Merge remote-tracking branch 'upstream/main' into fix-for-issue-8911

* upstream/main:
  Fix for Dark theme not readable (JabRef#8929)
  Find Unlinked files should ignore Thumbs.db, etc (JabRef#8800)
  Try to  make reproducible builds (JabRef#8925)
  Link to new board (and refine text)
  Pass the data as a string (JabRef#8923)
  Add IntelliJ plugins to Gitpod configuration
  Add gradle support
  Fix extension name
  Remove obsolete closing bracket
  Add gitpod config (JabRef#8921)
  Fix javafx version not displayed in About Dialog (JabRef#8918)
  Redesign "Manage field names & content" dialog (JabRef#8892)

.gitpod.Dockerfile

@@ -0,0 +1,8 @@
+# See https://www.gitpod.io/docs/java-in-gitpod/ for a full documentation of Java in GitPod
+
+FROM gitpod/workspace-full
+
+# All available versions can be listed using sdk ls java
+# More information about SDKMAN available at https://github.com/sdkman/sdkman-cli#sdkman-cli
+RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh \
+             && sdk install java 18.0.1.1-open"

.gitpod.yml

@@ -0,0 +1,16 @@
+image:
+  file: .gitpod.Dockerfile
+tasks:
+  - init: ./gradlew assemble
+jetbrains:
+  intellij:
+    plugins:
+      - CheckStyle-IDEA
+      - zielu.gittoolbox
+vscode:
+  extensions:
+    - redhat.java
+    - richardwillis.vscode-gradle
+    - vscjava.vscode-java-debug
+    - kiteco.kite
+    - DavidAnson.vscode-markdownlint

CHANGELOG.md

@@ -13,11 +13,13 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
+- 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)
 
 ### Changed
 
+- Change in the color of the selection entries and the color of the summary in the Import Entries Dialog. [#7927](https://github.com/JabRef/jabref/issues/7927)
 - We upgraded to Lucene 9.2 for the fulltext search.
   Thus, the now created search index cannot be read from older versions of JabRef anylonger.
   ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
@@ -30,6 +32,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The Medline/Pubmed search now also supports the [default fields and operators for searching](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax). [forum#3554](https://discourse.jabref.org/t/native-pubmed-search/3354)
 - We improved group expansion arrow that prevent it from activating group when expanding or collapsing. [#7982](https://github.com/JabRef/jabref/issues/7982), [#3176](https://github.com/JabRef/jabref/issues/3176)
 - 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 fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
 
 ### Fixed

README.md

@@ -71,7 +71,7 @@ An explanation of donation possibilities and usage of donations is available at
 [![OpenHub](https://www.openhub.net/p/jabref/widgets/project_thin_badge.gif)](https://www.openhub.net/p/jabref)
 [![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
 [![Test Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests)
-[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
+[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=main)
 
 Want to be part of a free and open-source project that tens of thousands of scientists use every day?
 Check out the ways you can contribute, below:

build.gradle

@@ -81,7 +81,7 @@ repositories {
     mavenLocal()
     mavenCentral()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
-    maven { url 'https://repository.apache.org/snapshots' }
+    maven { url 'https://jitpack.io' }
 }
 
 configurations {
@@ -95,6 +95,10 @@ configurations {
     }
 }
 
+dependencyLocking {
+    lockAllConfigurations()
+}
+
 javafx {
     version = "18"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
@@ -166,7 +170,7 @@ dependencies {
     // JavaFX stuff
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
-    implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
+    implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
     implementation 'org.fxmisc.flowless:flowless:0.6.10'
@@ -208,15 +212,13 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
-    testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
-    testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:4.6.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.23.1'
-    testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
-    testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
+    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:10.1'

buildres/linux/jabrefHost.py

@@ -74,7 +74,7 @@ def send_message(message):
 
 def add_jabref_entry(data):
     """Send string via cli as literal to preserve special characters"""
-    cmd = str(JABREF_PATH).split() + ["--importBibtex", r"{}".format(data)]
+    cmd = str(JABREF_PATH).split() + ["--importBibtex", r"'{}'".format(data)]
     logging.info("Try to execute command {}".format(cmd))
     response = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
     logging.info("Called JabRef and got: {}".format(response))

docs/teaching.md

@@ -15,27 +15,31 @@ By using JabRef as training object in exercises and labs, students can level-up
 
