Merge remote-tracking branch 'origin/fix-for-issue-13241' into fix-for-issue-13241

Author: ZodGaz

.github/workflows/binaries-ea.yml

@@ -224,10 +224,17 @@ jobs:
         shell: bash
         run: mv ~/AppData/Local/mise ~/.asdf
       - name: Setup JDK for gradle itself
+        if: false
         uses: actions/setup-java@v4
         with:
           java-version: '21'
           distribution: 'temurin'
+      - name: Setup JDK ${{ env.jdk_version }}
+        uses: actions/setup-java@v4
+        with:
+          java-version: '${{ env.jdk_version }}'
+          distribution: 'corretto'
+          java-package: 'jdk'
       # endregion
 
       # region JavaFX
@@ -283,9 +290,9 @@ jobs:
           cd jabgui
 
           # see https://github.com/jdx/mise/discussions/4973
-          eval $(mise hook-env -f | grep 'export JAVA_HOME')
-          eval $(mise hook-env -f | grep 'export PATH')
-          echo $JAVA_HOME
+          # eval $(mise hook-env -f | grep 'export JAVA_HOME')
+          # eval $(mise hook-env -f | grep 'export PATH')
+          # echo $JAVA_HOME
 
           jpackage \
           --module org.jabref/org.jabref.Launcher \
@@ -335,9 +342,9 @@ jobs:
           cd jabgui
 
           # see https://github.com/jdx/mise/discussions/4973
-          eval $(mise hook-env -f | grep 'export JAVA_HOME')
-          eval $(mise hook-env -f | grep 'export PATH')
-          echo $JAVA_HOME
+          # eval $(mise hook-env -f | grep 'export JAVA_HOME')
+          # eval $(mise hook-env -f | grep 'export PATH')
+          # echo $JAVA_HOME
 
           jpackage \
           --module org.jabref/org.jabref.Launcher \

.github/workflows/binaries.yml

@@ -10,7 +10,7 @@ on:
       - 'src/test/**'
       - 'README.md'
     tags:
-       - '*'
+      - '*'
   pull_request:
     types:
       - opened
@@ -212,32 +212,6 @@ jobs:
       - name: Setup JBang
         uses: jbangdev/setup-jbang@main
 
-      # region Publish JabLib on Maven Central
-      - name: Decode secretKeyRingFile
-        if: (needs.conditions.outputs.upload-to-builds-jabref-org == 'true') && (startsWith(matrix.os, 'ubuntu'))
-        id: secring
-        uses: timheuer/base64-to-file@v1
-        with:
-          fileName: 'secring.gpg'
-          encodedString: ${{ secrets.KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64 }}
-      - name: store secrets
-        if: (needs.conditions.outputs.upload-to-builds-jabref-org == 'true') && (startsWith(matrix.os, 'ubuntu'))
-        run: |
-          cat >> gradle.properties <<EOF
-          signing.keyId=${{ secrets.KOPPOR_SIGNING_KEYID }}
-          signing.password=${{ secrets.KOPPOR_SIGNING_PASSWORD }}
-          signing.secretKeyRingFile=${{ steps.secring.outputs.filePath }}
-          mavenCentralUsername=${{ secrets.KOPPOR_MAVENCENTRALUSERNAME }}
-          mavenCentralPassword=${{ secrets.KOPPOR_MAVENCENTRALPASSWORD }}
-          EOF
-          grep secretKeyRingFile gradle.properties
-          file ${{ steps.secring.outputs.filePath }}
-          md5sum ${{ steps.secring.outputs.filePath }}
-      - name: publishAllPublicationsToMavenCentralRepository
-        if: (needs.conditions.outputs.upload-to-builds-jabref-org == 'true') && (matrix.os == 'ubuntu-22.04')
-        run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" -Ptagbuild="${{ needs.conditions.outputs.tagbuild }}" :jablib:publishAllPublicationsToMavenCentralRepository
-      # endregion
-
       - name: Basic build (assemble)
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" assemble
 

