arfazhxss · arfazhxss · Sep 16, 2024 · Sep 8, 2024 · Sep 8, 2024 · Sep 8, 2024
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -332,6 +332,22 @@ jobs:
         env:
           CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
 
+  requirements_coverage:
+    name: "Validate requiremenet coverage"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: 21.0.2
+          distribution: 'temurin'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v4
+      - run: ./gradlew traceRequirements
+
   # This is https://github.com/marketplace/actions/gradle-wrapper-validation
   # It ensures that the jar file is from gradle and not by a strange third party.
   gradlevalidation:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,8 +26,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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 improved [cleanup](https://docs.jabref.org/finding-sorting-and-cleaning-entries/cleanupentries) of `arXiv` IDs in distributed in the fields `note`, `version`, `institution`, and `eid` fields. [#11306](https://github.com/JabRef/jabref/issues/11306)
+- We added a switch not to store the linked file URL, because it caused troubles at other apps. [#11735](https://github.com/JabRef/jabref/pull/11735)
 - When starting a new SLR, the selected catalogs now persist within and across JabRef sessions. [koppor#614](https://github.com/koppor/jabref/issues/614)
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
+- We added a setting which always adds the literal "Cited on pages" text before each JStyle citation. [#11691](https://github.com/JabRef/jabref/pull/11732)
 
 ### Changed
 
@@ -44,6 +47,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - The browse button for a Custom theme now opens in the directory of the current used CSS file. [#11597](https://github.com/JabRef/jabref/pull/11597)
 - The browse button for a Custom exporter now opens in the directory of the current used exporter file. [#11717](https://github.com/JabRef/jabref/pull/11717)
 - We improved the display of long messages in the integrity check dialog. [#11619](https://github.com/JabRef/jabref/pull/11619)
+- We improved the undo/redo buttons in the main toolbar and main menu to be disabled when there is nothing to undo/redo. [#8807](https://github.com/JabRef/jabref/issues/8807)
 
 ### Fixed
 
@@ -65,7 +69,9 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the full-text search results were incomplete. [#8626](https://github.com/JabRef/jabref/issues/8626)
 - We fixed an issue where search result highlighting was incorrectly highlighting the boolean operators. [#11595](https://github.com/JabRef/jabref/issues/11595)
 - We fixed an issue where search result highlighting was broken at complex searches. [#8067](https://github.com/JabRef/jabref/issues/8067)
-- We fixed an issue where unescaped braces in the arXiv fetcher were not treated [#11704](https://github.com/JabRef/jabref/issues/11704)
+- We fixed an exception when searching for unlinked files. [#11731](https://github.com/JabRef/jabref/issues/11731)
+- We fixed an issue where two contradicting notifications were shown when cutting an entry in the main table. [#11724](https://github.com/JabRef/jabref/pull/11724)
+- We fixed an issue where unescaped braces in the arXiv fetcher were not treated. [#11704](https://github.com/JabRef/jabref/issues/11704)
 
 ### Removed
 

diff --git a/PRIVACY.md b/PRIVACY.md
diff --git a/build.gradle b/build.gradle
@@ -30,6 +30,8 @@ plugins {
     id 'idea'
 
     id 'org.openrewrite.rewrite' version '6.20.0'
+
+    id "org.itsallcode.openfasttrace" version "3.0.0"
 }
 
 // Enable following for debugging
@@ -236,7 +238,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.3'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.43.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.48.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
@@ -323,20 +325,21 @@ dependencies {
     implementation 'com.github.vatbub:mslinks:1.0.6.2'
 
     // YAML formatting
-    implementation 'org.yaml:snakeyaml:2.2'
+    implementation 'org.yaml:snakeyaml:2.3'
 
