Merge remote-tracking branch 'upstream/main' into fix-for-JabRef#10935

* upstream/main: (40 commits) Improve citation relations (JabRef#11016) Keep enclosing braces of authors (JabRef#11034) Bump org.apache.pdfbox:fontbox from 3.0.1 to 3.0.2 (JabRef#11042) Bump com.dlsc.gemsfx:gemsfx from 2.2.0 to 2.4.0 (JabRef#11044) Bump org.apache.pdfbox:xmpbox from 3.0.1 to 3.0.2 (JabRef#11041) Bump com.googlecode.plist:dd-plist from 1.23 to 1.28 (JabRef#11040) Bump gittools/actions from 0.13.4 to 1.1.1 (JabRef#11039) Change copy-paste function to handle string constants (follow up PR) (JabRef#11037) Fixes Zotero file handling for absolute paths (JabRef#11038) Speed up failure reporting (JabRef#11030) Importing of BibDesk Groups and Linked Files (JabRef#10968) Convert RemoveBracesFormatterTest to @ParameterizedTest (JabRef#11033) Update teaching.md Remove non-existing recipe (JabRef#11029) Update CSL styles (JabRef#11031) Clean up defintions of entry types (JabRef#11013) Fix log file path on Windows (JabRef#11028) Change to rolling logs (JabRef#11023) chore: remove repetitive words (JabRef#11015) Fix test names (JabRef#11014) ...
Anirudhxx · Mar 18, 2024 · 660b6d2 · 660b6d2
2 parents 2f88cc9 + 2ac5335
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diff --git a/.gitattributes b/.gitattributes
@@ -11,5 +11,4 @@ gradlew text eol=lf
 *.java text eol=lf
 *.properties text eol=lf
 
-# disable after a release (otherwise, duplicate CHANGELOG.md entries will be generated)
-# CHANGELOG.md merge=union
+CHANGELOG.md merge=union
diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -66,12 +66,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.13.2
+        uses: gittools/actions/gitversion/setup@v1.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.13.2
+        uses: gittools/actions/gitversion/execute@v1.1.1
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.github/workflows/deployment-jdk-ea.yml b/.github/workflows/deployment-jdk-ea.yml
@@ -87,12 +87,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.13.2
+        uses: gittools/actions/gitversion/setup@v1.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.13.2
+        uses: gittools/actions/gitversion/execute@v1.1.1
       - name: 'Set up JDK ${{ matrix.jdk }}'
         uses: oracle-actions/setup-java@v1
         with:

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -79,12 +79,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.13.2
+        uses: gittools/actions/gitversion/setup@v1.1.1
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.13.2
+        uses: gittools/actions/gitversion/execute@v1.1.1
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -171,11 +171,15 @@ jobs:
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest -x modernizer
         env:
           CI: "true"
+      - name: Prepare format failed test results
+        if: failure()
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: xml-twig-tools xsltproc
+          version: 1.0
       - name: Format failed test results
         if: failure()
-        run: |
-          sudo apt-get install -qq -y xml-twig-tools xsltproc
-          scripts/after-failure.sh
+        run: scripts/after-failure.sh
   databasetests:
     name: Database tests
     runs-on: ubuntu-latest

diff --git a/.github/workflows/upload-release.yml b/.github/workflows/upload-release.yml
@@ -18,7 +18,7 @@ jobs:
           cd build
           wget -q -m -r -nH --cut-dirs 2 --no-parent --accept=tar.gz,dmg,pkg,deb,rpm,zip,msi https://builds.jabref.org/tags/
       - name: Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         with:
           draft: true
           files: build/**
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,9 +24,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
 - We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
+- We added importing of static groups and linked files from BibDesk .bib files. [#10381](https://github.com/JabRef/jabref/issues/10381)
 - We added ability to export in CFF (Citation File Format) [#10661](https://github.com/JabRef/jabref/issues/10661).
 - We added ability to push entries to TeXworks. [#3197](https://github.com/JabRef/jabref/issues/3197)
 - We added the ability to zoom in and out in the document viewer using <kbd>Ctrl</kbd> + <kbd>Scroll</kbd>. [#10964](https://github.com/JabRef/jabref/pull/10964)
+- We added a Cleanup for removing non-existent files and grouped the related options [#10929](https://github.com/JabRef/jabref/issues/10929)
+- We added the functionality to parse the bibliography of PDFs using the GROBID online service. [#10200](https://github.com/JabRef/jabref/issues/10200)
+- We added support for BibTeX String constants during copy & paste between libraries [#10872](https://github.com/JabRef/jabref/issues/10872)
 
