Merge remote-tracking branch 'upstream/ai-pr-1' into ai-pr-1

.github/workflows/add-greeting-to-issue.yml

@@ -24,6 +24,8 @@ jobs:
 
           Newcomers, we're excited to have you on board. Start by exploring our [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) guidelines, and don't forget to check out our [workspace setup guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) to get started smoothly.
 
+          In case you encounter failing tests during development, please check our [developer FAQs](https://devdocs.jabref.org/code-howtos/faq.html)!
+
           Having any questions or issues? Feel free to ask here on GitHub. Need help setting up your local workspace? Join the conversation on [JabRef's Gitter chat](https://gitter.im/JabRef/jabref). And don't hesitate to open a (draft) pull request early on to show the direction it is heading towards. This way, you will receive valuable feedback.
 
           Happy coding! 🚀

.github/workflows/deployment-arm64.yml

@@ -98,7 +98,7 @@ jobs:
           create-keychain: false
           keychain-password: jabref
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Prepare merged jars and modules dir (macOS)

.github/workflows/deployment-jdk-ea.yml

@@ -191,7 +191,7 @@ jobs:
           java-version: 21
           distribution: 'temurin'
       - name: Set up Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Prepare merged jars and modules dir

.github/workflows/deployment.yml

@@ -93,7 +93,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Prepare merged jars and modules dir (macOS)

.github/workflows/tests-fetchers.yml

@@ -51,7 +51,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run fetcher tests

.github/workflows/tests.yml

@@ -47,7 +47,7 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run checkstyle using gradle
@@ -82,7 +82,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run OpenRewrite
@@ -117,7 +117,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run modernizer
@@ -237,7 +237,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run tests
@@ -280,7 +280,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run tests on PostgreSQL
@@ -321,7 +321,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Run GUI tests
@@ -371,7 +371,7 @@ jobs:
           java-version: 21.0.2
           distribution: 'temurin'
       - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v3
+        uses: gradle/actions/setup-gradle@v4
         with:
           gradle-home-cache-cleanup: true
       - name: Update test coverage metrics
@@ -400,7 +400,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           show-progress: 'false'
-      - uses: gradle/actions/wrapper-validation@v3
+      - uses: gradle/actions/wrapper-validation@v4
 
   # This ensures that no git merge conflict markers (<<<, ...) are contained
   merge_conflict_job:

CHANGELOG.md

@@ -20,6 +20,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - The dialog for [adding an entry using reference text](https://docs.jabref.org/collect/newentryfromplaintext) is now filled with the clipboard contents as default. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - Added minimal support for [biblatex data annotation](https://mirrors.ctan.org/macros/latex/contrib/biblatex/doc/biblatex.pdf#subsection.3.7) fields in `.layout` files. [#11505](https://github.com/JabRef/jabref/issues/11505)
 - Added saving of selected options in the [Lookup -> Search for unlinked local files dialog](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [#11439](https://github.com/JabRef/jabref/issues/11439)
+- We fixed ans issue where text in Dark mode inside "Citation information" was not readable [#11512](https://github.com/JabRef/jabref/issues/11512)
+- We enabled creating a new file link manually. [#11017](https://github.com/JabRef/jabref/issues/11017)
 - We added a toggle button to invert the selected groups. [#9073](https://github.com/JabRef/jabref/issues/9073)
 - We reintroduced the floating search in the main table. [#4237](https://github.com/JabRef/jabref/issues/4237)
 - We fixed an issue where the selection of an entry in the table lost after searching for a group. [#3176](https://github.com/JabRef/jabref/issues/3176)
@@ -37,14 +39,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We fixed an issue where the "Check for updates" preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
+- We fixed an issue where JabRef put file paths as absolute path when an entry was created using drag and drop of a PDF file. [#11173](https://github.com/JabRef/jabref/issues/11173)
 - We fixed an issue that online and offline mode for new library creation were handled incorrectly. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - We fixed an issue with colors in the search bar when dark theme is enabled. [#11569](https://github.com/JabRef/jabref/issues/11569)
 - We fixed an issue where a new unsaved library was not marked with an asterisk. [#11519](https://github.com/JabRef/jabref/pull/11519)
 - We fixed an issue where JabRef starts without window decorations. [#11440](https://github.com/JabRef/jabref/pull/11440)
 
 ### Removed
 
-
+- We removed support for importing using the SilverPlatterImporter (`Record INSPEC`). [#11576](https://github.com/JabRef/jabref/pull/11576)
 
 
 