     // AI
-    implementation 'dev.langchain4j:langchain4j:0.33.0'
+    implementation 'dev.langchain4j:langchain4j:0.34.0'
     // Even though we use jvm-openai for LLM connection, we still need this package for tokenization.
-    implementation('dev.langchain4j:langchain4j-open-ai:0.33.0') {
+    implementation('dev.langchain4j:langchain4j-open-ai:0.34.0') {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
     }
-    implementation('dev.langchain4j:langchain4j-mistral-ai:0.33.0')
-    implementation('dev.langchain4j:langchain4j-hugging-face:0.33.0')
+    implementation('dev.langchain4j:langchain4j-mistral-ai:0.34.0')
+    implementation('dev.langchain4j:langchain4j-google-ai-gemini:0.34.0')
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.34.0')
     implementation 'ai.djl:api:0.29.0'
     implementation 'ai.djl.pytorch:pytorch-model-zoo:0.29.0'
     implementation 'ai.djl.huggingface:tokenizers:0.29.0'
-    implementation 'io.github.stefanbratanov:jvm-openai:0.10.0'
+    implementation 'io.github.stefanbratanov:jvm-openai:0.11.0'
     // openai depends on okhttp, which needs kotlin - see https://github.com/square/okhttp/issues/5299 for details
     implementation ('com.squareup.okhttp3:okhttp:4.12.0') {
         exclude group: 'org.jetbrains.kotlin', module: 'kotlin-stdlib-jdk8'
@@ -367,7 +370,7 @@ 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:2.17.0"))
+    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.18.0"))
     rewrite("org.openrewrite.recipe:rewrite-static-analysis")
     rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
     rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
@@ -776,6 +779,7 @@ jlink {
         uses 'org.eclipse.jgit.transport.SshSessionFactory'
         uses 'org.eclipse.jgit.lib.GpgSigner'
         uses 'kong.unirest.core.json.JsonEngine';
+        uses 'ai.djl.repository.zoo.ZooProvider';
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'
         provides 'org.mariadb.jdbc.authentication.AuthenticationPlugin' with 'org.mariadb.jdbc.internal.com.send.authentication.CachingSha2PasswordPlugin',
@@ -792,7 +796,10 @@ jlink {
         provides 'java.security.Provider' with 'org.bouncycastle.jce.provider.BouncyCastleProvider',
                 'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'
         provides 'kong.unirest.core.json.JsonEngine' with 'kong.unirest.modules.gson.GsonEngine';
-
+        provides 'ai.djl.repository.zoo.ZooProvider' with 'ai.djl.engine.rust.zoo.RsZooProvider',
+                'ai.djl.huggingface.zoo.HfZooProvider',
+                'ai.djl.pytorch.zoo.PtZooProvider',
+                'ai.djl.repository.zoo.DefaultZooProvider';
     }
 
     jpackage {
@@ -898,3 +905,7 @@ jmh {
     iterations = 10
     fork = 2
 }
+
+requirementTracing {
+    inputDirectories = files('docs', 'src/main/java', 'src/test/java')
+}
diff --git a/buildres/abbrv.jabref.org b/buildres/abbrv.jabref.org
diff --git a/docs/code-howtos/index.md b/docs/code-howtos/index.md
@@ -47,7 +47,7 @@ JabRef stores files relative to one of [multiple possible directories](https://d
 The convert the relative path to an absolute one, there is the `find` method in `FileUtil`:
 
 ```java
-org.jabref.logic.util.io.FileUtil.find(org.jabref.model.database.BibDatabaseContext, java.lang.String, org.jabref.preferences.FilePreferences)
+org.jabref.logic.util.io.FileUtil.find(org.jabref.model.database.BibDatabaseContext, java.lang.String, org.jabref.logic.FilePreferences)
 ```
 
 `String path` Can be the files name or a relative path to it. The Preferences should only be directly accessed in the GUI. For the usage in logic pass them as parameter
@@ -59,7 +59,7 @@ When adding a file to a library, the path should be stored relative to "the best
 This is implemented in `FileUtil`:
 
 ```java
-org.jabref.logic.util.io.FileUtil.relativize(java.nio.file.Path, org.jabref.model.database.BibDatabaseContext, org.jabref.preferences.FilePreferences)
+org.jabref.logic.util.io.FileUtil.relativize(java.nio.file.Path, org.jabref.model.database.BibDatabaseContext, org.jabref.logic.FilePreferences)
 ```
 
 ## Setting a Directory for a .bib File

diff --git a/docs/contributing.md b/docs/contributing.md
@@ -112,3 +112,5 @@ If you want to indicate that a pull request is not yet complete **before** creat
 
