Merge branch 'main' into jackson3

* main:
  Fix calling JBang command (#14282)
  .jbang scripts should not be included inside themselves (#14278)
  Fix typos (#14277)
  Refactor importDatabase for better readability (#14274)
  fix jbang (#14276)
  Feat: Add definition links for TeX Files (#14260)
  Update preventing module commits (#14273)
  Fix JabKitLuancher
  Rename packages in jabkit to start with org.jabref.toolkit to avoid split packages between jabkit and jabgui (#14052). (#14271)
  Add doi-to-bibtex to examples and JabKit (#14244)

Author: Siedlerchr

.github/workflows/tests-code.yml

@@ -469,6 +469,7 @@ jobs:
         run: |
           echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
       - name: Use cache
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
         uses: actions/cache@v4
         with:
           path: ~/.jbang
@@ -480,17 +481,17 @@ jobs:
         uses: jbangdev/setup-jbang@main
 
       # Build all JBang scripts
-      - run: jbang build .jbang/CheckoutPR.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build .jbang/CloneJabRef.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh .jbang/JabKitLauncher.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh .jbang/JabLsLauncher.java
-        if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh .jbang/JabSrvLauncher.java
+      - run: |
+          for f in .jbang/*.java; do
+            echo "Building $f..."
+            jbang build --fresh "$f"
+          done
         if: steps.changed-jablib-files.outputs.any_changed != 'true'
-      - run: jbang build --fresh jablib-examples/*.java
+      - run: |
+          for f in jablib-examples/*.java; do
+            echo "Building $f..."
+            jbang build --fresh "$f"
+          done
         if: steps.changed-jablib-files.outputs.any_changed != 'true'
 
       # *Launcher.java should support "--help"
@@ -522,6 +523,7 @@ jobs:
         with:
           files: |
             .jbang/*.java
+            jabkit/src/main/java/**/*.java
             jablib/src/main/java/**/*.java
             jablib-examples/**/*.java
           files_ignore: |
@@ -553,7 +555,20 @@ jobs:
           # We modify the JBang scripts directly to avoid issues with relative paths
           for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
             case "$f" in
-              jablib-examples/*) continue ;; # skip scripts
+              .jbang/*)
+                # skip scripts
+                continue
+                ;;
+              jablib-examples/*)
+                # skip scripts
+                continue
+                ;;
+              jabkit/*)
+                # only JabKit needs its modified sources if jabkit was modified
+                if [ "${{ matrix.script }}" != ".jbang/JabKitLauncher.java" ]; then
+                  continue
+                fi
+                ;;
             esac
             echo "//SOURCES ../$f" >> "${{ matrix.script }}"
           done

.gitignore

@@ -16,7 +16,7 @@ jablib/src/main/resources/csl-locales
 
 javafx/
 
-# genreated by gg.cmd
+# generated by gg.cmd
 m2
 gg.cmd
 

.jbang/JabKitLauncher.java

@@ -5,20 +5,21 @@
 //JAVA 24
 //RUNTIME_OPTIONS --enable-native-access=ALL-UNNAMED
 
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/converter/CygWinPathConverter.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/CheckConsistency.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/CheckIntegrity.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Convert.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Fetch.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/GenerateBibFromAux.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/GenerateCitationKeys.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Pdf.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/PdfUpdate.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Preferences.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Pseudonymize.java
-//SOURCES ../jabkit/src/main/java/org/jabref/cli/Search.java
-//SOURCES ../jabkit/src/main/java/org/jabref/JabKit.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/converter/CygWinPathConverter.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/ArgumentProcessor.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/CheckConsistency.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/CheckIntegrity.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Convert.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/DoiToBibtex.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Fetch.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/GenerateBibFromAux.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/GenerateCitationKeys.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Pdf.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/PdfUpdate.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Preferences.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Pseudonymize.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/cli/Search.java
+//SOURCES ../jabkit/src/main/java/org/jabref/toolkit/JabKit.java
 //FILES tinylog.properties=../jabkit/src/main/resources/tinylog.properties
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/
@@ -38,11 +39,9 @@
 //DEPS info.picocli:picocli:4.7.7
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
 
-import org.jabref.JabKit;
-
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabKitLauncher {
     public static void main(String[] args) {
-        org.jabref.JabKit.main(args);
+        org.jabref.toolkit.JabKit.main(args);
     }
 }

.jbang/JabLsLauncher.java

@@ -23,6 +23,7 @@
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/LspRangeUtil.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/DefinitionProviderFactory.java
+//SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/LatexDefinitionProvider.java
 //SOURCES ../jabls/src/main/java/org/jabref/languageserver/util/definition/MarkdownDefinitionProvider.java
 
 // REPOS mavencentral,snapshots=https://central.sonatype.com/repository/maven-snapshots/

CHANGELOG.md

@@ -13,9 +13,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
 - We added automatic date-based groups that create year/month/day subgroups from an entry’s date fields. [#10822](https://github.com/JabRef/jabref/issues/10822)
+- We added `doi-to-bibtex` to `JabKit`. [#14244](https://github.com/JabRef/jabref/pull/14244)
 
 ### Changed
 
+- `JabKit`: `--porcelain` does not output any logs to the console anymore. [#14244](https://github.com/JabRef/jabref/pull/14244)
 - <kbd>Ctrl</kbd> + <kbd>Shift</kbd> + <kbd>L</kbd> now opens the terminal in the active library directory. [#14130](https://github.com/JabRef/jabref/issues/14130)
 
 ### Fixed

docs/code-howtos/faq.md

@@ -163,7 +163,13 @@ git push
 
 ### Prevention
 
-To avoid this, avoid staging using `git add .` from CLI. Preferably use a GUI-based git manager, such as the one built in IntelliJ or open git gui from the command line. Even if you accidentally stage them, don't commit all files, selectively commit the files you touched using the GUI based tool, and push.
+To avoid this, avoid staging using any of these commands:
+
+* `git add .`
+* `git add jablib/src/main` (or any path prefix)
+* `git commit -a`
+
+Preferably use a GUI-based git manager, such as the one built in IntelliJ or open git gui from the command line. Even if you accidentally stage them, don't commit all files, selectively commit the files you touched using the GUI based tool, and push.
 