PRIVACY.md

@@ -1,6 +1,6 @@
 # Privacy Policy
 
-Last updated: 2023-08-24
+Last updated: 2024-08-06
 
 Your privacy is a fundamental right JabRef e.V. respects and supports.
 By using JabRef and its related online services, you choose to share some of your personal information.
@@ -58,6 +58,7 @@ These third-party services are the following:
 | [IACR](https://www.iacr.org/)                                                                                                | <https://www.iacr.org/privacy.html> |
 | [IEEEXplore](https://ieeexplore.ieee.org/Xplore/home.jsp)                                                                    | <https://www.ieee.org/security-privacy.html> |
 | [INSPIRE](https://inspirehep.net/)                                                                                           | <https://cern.service-now.com/service-portal?id=privacy_policy&se=INSPIRE-Online&notice=main> |
+| [ISIDORE](https://isidore.science/)                                                                                          | <https://isidore.science/credit> |
 | [JSTOR](https://www.jstor.org/)                                                                                              | <https://www.ithaka.org/privacypolicy/> |
 | [Library of Congress](https://lccn.loc.gov/)                                                                                 | <https://www.loc.gov/legal/> |
 | [National Library of Medicine](https://www.ncbi.nlm.nih.gov/)                                                                | <https://www.nlm.nih.gov/web_policies.html> |
@@ -73,9 +74,8 @@ These third-party services are the following:
 | [The SAO/NASA Astrophysics Data System](https://ui.adsabs.harvard.edu/)                                                      | <https://ui.adsabs.harvard.edu/help/privacy/> |
 | [Unpaywall](https://unpaywall.org/)                                                                                          | <https://unpaywall.org/legal/privacy> |
 | [zbMATH Open](https://www.zbmath.org)                                                                                        | <https://zbmath.org/privacy-policy/> |
-| [ISIDORE](https://isidore.science/)                                                                                          | <https://isidore.science/credit> |
 
-[1]: *Note: The Mr. DLib service is used for the related articles tab in the entry editor and collects also your language, your browser and operating system (by default*disabled*).*
+[1]: *Note: The Mr. DLib service is used for the related articles tab in the entry editor and collects also your language, your browser and operating system (*disabled* by default).*
 
 ## JabRef Browser Extension
 

build.gradle

@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.16.4'
+    id 'org.openrewrite.rewrite' version '6.17.1'
 }
 
 // Enable following for debugging
@@ -190,7 +190,7 @@ dependencies {
     implementation 'com.github.javakeyring:java-keyring:1.0.4'
 
     antlr4 'org.antlr:antlr4:4.13.1'
-    implementation 'org.antlr:antlr4-runtime:4.13.1'
+    implementation 'org.antlr:antlr4-runtime:4.13.2'
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.10.0.202406032230-r'
 
@@ -302,8 +302,8 @@ dependencies {
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
     // HTTP server
     // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
-    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.7'
-    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.7'
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.8'
+    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.8'
     // Allow objects "magically" to be mapped to JSON using GSON
     // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'
 
@@ -358,7 +358,7 @@ dependencies {
     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:2.15.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.16.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")

docs/code-howtos/faq.md

@@ -19,7 +19,7 @@ Following is a list of common errors encountered by developers which lead to fai
       Read more about the background and format of localization in JabRef [here](https://devdocs.jabref.org/code-howtos/localization.html).
 
 * `org.jabref.logic.l10n.LocalizationConsistencyTest` `findObsoleteLocalizationKeys` <span style="color:red">FAILED</span>
-  * <span style="color:green">Fix</span>: There are localization keys [localization properties file](https://github.com/JabRef/jabref/blob/main/src/main/resources/l10n/JabRef_en.properties) that are not used in the code, probably due to the removal of existing code. Navigate to the unused key-value pairs in the file and remove them. You can always click on the details of the failing test to pinpoint which keys are unused.
+  * <span style="color:green">Fix</span>: There are localization keys in the [localization properties file](https://github.com/JabRef/jabref/blob/main/src/main/resources/l10n/JabRef_en.properties) that are not used in the code, probably due to the removal of existing code. Navigate to the unused key-value pairs in the file and remove them. You can always click on the details of the failing test to pinpoint which keys are unused.
     Read more about the background and format of localization in JabRef [here](https://devdocs.jabref.org/code-howtos/localization.html).
 
 * `org.jabref.logic.citationstyle.CitationStyle` `discoverCitationStyles` <span style="color:red">ERROR: Could not find any citation style. Tried with /ieee.csl.</span>

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-11-code-into-ide.md

@@ -43,7 +43,8 @@ Press <kbd>Alt</kbd>+<kbd>0</kbd> to open the commit dialog.
 Unfortunately, IntelliJ has no support for ignored sub modules [[IDEA-285237](https://youtrack.jetbrains.com/issue/IDEA-285237/ignored-changes-in-submodules-are-still-visible-in-the-commit-window)].
 Fortunately, there is a workaround:
 
-Go to **File > Settings... > Version Control > Directory Mappings**.
+Go to **File > Settings... > Version Control > Directory Mappings**.<br>
+**Note:** In some MacBooks, `Settings` can be found at the "IntelliJ" button of the app menu instead of at "File".
 
