Merge remote-tracking branch 'upstream/main' into fix-for-issue-348

* upstream/main: (24 commits)
  Clean up test code (JabRef#10658)
  Bump org.openrewrite.rewrite from 6.4.0 to 6.5.4 (JabRef#10650)
  Bump com.puppycrawl.tools:checkstyle from 10.12.4 to 10.12.5 (JabRef#10654)
  Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml (JabRef#10653)
  Bump com.github.Dansoftowner:jSystemThemeDetector from 3.6 to 3.8
  Remove comments - don't work on forks
  Update journal abbreviation lists (JabRef#10645)
  Use clparse (instead of heylogs) (JabRef#10641)
  Update CSL styles (JabRef#10642)
  Added parent field to Hayagriva YAML export (JabRef#10633)
  Bump org.fxmisc.richtext:richtextfx from 0.11.1 to 0.11.2 (JabRef#10637)
  Bump io.github.classgraph:classgraph from 4.8.163 to 4.8.164 (JabRef#10634)
  Bump org.junit.platform:junit-platform-launcher from 1.10.0 to 1.10.1 (JabRef#10635)
  Bump org.mockito:mockito-core from 5.6.0 to 5.7.0 (JabRef#10638)
  Bump com.tngtech.archunit:archunit-junit5-engine from 1.1.0 to 1.2.0 (JabRef#10636)
  add some more spaces
  Fix CHANGELOG.md
  Remove SearchListener
  Refactor method name to reflect usage
  Revert "Remove filtering on query in maintable"
  ...

.github/workflows/tests.yml

@@ -49,20 +49,6 @@ jobs:
           checkstyle_version: '10.3'
       - name: Run checkstyle using gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
-              The tool reviewdog already placed comments on GitHub to indicate the places. See the tab "Files" in you PR.
-              Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
-              Afterwards, please run checkstyle locally and fix the issues.
-
-
-              More information on code quality in JabRef is available at <https://devdocs.jabref.org/getting-into-the-code/development-strategy.html>.
-          comment_tag: checkstyle
   openrewrite:
     name: OpenRewrite
     runs-on: ubuntu-latest
@@ -81,19 +67,6 @@ jobs:
       - name: Run OpenRewrite
         run: |
           ./gradlew rewriteDryRun
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [OpenRewrite](https://docs.openrewrite.org/) to ensure "modern" Java coding practices.
-              The issues found can be **automatically fixed**.
-              Please execute the gradle task *`rewriteRun`*, check the results, commit, and push.
-
-
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "OpenRewrite".
-          comment_tag: openrewrite
   modernizer:
     name: Modernizer
     runs-on: ubuntu-latest
@@ -114,18 +87,6 @@ jobs:
           # enable failing of this task if modernizer complains
           sed -i "s/failOnViolations = false/failOnViolations = true/" build.gradle
           ./gradlew modernizer
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              Your code currently does not meet JabRef's code guidelines.
-              We use [Gradle Modernizer Plugin](https://github.com/andygoossens/gradle-modernizer-plugin#gradle-modernizer-plugin) to ensure "modern" Java coding practices.
-              Please fix the detected errors, commit, and push.
-
-
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "Modernizer".
-          comment_tag: modernizer
   markdown:
     name: Markdown
     runs-on: ubuntu-latest
@@ -141,18 +102,7 @@ jobs:
           globs: |
             *.md
             docs/**/*.md
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
-        with:
-          message: >
-              You modified Markdown (*.md) files.
-              To ensure consistent styling, we have [markdown-lint](https://github.com/DavidAnson/markdownlint) in place.
-              [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
-
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "Markdown".
-          comment_tag: markdown
-  changelog-non-frozen:
+  changelog:
     name: CHANGELOG.md
     runs-on: ubuntu-latest
     steps:
@@ -161,41 +111,43 @@ jobs:
         with:
           submodules: 'false'
           show-progress: 'false'
-          fetch-depth: 0
       - name: Lint CHANGELOG.md
         run: |
           # Install jbang
           curl -Ls https://sh.jbang.dev | bash -s - app setup
           export PATH=$PATH:$HOME/.jbang/bin
 