 For improving developer's documentation, go on at the [docs/ subdirectory of JabRef's code](https://github.com/JabRef/jabref/tree/main/docs) and edit the file.
 GitHub offers a good guide at [Editing files in another user's repository](https://help.github.com/en/github/managing-files-in-a-repository/editing-files-in-another-users-repository).
+
+One can also add [callouts](https://just-the-docs.github.io/just-the-docs-tests/components/callouts/).
diff --git a/docs/requirements/ai.md b/docs/requirements/ai.md
@@ -0,0 +1,16 @@
+---
+parent: Requirements
+---
+# AI
+
+## User Interface
+
+### Chatting with AI
+`req~ai.chat.new-message-based-on-previous~1`
+
+To enable simple editing and resending of previous messages, <kbd>Cursor Up</kbd> should show last message.
+This should only happen if the current text field is empty.
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->
diff --git a/docs/requirements/index.md b/docs/requirements/index.md
@@ -0,0 +1,49 @@
+---
+nav_order: 7
+has_children: true
+---
+# Requirements
+
+This part of the documentation collects requirements using [OpenFastTrace](https://github.com/itsallcode/openfasttrace).
+
+## Specifying requirements
+
+One writes directly below a Markdown heading a requirement identifier.
+
+Example:
+
+```markdown
+### Example
+`req~ai.example~1`
+```
+
+It is important that there is no empty line directly after the heading.
+
+{: note}
+One needs to add `<!-- markdownlint-disable-file MD022 -->` to the end of the file, because the id of the requirement needs to follow the heading directly.
+
+## Linking implementations
+
+Then, one writes down at the requirement.
+Directly at the end, one writes that it requires an implementation:
+
+```markdown
+Needs: impl
+```
+
+One can also state that there should be detailed design document (`dsn`).
+However, typically in JabRef, we go from the requirement directly to the implementation.
+
+Then, at the implementation, a comment is added this implementation is covered:
+
+```java
+// [impl->req~ai.example~1]
+```
+
+When executing the gradle task `traceRequirements`, `build/tracing.txt` is generated.
+In case of a tracing error, one can inspect this file to see which requirements were not covered.
+
+## More Information
+
+- [User manual of OpenFastTrace](https://github.com/itsallcode/openfasttrace/blob/main/doc/user_guide.md)
+- We cannot copy and paste real examples here, because of [openfasttrace#280](https://github.com/itsallcode/openfasttrace/issues/280).
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=5b9c5eb3f9fc2c94abaea57d90bd78747ca117ddbbf96c859d3741181a12bf2a
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.10-bin.zip
+distributionSha256Sum=1541fa36599e12857140465f3c91a97409b4512501c26f9631fb113e392c5bd1
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

diff --git a/scripts/vms/README.md b/scripts/vms/README.md
@@ -55,7 +55,8 @@ Then, everything is removed.
 | [`fedora`](fedora/)                             | source  | --      | --          | --        |
 | [`Linux Mint (Cinnamon)`](linux-mint-cinnamon/) | source  | Firefox | yes         | --        |
 | [`ubuntu`](ubuntu/)                             | snap    | Firefox | yes         | --        |
-| [`windows`](windows/)                           | source  | Edge    | --          | --        |
+| [`windows 10`](windows10/)                      | source  | Edge    | --          | --        |
+| [`windows 11`](windows11/)                      | source  | Edge    | --          | --        |
 
 ## Troubleshooting
 

diff --git a/scripts/vms/windows/README.md → scripts/vms/windows10/README.md b/scripts/vms/windows/README.md → scripts/vms/windows10/README.md
@@ -1,4 +1,4 @@
-# Windows VM
+# Windows 10 VM
 
 A Windows-based VM to test JabRef.
 As user, you need to ensure to have the proper Windows license to use this VM.

diff --git a/scripts/vms/windows/Vagrantfile → scripts/vms/windows10/Vagrantfile b/scripts/vms/windows/Vagrantfile → scripts/vms/windows10/Vagrantfile
@@ -1,7 +1,7 @@
 # -*- mode: ruby -*-
 # vi: set ft=ruby :
 
-NAME = "jabref-windows-sandbox"
+NAME = "jabref-windows-10-sandbox"
 
