Merge remote-tracking branch 'upstream/master' into multiline

* upstream/master:
  Update label names
  Squashed 'src/main/resources/csl-locales/' changes from d0ee4d13c9..79845b087b
  Squashed 'src/main/resources/csl-styles/' changes from c1793d2..143464e
  Cite work by @ayaankazerouni
  Improve performance for loading files (#6332)
  Add ADR von JUnit vs. AssertJ (#6335)
  'Name' textfield on focus instead of 'OK' button when user clicks on 'Add subgroup' option (#6330)
  Bump jurt from 6.3.2 to 6.4.3 (#6325)
  Bump unoil from 6.3.2 to 6.4.3 (#6320)
  Bump ridl from 6.3.2 to 6.4.3 (#6326)
  Bump classgraph from 4.8.69 to 4.8.71 (#6322)
  Bump flexmark from 0.61.6 to 0.61.16 (#6318)
  Bump richtextfx from 0.10.4 to 0.10.5 (#6319)
  Bump guava from 28.2-jre to 29.0-jre (#6323)
  Bump flexmark-ext-gfm-tasklist from 0.61.6 to 0.61.16 (#6327)
  Bump org.beryx.jlink from 2.17.5 to 2.17.7 (#6324)
  Improve performance massively by fixing a stupid binding mistake (#6316)
  Fixed missing paste command (#6313)
  Remove cache of auto completion results (#6310)

.github/workflows/stale.yml

@@ -13,6 +13,6 @@ jobs:
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         stale-issue-message: 'This issue will be closed in 7 days due to inactivity :zzz: Please provide the requested information if the problem persists.'
-        stale-issue-label: 's: stale'
+        stale-issue-label: 'status: stale'
         days-before-stale: 30
-        only-labels: 's: waiting-for-customer-feedback'
+        only-labels: 'status: waiting-for-customer-feedback'

CHANGELOG.md

@@ -39,6 +39,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where custom jstyles for Open/LibreOffice where not saved correctly. [#6170](https://github.com/JabRef/jabref/issues/6170)
 - We fixed an issue where the INSPIRE fetcher was no longer working [#6229](https://github.com/JabRef/jabref/issues/6229)
 - We fixed the display of icon both in the main table and linked file editor. [#6169](https://github.com/JabRef/jabref/issues/6169)
+- We fixed the paste entry command in the menu and toolbar, that did not do anything. [#6293](https://github.com/JabRef/jabref/issues/6293)
 - We fixed an issue where the windows installer did not create an entry in the start menu [bug report in the forum](https://discourse.jabref.org/t/error-while-fetching-from-doi/2018/3)
 
 ### Removed
@@ -245,6 +246,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a 'LaTeX citations' tab to the entry editor, to search for citations to the active entry in the LaTeX file directory. It can be disabled in the preferences dialog.
 - We added an option in preferences to allow for integers in field "edition" when running database in bibtex mode. [#4680](https://github.com/JabRef/jabref/issues/4680)
 - We added the ability to use negation in export filter layouts. [#5138](https://github.com/JabRef/jabref/pull/5138)
+- Focus on Name Area instead of 'OK' button whenever user presses 'Add subgroup'. [#6307](https://github.com/JabRef/jabref/issues/6307)
 
 ### Fixed
 

build.gradle

@@ -22,7 +22,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.28.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
-    id 'org.beryx.jlink' version '2.17.5'
+    id 'org.beryx.jlink' version '2.17.7'
 
     // nicer test outputs during running and completion
     id 'com.adarshr.test-logger' version '2.0.0'
@@ -128,10 +128,10 @@ dependencies {
     // See https://bugs.documentfoundation.org/show_bug.cgi?id=117331#c8 for background information
     // Use the task bundleLibreOffice to update the bundled jar
     // DO NOT CHANGE THE libreoffice PREFIX
-    libreoffice 'org.libreoffice:juh:6.3.2'
-    libreoffice 'org.libreoffice:jurt:6.3.2'
-    libreoffice 'org.libreoffice:ridl:6.3.2'
-    libreoffice 'org.libreoffice:unoil:6.3.2'
+    libreoffice 'org.libreoffice:juh:6.4.3'
+    libreoffice 'org.libreoffice:jurt:6.4.3'
+    libreoffice 'org.libreoffice:ridl:6.4.3'
+    libreoffice 'org.libreoffice:unoil:6.4.3'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.5'
     implementation 'info.debatty:java-string-similarity:1.2.1'
@@ -151,7 +151,7 @@ dependencies {
         exclude module: 'oraclepki'
     }
 
-    implementation ('com.google.guava:guava:28.2-jre') {
+    implementation ('com.google.guava:guava:29.0-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -165,7 +165,7 @@ dependencies {
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'org.fxmisc.easybind:easybind:1.0.3'
     implementation 'org.fxmisc.flowless:flowless:0.6.1'
-    implementation 'org.fxmisc.richtext:richtextfx:0.10.4'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.5'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.9'
     implementation 'org.controlsfx:controlsfx:11.0.1'
@@ -196,11 +196,11 @@ dependencies {
         exclude module: "log4j-core"
     }
 