 Currently, it looks as follows:
 
@@ -60,3 +61,5 @@ This will make these directories "Unregistered roots:", which is fine.
 {% figure caption:"Directory Mappings having three unregistered roots" %}
 ![Directory Mappings having three repositories unregsitered](intellij-directory-mappings-unregistered-roots.png)
 {% endfigure %}
+
+<!-- markdownlint-disable-file MD033 -->

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md

@@ -8,7 +8,8 @@ nav_order: 12
 
 ## Ensure that JDK 21 is available to IntelliJ
 
-Ensure you have a Java 21 SDK configured by navigating to **File > Project Structure... > Platform Settings > SDKs**.
+Ensure you have a Java 21 SDK configured by navigating to **File > Project Structure... > Platform Settings > SDKs**.<br>
+**Note:** In some MacBooks, `Project Structure` can be found at the "IntelliJ" button of the app menu instead of at "File".
 
 {% figure caption:"JDKs 11, 14, and 15 shown in available SDKs. JDK 21 is missing." %}
 ![Plattform Settings - SDKs](intellij-choose-jdk-adoptopenjdk-on-windows-project-settings.png)
@@ -197,3 +198,5 @@ A right-click on "BibEntryTests" enables the debugger to start.
 {% figure caption:"Run window for the BibEntry test case" %}
 ![Run window for the BibEntry test case](guidelines-intellij-tests-are-green.png)
 {% endfigure %}
+
+<!-- markdownlint-disable-file MD033 -->

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.md

@@ -12,7 +12,8 @@ Install the [CheckStyle-IDEA plugin](http://plugins.jetbrains.com/plugin/1065?pr
 Navigate to **File > Settings... > Plugins"**.
 On the top, click on "Marketplace".
 Then, search for "Checkstyle".
-Click on "Install" choose "CheckStyle-IDEA".
+Click on "Install" choose "CheckStyle-IDEA".<br>
+**Note:** In some MacBooks, `Settings` can be found at the "IntelliJ" button of the app menu instead of at "File".
 
 {% figure caption:"Install CheckStyle" %}
 ![Install CheckStyle](guidelines-intellij-install-checkstyle.png)
@@ -159,3 +160,5 @@ Press "OK".
 > Finally, you have Checkstyle running locally so that you can check for styling errors before submitting the pull request.
 
 Got it running? GREAT! You are ready to lurk the code and contribute to JabRef. Please make sure to also read our [contribution guide](https://devdocs.jabref.org/contributing#contribute-code).
+
+<!-- markdownlint-disable-file MD033 -->

scripts/vms/README.md

@@ -13,14 +13,14 @@ This folder contains directories making use of [Vagrant](https://www.vagrantup.c
 
 ### Setup VM
 
-1. `cd` into `ubuntu`
+1. `cd` into `{vmdir}`, e..g, `cd ubuntu`
 2. Start the vm `vagrant up`
-3. Store ssh configuration: `vagrant ssh-config > default`
+3. Linux machines: Store ssh configuration: `vagrant ssh-config > default`
 
 ### Use VM
 
 You can use the UI offered by the VirtualBox client.
-You can also do `ssh -Y -F vagrant-ssh default` to SSH into the machine.
+On Linux, you can also do `ssh -Y -F vagrant-ssh default` to SSH into the machine.
 
 If asked for a password, this is `vagrant`.
 
@@ -31,8 +31,11 @@ Then, everything is removed.
 
 ## Available VMs
 
-- `ubuntu`: Ubuntu with JabRef snap and libreoffice-connection pre-installed. One has to install the [JabRef Browser Extension](https://addons.mozilla.org/en-US/firefox/addon/jabref/) manually.
-- `fedora`: Fedora 39 with KDE plasma and JDK. During the build, the JabRef sources will be fetched and an initial build will be triggered. Login and then type `startx`. Now KDE Plasma should start. Open Konsole. Then `cd jabref`. Then `./gradlew run`.
+| VM                    | JabRef | Browser | LibreOffice |
+|-----------------------|--------|---------|-------------|
+| [`fedora`](fedora/)   | source | --      | --          |
+| [`ubuntu`](ubuntu/)   | snap   | Firefox | yes         |
+| [`windows`](windows/) | source | Firefox | yes         |
 
 ## Troubleshooting
 

scripts/vms/fedora/README.md

@@ -0,0 +1,6 @@
+# Fedora VM
+
+Fedora 39 with KDE plasma and JDK.
+During the build, the JabRef sources will be fetched and an initial build will be triggered.
+
+Login and then type `startx`. Now KDE Plasma should start. Open Konsole. Then `cd jabref`. Then `./gradlew run`.

scripts/vms/ubuntu/README.md

@@ -0,0 +1,5 @@
+# Ubuntu VM
+
+Ubuntu with JabRef snap and libreoffice-connection pre-installed.
+
+One has to install the [JabRef Browser Extension](https://addons.mozilla.org/en-US/firefox/addon/jabref/) manually.