 ### Changed
 
@@ -40,8 +44,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed the duplicate handling in the Import entries dialog. Potential duplicate entries are marked with an icon and importing will now trigger the merge dialog [#10914](https://github.com/JabRef/jabref/pull/10914)
 - We made the command "Push to TexShop" more robust to allow cite commands with a character before the first slash. [forum#2699](https://discourse.jabref.org/t/push-to-texshop-mac/2699/17?u=siedlerchr)
 - We only show the notification "Saving library..." if the library contains more than 2000 entries. [#9803](https://github.com/JabRef/jabref/issues/9803)
+- JabRef now keeps previous log files upon start. [#11023](https://github.com/JabRef/jabref/pull/11023)
+- When normalizing author names, complete enclosing braces are kept. [#10031](https://github.com/JabRef/jabref/issues/10031)
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
+- We store the citation relations in an LRU cache to avoid bloating the memory and out-of-memory exceptions. [#10958](https://github.com/JabRef/jabref/issues/10958)
 - Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
+- Citation relations now get more information, and have quick access to view the articles in a browser without adding them to the library [#10869](https://github.com/JabRef/jabref/issues/10869)
 
 ### Fixed
 
@@ -50,6 +58,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the preview panel showing the wrong entry (an entry that is not selected in the entry table). [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where HTML-reserved characters like '&' and '<', in addition to HTML entities like '&amp;' were not rendered correctly in entry preview. [#10677](https://github.com/JabRef/jabref/issues/10677)
 - The last page of a PDF is now indexed by the full text search. [#10193](https://github.com/JabRef/jabref/issues/10193)
+- The entry editor respects the configured custom tabs when showing "Other fields". [#11012](https://github.com/JabRef/jabref/pull/11012)
 - The default owner of an entry can be changed again. [#10924](https://github.com/JabRef/jabref/issues/10924)
 - We fixed an issue where the duplicate check did not take umlauts or other LaTeX-encoded characters into account. [#10744](https://github.com/JabRef/jabref/pull/10744)
 - We fixed the colors of the icon on hover for unset special fields. [#10431](https://github.com/JabRef/jabref/issues/10431)
@@ -58,6 +67,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the `CommentsTab` was not properly formatted when the `defaultOwner` contained capital or special letters. [#10870](https://github.com/JabRef/jabref/issues/10870)
 - We fixed an issue where the `File -> Close library` menu item was not disabled when no library was open. [#10948](https://github.com/JabRef/jabref/issues/10948)
 - We fixed an issue where the Document Viewer would show the PDF in only half the window when maximized. [#10934](https://github.com/JabRef/jabref/issues/10934)
+- Clicking on the crossref and related tags in the entry editor jumps to the linked entry. [#5484](https://github.com/JabRef/jabref/issues/5484) [#9369](https://github.com/JabRef/jabref/issues/9369)
+- We fixed an issue where JabRef could not parse absolute file paths from Zotero exports [#10959](https://github.com/JabRef/jabref/issues/10959)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -9,7 +9,7 @@ plugins {
 
     id 'me.champeau.jmh' version '0.7.2'
 
-    id 'org.javamodularity.moduleplugin' version '1.8.14'
+    id 'org.javamodularity.moduleplugin' version '1.8.15'
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
@@ -114,8 +114,8 @@ dependencies {
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
     implementation 'org.apache.pdfbox:pdfbox:3.0.1'
-    implementation 'org.apache.pdfbox:fontbox:3.0.1'
-    implementation ('org.apache.pdfbox:xmpbox:3.0.1') {
+    implementation 'org.apache.pdfbox:fontbox:3.0.2'
+    implementation ('org.apache.pdfbox:xmpbox:3.0.2') {
         exclude group: 'org.junit.jupiter'
     }
 