-    implementation 'com.vladsch.flexmark:flexmark:0.61.6'
+    implementation 'com.vladsch.flexmark:flexmark:0.61.16'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.6'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.6'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.16'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.69'
+    testImplementation 'io.github.classgraph:classgraph:4.8.71'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.6.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.6.2'

docs/adr/0009-use-plain-junit5-for-testing.md

@@ -0,0 +1,83 @@
+# Use Plain JUnit5 for advanced test assertions
+
+## Context and Problem Statement
+
+How to write readable test assertions?
+How to write readable test assertions for advanced tests?
+
+## Considered Options
+
+* Plain JUnit5
+* Hamcrest
+* AssertJ
+
+## Decision Outcome
+
+Chosen option: "Plain JUnit5", because comes out best \(see below\).
+
+### Positive Consequences
+
+* Tests are more readable
+* More easy to write tests
+* More readable assertions
+
+### Negative Consequences
+
+* More complicated testing leads to more complicated assertions
+
+## Pros and Cons of the Options
+
+### Plain JUnit5
+
+Homepage: <https://junit.org/junit5/docs/current/user-guide/>
+JabRef testing guidelines: <https://devdocs.jabref.org/getting-into-the-code/code-howtos#test-cases>
+
+Example:
+
+```java
+String actual = markdownFormatter.format(source);
+assertTrue(actual.contains("Markup<br />"));
+assertTrue(actual.contains("<li>list item one</li>"));
+assertTrue(actual.contains("<li>list item 2</li>"));
+assertTrue(actual.contains("> rest"));
+assertFalse(actual.contains("\n"));
+```
+
+* Good, because Junit5 is "common Java knowledge"
+* Bad, because complex assertions tend to get hard to read
+* Bad, because no fluent API
+
+### Hamcrest
+
+Homepage: <http://hamcrest.org/JavaHamcrest/>
+
+* Good, because offers advanced matchers (such as `contains`)
+* Bad, because not full fluent API
+* Bad, because entry barrier is increased
+
+### AssertJ
+
+Homepage: <https://joel-costigliola.github.io/assertj/>
+
+Example:
+
+```java
+assertThat(markdownFormatter.format(source))
+        .contains("Markup<br />")
+        .contains("<li>list item one</li>")
+        .contains("<li>list item 2</li>")
+        .contains("> rest")
+        .doesNotContain("\n");
+```
+
+* Good, because offers fluent assertions
+* Good, because allows partial string testing to focus on important parts
+* Good, because assertions are more readable
+* Bad, because not commonly used
+* Bad, because newcomers have to learn an additional language to express test cases
+* Bad, because entry barrier is increased
+* Bad, because expressions of test cases vary from unit test to unit test
+
+## Links
+
+* German comparison between Hamcrest and AssertJ: <https://www.sigs-datacom.de/uploads/tx_dmjournals/philipp_JS_06_15_gRfN.pdf>

docs/teaching.md

@@ -120,6 +120,15 @@ Course [Open Source Software](https://github.com/igorsteinmacher/DSL-UTFPR)
 - Summary: Students are requested to contribute to an Open Source project to learn about the maintenance and evolution of software projects. This project is the predecessor of NAU's CS499.
 - Course offered from 2013 to 2016 with different names
 
+## Interesting Read for Students and Advisors
+
+- [Developing Procrastination Feedback for Student Software Developers](https://medium.com/@ayaankazerouni/developing-procrastination-feedback-for-student-software-developers-1652de60db7f) by [@ayaankazerouni](https://github.com/ayaankazerouni?tab=overview&from=2015-12-01&to=2015-12-31)  
+  > When students worked earlier and more often, they produced projects that:
+  >
+  > - were more correct,
+  > - were completed earlier,
+  > - took no more or less time to complete
+
 ## References
 
 <a id="LientzSwanson" href="#a1">1</a>: Lientz B., Swanson E., 1980: Software Maintenance Management. Addison Wesley, Reading, MA.

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

@@ -14,9 +14,7 @@
 import javafx.scene.layout.StackPane;
 
 import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
 import org.jabref.gui.autocompleter.AutoCompletePreferences;
-import org.jabref.gui.autocompleter.AutoCompleteUpdater;
 import org.jabref.gui.autocompleter.PersonNameSuggestionProvider;
 import org.jabref.gui.autocompleter.SuggestionProviders;
 import org.jabref.gui.collab.DatabaseChangeMonitor;
@@ -40,9 +38,7 @@
 import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.KeyCollisionException;
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
-import org.jabref.model.database.event.CoarseChangeFilter;
 import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.database.event.EntriesRemovedEvent;
 import org.jabref.model.database.shared.DatabaseLocation;
@@ -93,12 +89,10 @@ public class BasePanel extends StackPane {
     // the query the user searches when this BasePanel is active
     private Optional<SearchQuery> currentSearchQuery = Optional.empty();
     private Optional<DatabaseChangeMonitor> changeMonitor = Optional.empty();
-    private JabRefExecutorService executorService;
 