 ## How to integrate JabRef in your class
 
-1. Get in touch with the JabRef team to discuss details. We offer email, skype, [gitter.im](https://gitter.im/JabRef/jabref), discord. Get in touch with [@koppor](https://github.com/koppor/) to find the right channel and to start forming the success of your course.
-2. Choose tasks from one of the following boards. Write a comment on each issue so that it can be reserved for your course.
-   * Candidates for university projects: [https://github.com/JabRef/jabref/projects/9](https://github.com/JabRef/jabref/projects/9)
-     * This board categorizes in small, medium, and large features
-   * Feature Board: [https://github.com/JabRef/jabref/projects/7](https://github.com/JabRef/jabref/projects/7)
-     * This is a general feature board. Recommended, if the board above is empty or you did not find something suitable
-   * Bug Board: [https://github.com/JabRef/jabref/projects/5](https://github.com/JabRef/jabref/projects/5)
-     * This is an excellent board to find issues training the maintenance knowledge which is essential for industry work
-   * General "good first issues". The JabRef team tags issues as [good first issues](https://github.com/jabref/jabref/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22) to indicate open tasks offering a good start into the JabRef code. These issues are more a list of random bugs and features. For a more structured comparison of the opened tasks, we recommend the project boards listed above.
-   * Be aware that the difficulty of bugs and feature vary. A task should be chosen with care. The JabRef team can help here: The majority of the team has experiences in teaching
+1. Choose task from the board [Candidates for university projects](https://github.com/orgs/JabRef/projects/3/views/3).
+   There, new functionality is categorized in small, medium, and large effort.
+   Morevoer, categorization on the main focus (UI, logic, or both),
+   implementation effort, testing effort, and "issue understanding effort".
+   The latter category is important, because some issues are "quick wins" and others need thorough thinking.   
+   In general, all issues of JabRef are free to take.
+   Be aware that the difficulty of bugs and feature vary.
+   For the brave, the [Bug Board](https://github.com/JabRef/jabref/projects/5) or the [Feature Board](https://github.com/JabRef/jabref/projects/7) provide other issue sources.
+   Especially for Master students, these are excellent boards to find issues that train maintenance knowledge (which is essential for industry work).
+2. Get in touch with the JabRef team to reserve issues for your student group and possibly to discuss details. We offer email, skype, [gitter.im](https://gitter.im/JabRef/jabref), discord. Get in touch with [@koppor](https://github.com/koppor/) to find the right channel and to start forming the success of your course.
 3. Schedule tasks with students
-4. Code reviews by JabRef maintainers
-5. Students address feedback and learn more about good coding practices by incoporating feedback
-6. Students update their pull request
-7. Pull request is merged
+4. Students implement code
+5. Students review other student's code (recommended: students of a previous year's project review current year's project code)
+6. Students address review feedback
+7. Students submit pull request
+8. Code reviews by JabRef maintainers
+9. Students address feedback and learn more about good coding practices by incoporating feedback
+10. Students update their pull request
+11. Pull request is merged
 
-For a near-to-perfect preparation and effect of the course, we ask you to get in touch with us **four weeks** in advance. Then, the JabRef team can a) learn about the starting skill level of the students, b) the aimed skill level at the end of the course, c) the amount of time the students are given to learn about and contribute to JabRef, d) check the [feature board](https://github.com/JabRef/jabref/projects/7) for appropriate tasks (and fill it as needed), e) recommend appropriate features.
+For a near-to-perfect preparation and effect of the course, we ask you to get in touch with us **four weeks** in advance. Then, the JabRef team can a) learn about the starting skill level of the students, b) the aimed skill level at the end of the course, c) the amount of time the students are given to learn about and contribute to JabRef, d) check the [Candidates for university projects](https://github.com/orgs/JabRef/projects/3/views/3) for appropriate tasks (and fill it as needed), e) recommend appropriate features.
 
-It is also possible to just direct students to our [Contribution Guide](https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#contributing-guide). The learning effect may be lower as the time of the students has to be spent to a) learn about JabRef and b) select an appropriate issue.
+It is also possible to just direct students to our [Contribution Guide](https://devdocs.jabref.org/contributing.html#contribute-code). The learning effect may be lower as the time of the students has to be spent to a) learn about JabRef and b) select an appropriate issue.
 