@@ -177,7 +177,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.2'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.2.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.4.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -196,14 +196,14 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.9'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.0'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.1'
 
     implementation('de.undercouch:citeproc-java:3.0.0-beta.2') {
         exclude group: 'org.antlr'
     }
 
     // jakarta.activation is already dependency of glassfish
-    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.1'
+    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.2'
     implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '4.0.3'
 
     implementation ('com.github.tomtung:latex2unicode_2.13:0.3.2') {
@@ -228,7 +228,7 @@ dependencies {
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.5'
     // injection framework
     implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.5'
-    implementation 'org.glassfish.hk2:hk2-api:3.0.6'
+    implementation 'org.glassfish.hk2:hk2-api:3.1.0'
     // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
     // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
     // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
@@ -242,7 +242,10 @@ dependencies {
     // Because of GraalVM quirks, we need to ship that. See https://github.com/jspecify/jspecify/issues/389#issuecomment-1661130973 for details
     implementation 'org.jspecify:jspecify:0.3.0'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.165'
+    // parse plist files
+    implementation 'com.googlecode.plist:dd-plist:1.28'
+
+    testImplementation 'io.github.classgraph:classgraph:4.8.168'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'
 

diff --git a/config/README.md b/config/README.md
@@ -20,7 +20,7 @@ Style-checks are done for each pull request and installing this code style confi
 # Eclipse:
 
 The Eclipse code formatter style is stored in the `eclipse.gradle` file and gets imported automatically.
-In case the formatter style needs to be adapted, configure it and export in in eclipse.
+In case the formatter style needs to be adapted, configure it and export in eclipse.
 
 1. Right click on the eclipse project "JabRef"
 2. Select "Export > General > Preferences"

diff --git a/docs/code-howtos/custom-svg-icons.md b/docs/code-howtos/custom-svg-icons.md
@@ -23,7 +23,14 @@ Good icon design requires years of experience and cannot be covered here. Adapti
 
 ## Step 2. Packing the icons into a font
 
-Use the [IcoMoon](https://icomoon.io) tool for packing the icons. Create a new set and import _all_ icons. Rearrange them so that they have the same order as in `org.jabref.gui.JabRefMaterialDesignIcon`. This will avoid that you have to change the code points for the existing glyphs. In the settings for your icon set, set the _Grid_ to 24. This is important to get the correct spacing. The name of the font is `JabRefMaterialDesign`. When your icon-set is ready, select all of them and download the font-package.
+Use the [IcoMoon](https://icomoon.io) tool for packing the icons.
+
+1. Create a new set by importing the json file
+2. Next to the icons, click on the hamburger menu, chose "Import to Set" to add a new icon (it will be added to the front)
+Rearrange them so that they have the same order as in `org.jabref.gui.JabRefMaterialDesignIcon`. This will avoid that you have to change the code points for the existing glyphs. In the settings for your icon set, set the _Grid_ to 24. This is important to get the correct spacing. The name of the font is `JabRefMaterialDesign`.
+3. Next to the icons, click on the hamburger menu and click "Select all".
+4. Proceed with the font creating, set the font property name to `JabRefMaterialDesign`
+When your icon-set is ready, select all of them and download the font-package.
 
 ## Step 3. Replace the existing `JabRefMaterialDesign.ttf`
 

diff --git a/docs/teaching.md b/docs/teaching.md
@@ -83,8 +83,6 @@ Course: BSc Computer Science Individual Project
 * Summary: Students experience the procedure of finding and fixing small and medium issues in an open source project.
 * Successfully run in 2022/2023
 
-Do you have additions/suggestions for improvement?
-
 #### Northern Arizona University (NAU), USA
 
 Course [CS499 - Open Source Software Development](https://github.com/igorsteinmacher/CS499-OSS)
@@ -129,7 +127,7 @@ Course "Programming and Software Development" as part of the [BSc Software Engin
 Course [DD2480 Software Engineering Fundamentals](https://www.kth.se/student/kurser/kurs/DD2480?l=en)
 
 * Summary: Groups of students from three to five persons experienced the whole software engineering process within a week: From the requirements' specification to the final pull request.
-* Successfully run in 2020
+* Successfully run in 2020, 2024, and other years.
 