     public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabaseContext bibDatabaseContext, ExternalFileTypes externalFileTypes) {
         this.preferences = Objects.requireNonNull(preferences);
         this.frame = Objects.requireNonNull(frame);
-        this.executorService = JabRefExecutorService.INSTANCE;
         this.bibDatabaseContext = Objects.requireNonNull(bibDatabaseContext);
         this.externalFileTypes = Objects.requireNonNull(externalFileTypes);
         this.undoManager = frame.getUndoManager();
@@ -114,6 +108,7 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         annotationCache = new FileAnnotationCache(bibDatabaseContext, Globals.prefs.getFilePreferences());
 
         setupMainPanel();
+        setupAutoCompletion();
 
         this.getDatabase().registerListener(new SearchListener());
         this.getDatabase().registerListener(new EntriesRemovedListener());
@@ -257,7 +252,6 @@ public void insertEntry(final BibEntry bibEntry) {
 
     public void insertEntries(final List<BibEntry> entries) {
         if (!entries.isEmpty()) {
-            try {
                 bibDatabaseContext.getDatabase().insertEntries(entries);
 
                 // Set owner and timestamp
@@ -276,9 +270,6 @@ public void insertEntries(final List<BibEntry> entries) {
                     showAndEdit(entries.get(0));
                 }
                 clearAndSelect(entries.get(0));
-            } catch (KeyCollisionException ex) {
-                LOGGER.info("Collision for bibtex key" + ex.getId(), ex);
-            }
         }
     }
 
@@ -379,11 +370,6 @@ public void setupMainPanel() {
 
         splitPane.getItems().add(mainTable);
 
-        // Set up name autocompleter for search:
-        setupAutoCompletion();
-        executorService.execute(this::instantiateSearchAutoCompleter);
-        this.getDatabase().registerListener(new SearchAutoCompleteListener());
-
         // Saves the divider position as soon as it changes
         // We need to keep a reference to the subscription, otherwise the binding gets garbage collected
         dividerPositionSubscription = EasyBind.monadic(Bindings.valueAt(splitPane.getDividers(), 0))
@@ -413,28 +399,18 @@ public void setupMainPanel() {
     private void setupAutoCompletion() {
         AutoCompletePreferences autoCompletePreferences = preferences.getAutoCompletePreferences();
         if (autoCompletePreferences.shouldAutoComplete()) {
-            suggestionProviders = new SuggestionProviders(autoCompletePreferences, Globals.journalAbbreviationLoader);
-            suggestionProviders.indexDatabase(getDatabase());
-            // Ensure that the suggestion providers are in sync with entries
-            CoarseChangeFilter changeFilter = new CoarseChangeFilter(bibDatabaseContext);
-            changeFilter.registerListener(new AutoCompleteUpdater(suggestionProviders));
+            suggestionProviders = new SuggestionProviders(getDatabase(), autoCompletePreferences, Globals.journalAbbreviationLoader);
         } else {
             // Create empty suggestion providers if auto completion is deactivated
             suggestionProviders = new SuggestionProviders();
         }
+        searchAutoCompleter = new PersonNameSuggestionProvider(FieldFactory.getPersonNameFields(), getDatabase());
     }
 
     public void updateSearchManager() {
         frame.getGlobalSearchBar().setAutoCompleter(searchAutoCompleter);
     }
 
-    private void instantiateSearchAutoCompleter() {
-        searchAutoCompleter = new PersonNameSuggestionProvider(FieldFactory.getPersonNameFields());
-        for (BibEntry entry : bibDatabaseContext.getDatabase().getEntries()) {
-            searchAutoCompleter.indexEntry(entry);
-        }
-    }
-
     private void adjustSplitter() {
         if (mode == BasePanelMode.SHOWING_EDITOR) {
             splitPane.setDividerPositions(preferences.getEntryEditorDividerPosition());
@@ -730,23 +706,6 @@ public void listen(EntriesRemovedEvent entriesRemovedEvent) {
         }
     }
 
-    /**
-     * Ensures that the search auto completer is up to date when entries are changed AKA Let the auto completer, if any,
-     * harvest words from the entry Actual methods for autocomplete indexing  must run in javafx thread
-     */
-    private class SearchAutoCompleteListener {
-
-        @Subscribe
-        public void listen(EntriesAddedEvent addedEntriesEvent) {
-            DefaultTaskExecutor.runInJavaFXThread(() -> addedEntriesEvent.getBibEntries().forEach(entry -> searchAutoCompleter.indexEntry(entry)));
-        }
-
-        @Subscribe
-        public void listen(EntryChangedEvent entryChangedEvent) {
-            DefaultTaskExecutor.runInJavaFXThread(() -> searchAutoCompleter.indexEntry(entryChangedEvent.getBibEntry()));
-        }
-    }
-
     /**
      * 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