-          # ensure that refs are available
-          BRANCH=`git rev-parse HEAD`
-          git checkout main
-
           # run heylogs verification
-          jbang --repos jitpack,central -m nbbrd.heylogs.cli.HeylogsCommand com.github.koppor.heylogs:heylogs-cli:jitpack-SNAPSHOT check CHANGELOG.md --gitdiff main...$BRANCH > heylogs.txt || true
+          jbang com.github.nbbrd.heylogs:heylogs-cli:0.7.2:bin check CHANGELOG.md > heylogs.txt || true
 
           # improve output
-          sed -i 's/consistent-separator/consistent-separator (ignored)/' heylogs.txt
           sed -i 's/all-h2-contain-a-version/all-h2-contain-a-version (ignored)/' heylogs.txt
 
           cat heylogs.txt
 
           # exit 1 in case of error
           # We have 1 "valid" issue in CHANGELOG.md
           grep -q "1 problem" heylogs.txt || exit 1
-      - name: Add comment on pull request
-        if: ${{ failure() }}
-        uses: thollander/actions-comment-pull-request@v2
+  changelog-unreleased-only:
+    name: CHANGELOG.md - only unreleased touched
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
         with:
-          message: >
-              While the PR was in progress, JabRef released a new version.
-              You have to merge `upstream/main` and move your entry in `CHANGELOG.md` to section `## [Unreleased]`.
-
-
-              It might also be that another CHANGELOG.md issue arose.
-              You can check the detailed error output at the tab "Checks", section "Tests" (on the left), subsection "CHANGELOG.md".
-          comment_tag: changelog
+          submodules: 'false'
+          show-progress: 'false'
+          fetch-depth: 0
+      - name: Install clparse
+        run: |
+          curl -LO https://github.com/marcaddeo/clparse/releases/download/0.9.1/clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
+          tar xzvf clparse-0.9.1-x86_64-unknown-linux-musl.tar.gz
+          sudo mv clparse /usr/local/bin/clparse
+      - name: Check CHANGELOG.md diff
+        run: |
+          diff \
+            <(git show origin/main:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)') \
+            <(git show HEAD:CHANGELOG.md | clparse --format=json --separator=– - | jq '.releases[] | select(.version != null)')
   tests:
     name: Unit tests
     runs-on: ubuntu-latest

CHANGELOG.md

@@ -32,9 +32,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the added protected term has unwanted leading and trailing whitespaces, where the formatted text has unwanted empty brackets and where the word at the cursor in the textbox can be added to the list. [#10415](https://github.com/JabRef/jabref/issues/10415)
 - We fixed an issue where in the merge dialog the file field of entries was not correctly merged when the first and second entry both contained values inside the file field. [#10572](https://github.com/JabRef/jabref/issues/10572)
 - We fixed some small inconsistencies in the user interface. [#10507](https://github.com/JabRef/jabref/issues/10507) [#10458](https://github.com/JabRef/jabref/issues/10458)
+- We fixed the issue where the Hayagriva YAML exporter would not include a parent field for the publisher/series. [#10596](https://github.com/JabRef/jabref/issues/10596)
 
 ### Removed
 
+- We removed duplicate filtering and sorting operations in the MainTable when editing BibEntries. [#10619](https://github.com/JabRef/jabref/pull/10619)
+
+
+
+
 ## [5.11] – 2023-10-22
 
 ### Added

build.gradle

@@ -27,7 +27,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.4.0'
+    id 'org.openrewrite.rewrite' version '6.5.4'
 }
 