-Since a huge fraction of software costs is spent on [software maintenance](https://en.wikipedia.org/wiki/Software\_maintenance), adding new features also educates in that aspect: perfective maintenance[1](teaching.md#LientzSwanson) is trained. When fixing bugs, corrective maintenance[2](teaching.md#LientzSwanson) is trained.
+Since a huge fraction of software costs is spent on [software maintenance](https://en.wikipedia.org/wiki/Software\_maintenance), adding new features also educates in that aspect: perfective maintenance[1](teaching.md#LientzSwanson) is trained. When fixing bugs, corrective maintenance [2](teaching.md#LientzSwanson) is trained.
 
 ## Process for contributions
 

src/main/java/org/jabref/gui/Base.css

@@ -98,6 +98,9 @@
     -jr-drag-target: -jr-purple;
     -jr-drag-target-hover: derive(-jr-purple, 80%);
 
+    -js-summary-text-color: #000000;
+    -js-summary-text-color-selected: #000000;
+
     /*
      Here are redefinitions of the default properties of modena. They should in principle all be derived from the
      above colors. Goal should be to make as few as possible direct color-changes to elements and only do this for

src/main/java/org/jabref/gui/Dark.css

@@ -55,6 +55,9 @@
 
     -jr-drag-target: -jr-accent;
     -jr-drag-target-hover: -jr-accent;
+
+    -js-summary-text-color: derive(-fx-light-text-color, 70%);
+    -js-summary-text-color-selected: derive( -fx-dark-text-color, 70%);
 }
 
 #previewBody {

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

@@ -67,9 +67,9 @@
 import org.jabref.gui.edit.CopyMoreAction;
 import org.jabref.gui.edit.EditAction;
 import org.jabref.gui.edit.ManageKeywordsAction;
-import org.jabref.gui.edit.MassSetFieldsAction;
 import org.jabref.gui.edit.OpenBrowserAction;
 import org.jabref.gui.edit.ReplaceStringAction;
+import org.jabref.gui.edit.automaticfiededitor.AutomaticFieldEditorAction;
 import org.jabref.gui.entryeditor.OpenEntryEditorAction;
 import org.jabref.gui.entryeditor.PreviewSwitchAction;
 import org.jabref.gui.exporter.ExportCommand;
@@ -750,8 +750,7 @@ private MenuBar createMenu() {
                 new SeparatorMenuItem(),
 
                 factory.createMenuItem(StandardActions.MANAGE_KEYWORDS, new ManageKeywordsAction(stateManager)),
-                factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(stateManager, dialogService, undoManager)));
-
+                factory.createMenuItem(StandardActions.AUTOMATIC_FIELD_EDITOR, new AutomaticFieldEditorAction(stateManager, dialogService)));
         SeparatorMenuItem specialFieldsSeparator = new SeparatorMenuItem();
         specialFieldsSeparator.visibleProperty().bind(prefs.getSpecialFieldsPreferences().specialFieldsEnabledProperty());
 

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -78,6 +78,8 @@ public enum StandardActions implements Action {
     REPLACE_ALL(Localization.lang("Find and replace"), KeyBinding.REPLACE_STRING),
     MANAGE_KEYWORDS(Localization.lang("Manage keywords")),
     MASS_SET_FIELDS(Localization.lang("Manage field names & content")),
+
+    AUTOMATIC_FIELD_EDITOR(Localization.lang("Automatic field editor")),
     TOGGLE_GROUPS(Localization.lang("Groups"), IconTheme.JabRefIcons.TOGGLE_GROUPS, KeyBinding.TOGGLE_GROUPS_INTERFACE),
     TOOGLE_OO(Localization.lang("OpenOffice/LibreOffice"), IconTheme.JabRefIcons.FILE_OPENOFFICE, KeyBinding.OPEN_OPEN_OFFICE_LIBRE_OFFICE_CONNECTION),
     TOGGLE_WEB_SEARCH(Localization.lang("Web search"), Localization.lang("Toggle web search interface"), IconTheme.JabRefIcons.WWW, KeyBinding.WEB_SEARCH),