 ## Q: I get `java: package org.jabref.logic.journals does not exist`
 

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

@@ -59,7 +59,7 @@ Allow also access for both cases and click "Allow access".
 
 ## Wait for IntelliJ IDEA to import the gradle project
 
-IntelliJ shows "Importing 'jabref' Gradle Project" at the lower right corner.
+IntelliJ shows "Importing 'jabref' Gradle Project" in the lower right corner.
 This will take several minutes.
 Wait until this disappears.
 

jabkit/build.gradle.kts

@@ -63,11 +63,14 @@ javaModuleTesting.whitebox(testing.suites["test"]) {
 }
 
 application {
-    mainClass.set("org.jabref.JabKit")
+    mainClass.set("org.jabref.toolkit.JabKit")
     mainModule.set("org.jabref.jabkit")
 
     // Also passed to launcher by java-module-packaging plugin
     applicationDefaultJvmArgs = listOf(
+        // JEP 158: Disable all java util logging
+        "-Xlog:disable",
+
         // Enable JEP 450: Compact Object Headers
         "-XX:+UnlockExperimentalVMOptions", "-XX:+UseCompactObjectHeaders",
 

jabkit/src/main/java/module-info.java

@@ -2,8 +2,8 @@
     requires org.jabref.jablib;
 
     requires info.picocli;
-    opens org.jabref.cli;
-    opens org.jabref.cli.converter;
+    opens org.jabref.toolkit.cli;
+    opens org.jabref.toolkit.cli.converter;
 
     requires transitive org.jspecify;
     requires java.prefs;

jabkit/src/main/java/org/jabref/JabKit.java renamed to jabkit/src/main/java/org/jabref/toolkit/JabKit.java

@@ -1,4 +1,4 @@
-package org.jabref;
+package org.jabref.toolkit;
 
 import java.io.File;
 import java.io.IOException;
@@ -7,13 +7,11 @@
 import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
 import javafx.util.Pair;
 
-import org.jabref.cli.ArgumentProcessor;
 import org.jabref.logic.importer.SearchBasedFetcher;
 import org.jabref.logic.importer.WebFetcher;
 import org.jabref.logic.importer.WebFetchers;
@@ -34,6 +32,7 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.toolkit.cli.ArgumentProcessor;
 
 import com.airhacks.afterburner.injection.Injector;
 import org.slf4j.Logger;
@@ -58,6 +57,8 @@ public class JabKit {
 
     private static final String JABKIT_BRAND = "JabKit - command line toolkit for JabRef";
 
+    /// Note: To test with gradle, use jabkit -> Tasks -> application -> run
+    ///       Use `--args="..."` as parameters to "Run"
     public static void main(String[] args) {
         initLogging(args);
 
@@ -143,11 +144,10 @@ public static void initLogging(String[] args) {
 
         // We must configure logging as soon as possible, which is why we cannot wait for the usual
         // argument parsing workflow to parse logging options e.g. --debug or --porcelain
+        boolean isPorcelain = Arrays.stream(args).anyMatch("--porcelain"::equalsIgnoreCase);
         Level logLevel;
         if (Arrays.stream(args).anyMatch("--debug"::equalsIgnoreCase)) {
             logLevel = Level.DEBUG;
-        } else if (Arrays.stream(args).anyMatch("--porcelain"::equalsIgnoreCase)) {
-            logLevel = Level.ERROR;
         } else {
             logLevel = Level.INFO;
         }
@@ -163,18 +163,23 @@ public static void initLogging(String[] args) {
             return;
         }
 
+        String fileWriterName;
+        if (isPorcelain) {
+            fileWriterName = "writer";
+        } else {
+            fileWriterName = "writerFile";
+        }
+
         // The "Shared File Writer" is explained at
         // https://tinylog.org/v2/configuration/#shared-file-writer
-        Map<String, String> configuration = Map.of(
-                "level", logLevel.name().toLowerCase(),
-                "writerFile", "rolling file",
-                "writerFile.logLevel", logLevel == Level.DEBUG ? "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);
+        Configuration.set("level", logLevel.name().toLowerCase());
+        Configuration.set(fileWriterName, "rolling file");
+        Configuration.set("%s.logLevel".formatted(fileWriterName), logLevel == Level.DEBUG ? "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
+        Configuration.set("%s.file".formatted(fileWriterName), directory + File.separator + "log_{date:yyyy-MM-dd_HH-mm-ss}.txt");
+        Configuration.set("%s.charset".formatted(fileWriterName), "UTF-8");
+        Configuration.set("%s.policies".formatted(fileWriterName), "startup");
+        Configuration.set("%s.backups".formatted(fileWriterName), "30");
 
         LOGGER = LoggerFactory.getLogger(JabKit.class);
     }