 // Enable following for debugging
@@ -144,7 +144,7 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.7.0.202309050840-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.15.3'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.16.0'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.15.3'
 
     implementation 'com.fasterxml:aalto-xml:1.3.2'
@@ -173,14 +173,14 @@ dependencies {
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
-    implementation 'org.fxmisc.richtext:richtextfx:0.11.1'
+    implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
     implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.90.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
 
     implementation 'org.controlsfx:controlsfx:11.2.0'
-    implementation 'com.github.Dansoftowner:jSystemThemeDetector:3.6'
+    implementation 'com.github.Dansoftowner:jSystemThemeDetector:3.8'
 
     implementation 'org.jsoup:jsoup:1.16.2'
     implementation 'com.konghq:unirest-java:3.14.5'
@@ -235,25 +235,25 @@ dependencies {
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.163'
+    testImplementation 'io.github.classgraph:classgraph:4.8.164'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.1'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.0'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.1'
 
-    testImplementation 'org.mockito:mockito-core:5.6.0'
+    testImplementation 'org.mockito:mockito-core:5.7.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.1'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.1'
-    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.1.0'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.2.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.2.0'
     testImplementation "org.testfx:testfx-core:4.0.16-alpha"
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.12.4'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.12.5'
     // 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'
 
-    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.4.1"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.5.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

buildSrc/src/main/groovy/org/jabref/build/xjc/XjcTask.groovy

@@ -103,8 +103,9 @@ class XjcTask extends DefaultTask {
     }
 
     private void updateOutput() {
-        if (outputDirectory != null && javaPackage != null)
-        outputs.dir(new File(getOutputDirectory(), packageAsPath(javaPackage)))
+        if (outputDirectory != null && javaPackage != null) {
+            outputs.dir(new File(getOutputDirectory(), packageAsPath(javaPackage)))
+        }
     }
 
     private static String packageAsPath(String pkg) {

rewrite.yml

@@ -163,7 +163,7 @@ recipeList:
   - org.openrewrite.staticanalysis.RemoveExtraSemicolons
   - org.openrewrite.staticanalysis.RemoveJavaDocAuthorTag
   - org.openrewrite.staticanalysis.RemoveHashCodeCallsFromArrayInstances
-  - org.openrewrite.staticanalysis.RemoveRedundantTypeCast
+#  - org.openrewrite.staticanalysis.RemoveRedundantTypeCast
   - org.openrewrite.staticanalysis.RemoveToStringCallsFromArrayInstances
   - org.openrewrite.staticanalysis.RemoveUnneededAssertion
   - org.openrewrite.staticanalysis.RemoveUnneededBlock
@@ -195,3 +195,6 @@ recipeList:
   - org.openrewrite.staticanalysis.UseSystemLineSeparator
   - org.openrewrite.staticanalysis.WhileInsteadOfFor
 #  - org.openrewrite.staticanalysis.WriteOctalValuesAsDecimal
+
+  - org.openrewrite.java.testing.junit5.CleanupAssertions
+#  - org.openrewrite.java.testing.junit5.JUnit5BestPractices

src/main/java/org/jabref/gui/LibraryTab.java

@@ -66,7 +66,6 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.entry.event.EntriesEventSource;
-import org.jabref.model.entry.event.EntryChangedEvent;
 import org.jabref.model.entry.event.FieldChangedEvent;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
@@ -156,7 +155,6 @@ public LibraryTab(BibDatabaseContext bibDatabaseContext,
         setupMainPanel();
         setupAutoCompletion();
 
-        this.getDatabase().registerListener(new SearchListener());
         this.getDatabase().registerListener(new IndexUpdateListener());
         this.getDatabase().registerListener(new EntriesRemovedListener());
 
@@ -277,7 +275,6 @@ public void feedData(BibDatabaseContext bibDatabaseContextFromParserResult) {
         setupMainPanel();
         setupAutoCompletion();
 
-        this.getDatabase().registerListener(new SearchListener());
         this.getDatabase().registerListener(new EntriesRemovedListener());
 
         // ensure that at each addition of a new entry, the entry is added to the groups interface
@@ -918,28 +915,6 @@ public void listen(EntriesRemovedEvent entriesRemovedEvent) {
         }
     }
 