 Vagrant.configure("2") do |config|
   config.vm.box = "gusztavvargadr/windows-10"

diff --git a/scripts/vms/windows11/README.md b/scripts/vms/windows11/README.md
@@ -0,0 +1,49 @@
+# Windows 11 VM
+
+A Windows-based VM to test JabRef.
+As user, you need to ensure to have the proper Windows license to use this VM.
+
+In case you have many CPU cores, you can adapt `vb.cpus` in `Vagrantfile` to a higher number.
+
+One has to install the [JabRef Browser Extension](https://addons.mozilla.org/en-US/firefox/addon/jabref/) manually.
+
+## Troubleshooting
+
+### "Waiting for machine to reboot..."
+
+In case Vagrant reports "Waiting for machine to reboot..." and nothing happens, one has to "power off" the machine, execute `vagrant destory`, and then run `vagrant up` again.
+
+### `fatal: early EOF`
+
+```console
+jabref-windows-sandbox: Cloning into 'jabref'...
+jabref-windows-sandbox: error: RPC failed; curl 92 HTTP/2 stream 5 was not closed cleanly: CANCEL (err 8)
+jabref-windows-sandbox: error: 6846 bytes of body are still expected
+jabref-windows-sandbox: fetch-pack: unexpected disconnect while reading sideband packet
+jabref-windows-sandbox: fatal: early EOF
+jabref-windows-sandbox: fatal: fetch-pack: invalid index-pack output
+```
+
+The `git clone` command did not work.
+
+Login, open `cmd` and then execute following commands:
+
+```cmd
+git clone --recurse-submodules https://github.com/JabRef/jabref.git
+cd jabref
+gradlew run
+```
+
+## Background
+
+`Vagrantfile` is based on [SeisoLLC/windows-sandbox](https://github.com/SeisoLLC/windows-sandbox/tree/main).
+
+The most use image seems to be the [Windows 10 image by `gusztavvargadr`](https://portal.cloud.hashicorp.com/vagrant/discover/gusztavvargadr/windows-10).
+List of all images at <https://portal.cloud.hashicorp.com/vagrant/discover/gusztavvargadr>.
+
+[Chocolatey](https://chocolatey.org/) is used instead of [winget-cli](https://learn.microsoft.com/en-us/windows/package-manager/), because Chocolatey installation does not hit GitHub's rate limits during unattended installation.
+
+## Atlernatives
+
+- Atlernative Vagrant images: <https://app.vagrantup.com/boxes/search?q=windows+10&utf8=%E2%9C%93>.
+- [Windows Sandbox](https://learn.microsoft.com/en-us/windows/security/application-security/application-isolation/windows-sandbox/windows-sandbox-overview)
diff --git a/scripts/vms/windows11/Vagrantfile b/scripts/vms/windows11/Vagrantfile
@@ -0,0 +1,46 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+NAME = "jabref-windows-11-sandbox"
+
+Vagrant.configure("2") do |config|
+  # config.vm.box = "Caden/windows-11-pro-jp-22h2-22621.1992"
+  config.vm.box = "stromweld/windows-11"
+
+  config.vm.define NAME
+  config.vm.hostname = NAME
+
+  config.vm.provider "virtualbox" do |vb|
+    vb.name = NAME
+
+    vb.memory = 6000
+    vb.cpus = 2
+
+    vb.customize ['modifyvm', :id, '--clipboard-mode', 'bidirectional']
+    vb.gui = true
+  end
+
+  config.vm.provision "shell", privileged: "true", powershell_elevated_interactive: "true", inline: <<-SHELL
+    # Install chocolatey
+    Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://community.chocolatey.org/install.ps1'))
+    choco feature enable -n=allowGlobalConfirmation
+
+    choco install libericajdk
+    choco install git.install -y --params "/GitAndUnixToolsOnPath /WindowsTerminal /WindowsTerminalProfile"
+
+    # Required by AI functionaltiy
+    choco choco install vcredist140
+
+    # choco install firefox
+    # choco install libreoffice-fresh
+  SHELL
+
+  config.vm.provision "shell", reboot: true
+
+  config.vm.provision "shell", privileged: "false", inline: <<-SHELL
+    cd \\users\\vagrant
+    git clone --depth=1 --recurse-submodules https://github.com/JabRef/jabref.git
+    # cd jabref
+    # .\\gradlew jar
+  SHELL
+end
Original file line number	Diff line number	Diff line change
Expand Up		@@ -112,3 +112,5 @@ If you want to indicate that a pull request is not yet complete before creat

		For improving developer's documentation, go on at the [docs/ subdirectory of JabRef's code](https://github.com/JabRef/jabref/tree/main/docs) and edit the file.
		GitHub offers a good guide at [Editing files in another user's repository](https://help.github.com/en/github/managing-files-in-a-repository/editing-files-in-another-users-repository).

		One can also add [callouts](https://just-the-docs.github.io/just-the-docs-tests/components/callouts/).