag }}
+        name: Release ${{ steps.tag_version.outputs.new_tag }}
+        body: Released ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')