.github/workflows/on-pr-closed.yml

@@ -40,8 +40,8 @@ jobs:
           ticketPrefix: '#'
           titleRegex: '^#(?<ticketNumber>\d+)'
           branchRegex: '^(?<ticketNumber>\d+)'
-          # Matches GitHub's closes/fixes/resolves #{number}, but does not match our example `Closes #12345` in PULL_REQUEST_TEMPLATE
-          bodyRegex: '(?<action>fixes|closes|resolves)\s+(?:https?:\/\/github\.com\/JabRef\/jabref\/issues\/)?#?(?<ticketNumber>(?!12345\b)\d+)'
+          # Matches GitHub's closes/fixes/resolves #{number}, but does not match our example `Closes #13109` in PULL_REQUEST_TEMPLATE
+          bodyRegex: '(?<action>fixes|closes|resolves)\s+(?:https?:\/\/github\.com\/JabRef\/jabref\/issues\/)?#?(?<ticketNumber>(?!13109\b)\d+)'
           bodyRegexFlags: 'i'
           outputOnly: true
       - run: echo "${{ steps.get_issue_number.outputs.ticketNumber }}"

.github/workflows/on-pr-opened-updated.yml

@@ -10,6 +10,7 @@ jobs:
     name: Determine issue number
     runs-on: ubuntu-latest
     if: >
+      (github.repository == 'JabRef/jabref') &&
       !(
         (github.actor == 'dependabot[bot]') ||
         (
@@ -53,7 +54,6 @@ jobs:
           echo "No valid ticket number found!"
           exit 1
   move_issue:
-    if: github.repository_owner == 'JabRef'
     name: Mark issue as in progress
     # after determine_issue_number to ensure that there is only one failure because of no ticket number
     needs: determine_issue_number
@@ -84,7 +84,6 @@ jobs:
           issue-number: ${{ needs.determine_issue_number.outputs.issue_number }}
           skip-if-not-in-project: true
   ensure_assignment:
-    if: github.repository_owner == 'JabRef'
     name: Ensure that contributor is assigned (fails if not commented on issue)
     # after determine_issue_number to ensure that there is only one failure because of no ticket number
     needs: determine_issue_number
@@ -126,6 +125,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   conflicts_with_target:
+    if: github.repository == 'JabRef/jabref'
     name: Conflicts with target branch
     runs-on: ubuntu-latest
     steps:
@@ -144,7 +144,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   upload-pr-number:
-    if: ${{ github.repository == 'JabRef/jabref' }}
+    if: github.repository == 'JabRef/jabref'
     runs-on: ubuntu-latest
     steps:
       - name: Create pr_number.txt

.github/workflows/on-pr-opened.yml

@@ -6,6 +6,7 @@ on:
 
 jobs:
   welcome-first-time-contributor:
+    if: github.repository == 'JabRef/jabref'
     runs-on: ubuntu-latest
     permissions:
       issues: write