 ### Portuguese
 

diff --git a/licenses/com.googlecode.plist_ddplist.txt b/licenses/com.googlecode.plist_ddplist.txt
@@ -0,0 +1,20 @@
+dd-plist - An open source library to parse and generate property lists
+Copyright (C) 2016 Daniel Dreibrodt
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/rewrite.yml b/rewrite.yml
@@ -103,8 +103,6 @@ recipeList:
   - org.openrewrite.java.migrate.lang.StringFormatted
   - org.openrewrite.java.migrate.util.SequencedCollection
 
-  - org.openrewrite.java.recipes.UseJavaParserBuilderInJavaTemplate
-
   - org.openrewrite.java.RemoveObjectsIsNull
   - org.openrewrite.java.ShortenFullyQualifiedTypeReferences
 

diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -144,4 +144,5 @@
     requires org.libreoffice.uno;
     requires de.saxsys.mvvmfx.validation;
     requires com.jthemedetector;
+    requires dd.plist;
 }
diff --git a/src/main/java/org/jabref/Launcher.java b/src/main/java/org/jabref/Launcher.java
@@ -11,15 +11,13 @@
 import java.util.List;
 import java.util.Map;
 
-import org.jabref.architecture.AllowedToUseStandardStreams;
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefGUI;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ProxyAuthenticator;
 import org.jabref.logic.net.ProxyPreferences;
 import org.jabref.logic.net.ProxyRegisterer;
@@ -48,7 +46,6 @@
  * - Handle the command line arguments
  * - Start the JavaFX application (if not in cli mode)
  */
-@AllowedToUseStandardStreams("Direct output to the user")
 public class Launcher {
     private static Logger LOGGER;
     private static boolean isDebugEnabled;
@@ -140,11 +137,14 @@ private static void addLogToDisk() {
         // The "Shared File Writer" is explained at
         // https://tinylog.org/v2/configuration/#shared-file-writer
         Map<String, String> configuration = Map.of(
-                "writerFile", "shared file",
-                "writerFile.level", isDebugEnabled ? "debug" : "info",
                 "level", isDebugEnabled ? "debug" : "info",
-                "writerFile.file", directory.resolve("log.txt").toString(),
-                "writerFile.charset", "UTF-8");
+                "writerFile", "rolling file",
+                "writerFile.level", isDebugEnabled ? "debug" : "info",
+                // We need to manually join the path, because ".resolve" does not work on Windows, because ":" is not allowed in file names on Windows
+                "writerFile.file", directory + File.separator + "log_{date:yyyy-MM-dd_HH-mm-ss}.txt",
+                "writerFile.charset", "UTF-8",
+                "writerFile.policies", "startup",
+                "writerFile.backups", "30");
 
         configuration.forEach(Configuration::set);
         initializeLogger();
@@ -169,9 +169,8 @@ private static boolean handleMultipleAppInstances(String[] args, RemotePreferenc
                 LOGGER.debug("Passing arguments passed on to running JabRef...");
                 if (remoteClient.sendCommandLineArguments(args)) {
                     // So we assume it's all taken care of, and quit.
-                    LOGGER.debug("Arguments passed on to running JabRef instance.");
-                    // Used for script-use output etc. to the user
-                    System.out.println(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
+                    // Output to both to the log and the screen. Therefore, we do not have an additional System.out.println.
+                    LOGGER.info("Arguments passed on to running JabRef instance. Shutting down.");
                     return false;
                 } else {
                     LOGGER.warn("Could not communicate with other running JabRef instance.");