-    /**
-     * Ensures that the results of the current search are updated when a new entry is inserted into the database Actual methods for performing search must run in javafx thread
-     */
-    private class SearchListener {
-
-        @Subscribe
-        public void listen(EntriesAddedEvent addedEntryEvent) {
-            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
-        }
-
-        @Subscribe
-        public void listen(EntryChangedEvent entryChangedEvent) {
-            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
-        }
-
-        @Subscribe
-        public void listen(EntriesRemovedEvent removedEntriesEvent) {
-            // IMO only used to update the status (found X entries)
-            DefaultTaskExecutor.runInJavaFXThread(() -> frame.getGlobalSearchBar().performSearch());
-        }
-    }
-
     private class IndexUpdateListener {
 
         @Subscribe

src/main/java/org/jabref/gui/search/GlobalSearchBar.java

@@ -201,7 +201,7 @@ public GlobalSearchBar(JabRefFrame frame, StateManager stateManager, Preferences
         this.setSpacing(4.0);
         this.setAlignment(Pos.CENTER_LEFT);
 
-        Timer searchTask = FxTimer.create(Duration.ofMillis(SEARCH_DELAY), this::performSearch);
+        Timer searchTask = FxTimer.create(Duration.ofMillis(SEARCH_DELAY), this::updateSearchQuery);
         BindingsHelper.bindBidirectional(
                 stateManager.activeSearchQueryProperty(),
                 searchField.textProperty(),
@@ -238,31 +238,31 @@ private void initSearchModifierButtons() {
         initSearchModifierButton(regularExpressionButton);
         regularExpressionButton.setOnAction(event -> {
             searchPreferences.setSearchFlag(SearchRules.SearchFlags.REGULAR_EXPRESSION, regularExpressionButton.isSelected());
-            performSearch();
+            updateSearchQuery();
         });
 
         caseSensitiveButton.setSelected(searchPreferences.isCaseSensitive());
         caseSensitiveButton.setTooltip(new Tooltip(Localization.lang("Case sensitive")));
         initSearchModifierButton(caseSensitiveButton);
         caseSensitiveButton.setOnAction(event -> {
             searchPreferences.setSearchFlag(SearchRules.SearchFlags.CASE_SENSITIVE, caseSensitiveButton.isSelected());
-            performSearch();
+            updateSearchQuery();
         });
 
         fulltextButton.setSelected(searchPreferences.isFulltext());
         fulltextButton.setTooltip(new Tooltip(Localization.lang("Fulltext search")));
         initSearchModifierButton(fulltextButton);
         fulltextButton.setOnAction(event -> {
             searchPreferences.setSearchFlag(SearchRules.SearchFlags.FULLTEXT, fulltextButton.isSelected());
-            performSearch();
+            updateSearchQuery();
         });
 
         keepSearchString.setSelected(searchPreferences.shouldKeepSearchString());
         keepSearchString.setTooltip(new Tooltip(Localization.lang("Keep search string across libraries")));
         initSearchModifierButton(keepSearchString);
         keepSearchString.setOnAction(evt -> {
             searchPreferences.setSearchFlag(SearchRules.SearchFlags.KEEP_SEARCH_STRING, keepSearchString.isSelected());
-            performSearch();
+            updateSearchQuery();
         });
 
         openGlobalSearchButton.disableProperty().bindBidirectional(globalSearchActive);
@@ -271,7 +271,7 @@ private void initSearchModifierButtons() {
         openGlobalSearchButton.setOnAction(evt -> {
             globalSearchActive.setValue(true);
             globalSearchResultDialog = new GlobalSearchResultDialog(undoManager);
-            performSearch();
+            updateSearchQuery();
             dialogService.showCustomDialogAndWait(globalSearchResultDialog);
             globalSearchActive.setValue(false);
         });
@@ -298,9 +298,9 @@ public void focus() {
         searchField.selectAll();
     }
 
-    public void performSearch() {
+    public void updateSearchQuery() {
         LOGGER.debug("Flags: {}", searchPreferences.getSearchFlags());
-        LOGGER.debug("Run search {}", searchField.getText());
+        LOGGER.debug("Updated search query: {}", searchField.getText());
 
         // An empty search field should cause the search to be cleared.
         if (searchField.getText().isEmpty()) {