.github/workflows/publish.yml

@@ -0,0 +1,100 @@
+name: Publish to maven central
+
+on:
+  pull_request:
+    paths:
+     - .github\workflows\publish.yml
+  push:
+    paths:
+     - .github\workflows\publish.yml
+    tags:
+      - '*'
+  schedule:
+    # run on each Monday
+    - cron: '2 3 * * 1'
+  workflow_dispatch:
+
+permissions:
+  actions: write
+  contents: read
+  pull-requests: write
+
+env:
+  GRADLE_OPTS: -Xmx4g -Dorg.gradle.vfs.watch=false
+  JAVA_OPTS: -Xmx4g
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}-${{ github.event_name }}"
+  cancel-in-progress: true
+
+jobs:
+  publish:
+    name: jablib
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Fetch all history for all tags and branches
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: 'true'
+          show-progress: 'false'
+      - name: Install GitVersion
+        uses: gittools/actions/gitversion/setup@v3.2.1
+        with:
+          versionSpec: "5.x"
+      - name: Run GitVersion
+        id: gitversion
+        uses: gittools/actions/gitversion/execute@v3.2.1
+      - name: Setup JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: '24'
+          distribution: 'corretto'
+          java-package: 'jdk'
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v4
+      - name: Generate JBang cache key
+        id: cache-key
+        shell: bash
+        run: |
+          echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
+      - name: Use cache
+        uses: actions/cache@v4
+        with:
+          lookup-only: true
+          path: ~/.jbang
+          key: ${{ steps.cache-key.outputs.cache_key }}
+          restore-keys:
+            jbang-
+      - name: Setup JBang
+        uses: jbangdev/setup-jbang@main
+
+      # region Publish JabLib on Maven Central
+      - id: istagbuild
+        run: |
+          if [[ "${GITHUB_REF}" == refs/tags/* ]]; then
+            echo "tagbuild=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "tagbuild=false" >> "$GITHUB_OUTPUT"
+          fi
+      - name: Decode secretKeyRingFile
+        id: secring
+        uses: timheuer/base64-to-file@v1
+        with:
+          fileName: 'secring.gpg'
+          encodedString: ${{ secrets.KOPPOR_SIGNING_SECRETKEYRINGFILE_BASE64 }}
+      - name: store secrets
+        run: |
+          cat >> gradle.properties <<EOF
+          signing.keyId=${{ secrets.KOPPOR_SIGNING_KEYID }}
+          signing.password=${{ secrets.KOPPOR_SIGNING_PASSWORD }}
+          signing.secretKeyRingFile=${{ steps.secring.outputs.filePath }}
+          mavenCentralUsername=${{ secrets.KOPPOR_MAVENCENTRALUSERNAME }}
+          mavenCentralPassword=${{ secrets.KOPPOR_MAVENCENTRALPASSWORD }}
+          EOF
+          grep secretKeyRingFile gradle.properties
+          file ${{ steps.secring.outputs.filePath }}
+          md5sum ${{ steps.secring.outputs.filePath }}
+      - name: publishAllPublicationsToMavenCentralRepository
+        run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" -Ptagbuild="${{ steps.istagbuild.outputs.tagbuild }}" :jablib:publishAllPublicationsToMavenCentralRepository
+      # endregion

.github/workflows/tests-fetchers.yml

@@ -24,8 +24,8 @@ on:
       - '.github/workflows/tests-fetchers.yml'
       - 'build.gradle'
   schedule:
-    # run on each Wednesday
-    - cron: '2 3 * * 3'
+    # run on each Monday
+    - cron: '2 3 * * 1'
   workflow_dispatch:
 
 env:

.jbang/JabSrvLauncher.java

@@ -25,6 +25,7 @@
 
 //DEPS org.jabref:jablib:6.+
 //DEPS info.picocli:picocli:4.7.7
+//DEPS org.jspecify:jspecify:1.0.0
 
 // from jabsrv
 //DEPS org.slf4j:slf4j-api:2.0.17

CHANGELOG.md

@@ -11,8 +11,9 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Added
 
-- We introduced a settings parameters to manage citations' relations local storage time-to-live with a default value set to 30 days. [#11189](https://github.com/JabRef/jabref/issues/11189)
+- We introduced a settings parameter to manage citations' relations local storage time-to-live with a default value set to 30 days. [#11189](https://github.com/JabRef/jabref/issues/11189)
 - We distribute arm64 images for Linux. [#10842](https://github.com/JabRef/jabref/issues/10842)
+- We added the field `monthfiled` to the default list of fields to resolve BibTeX-Strings for [#13375](https://github.com/JabRef/jabref/issues/13375)
 
 ### Changed
 
@@ -36,6 +37,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new `jabkit` command `pseudonymize` to pseudonymize the library. [#13109](https://github.com/JabRef/jabref/issues/13109)
 - We added functionality to focus running instance when trying to start a second instance. [#13129](https://github.com/JabRef/jabref/issues/13129)
 - We added a new setting in the 'Entry Editor' preferences to hide the 'File Annotations' tab when no annotations are available. [#13143](https://github.com/JabRef/jabref/issues/13143)
+- We added support for multi-file import across different formats. [#13269](https://github.com/JabRef/jabref/issues/13269)
 
 ### Changed
 
@@ -65,6 +67,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the tab showing the fulltext search results was not displayed. [#12865](https://github.com/JabRef/jabref/issues/12865)
 - We fixed an issue showing an empty tooltip in maintable. [#11681](https://github.com/JabRef/jabref/issues/11681)
 - We fixed an issue where Document Viewer showed technical exceptions when opening entries with non-PDF files. [#13198](https://github.com/JabRef/jabref/issues/13198)
+- When creating a library, if you drag a PDF file containing only a single column, the dialog will now automatically close. [#13262](https://github.com/JabRef/jabref/issues/13262)
 - We fixed an issue where the tab showing the fulltext search results would appear blank after switching library. [#13241](https://github.com/JabRef/jabref/issues/13241)
 
 ### Removed

build-logic/src/main/kotlin/org.jabref.gradle.base.repositories.gradle.kts

@@ -8,5 +8,5 @@ repositories {
     // Required for one.jpro.jproutils:tree-showing
     maven { url = uri("https://sandec.jfrog.io/artifactory/repo") }
 
-    maven { url = uri("file:${rootDir.absolutePath}/jablib/lib")}
+    maven { url = rootDir.resolve("jablib/lib").toURI() }
 }

build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts

@@ -9,6 +9,7 @@ java {
         // - .devcontainer/devcontainer.json#L34 and
         // - .moderne/moderne.yml
         // - .github/workflows/binaries*.yml
+        // - .github/workflows/publish.yml
         // - .github/workflows/tests*.yml
         // - .github/workflows/update-gradle-wrapper.yml
         // - docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md

docs/requirements/ux.md

@@ -0,0 +1,18 @@
+---
+parent: Requirements
+---
+# UX
+
+This page collects general UX requirements
+
+## Auto close of merge entries dialog
+`req~ux.auto-close.merge-entries~1`
+
+The merge entries dialog collects and merges data from multiple sources.
+In case there is only one source, it should not be shown.
+Since some data fetchers take time, we need to open the dialog and wait until all sources are available.
+[As soon as only one source is available, the dialog should be closed to speed up the user's workflow](https://github.com/JabRef/jabref/issues/13262).
+
+Needs: impl
+
+<!-- markdownlint-disable-file MD022 -->

jabgui/build.gradle.kts

@@ -213,8 +213,6 @@ jlink {
     forceMerge(
         "controlsfx",
         "bcprov",
-        "jaxb",
-        "istack",
         "stax"
     )
 
@@ -224,7 +222,6 @@ jlink {
         requires("com.fasterxml.jackson.databind")
         requires("com.fasterxml.jackson.core")
         requires("com.fasterxml.jackson.datatype.jdk8")
-        requires("jakarta.xml.bind")
         requires("java.compiler")
         requires("java.datatransfer")
         requires("java.desktop")

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

@@ -76,14 +76,11 @@
     // endregion
 
     // region: data mapping
-    // requires jakarta.xml.bind;
     requires jdk.xml.dom;
     // requires com.google.gson;
     // requires com.fasterxml.jackson.databind;
     // requires com.fasterxml.jackson.dataformat.yaml;
     // requires com.fasterxml.jackson.datatype.jsr310;
-    // needs to be loaded here as it's otherwise not found at runtime
-    // requires org.glassfish.jaxb.runtime;
     // endregion
 
     // dependency injection using HK2

jabgui/src/main/java/org/jabref/gui/JabRefDialogService.java

@@ -462,6 +462,7 @@ public Optional<Path> showDirectorySelectionDialog(DirectoryDialogConfiguration
     public List<Path> showFileOpenDialogAndGetMultipleFiles(FileDialogConfiguration fileDialogConfiguration) {
         FileChooser chooser = getConfiguredFileChooser(fileDialogConfiguration);
         List<File> files = chooser.showOpenMultipleDialog(mainWindow);
+        Optional.ofNullable(chooser.getSelectedExtensionFilter()).ifPresent(fileDialogConfiguration::setSelectedExtensionFilter);
         return files != null ? files.stream().map(File::toPath).toList() : List.of();
     }