Merge branch 'main' into fix-lucene-query

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,7 +9,7 @@ Link the issue that will be closed, e.g., "Closes #333". If your PR closes a kop
 -->
 
 - [x] I own the copyright of the code submitted and I licence it under the [MIT license](https://github.com/JabRef/jabref/blob/main/LICENSE)
-- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
+- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if change is visible to the user)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
 - [ ] Screenshots added in PR description (for UI changes)

.github/workflows/assign-issue.yml

@@ -9,6 +9,7 @@ on:
 
 jobs:
   assign:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     permissions:
       issues: write

.github/workflows/check-links.yml

@@ -18,6 +18,7 @@ concurrency:
 
 jobs:
   lychee:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/cleanup-pr.yml

@@ -6,6 +6,7 @@ on:
 
 jobs:
   cleanup:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - name: Cancel deployment run

.github/workflows/deployment-arm64.yml

@@ -34,6 +34,7 @@ concurrency:
 
 jobs:
   build:
+    if: github.repository_owner == 'JabRef'
     strategy:
       fail-fast: false
       matrix:

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

@@ -32,6 +32,7 @@ concurrency:
 
 jobs:
   build:
+    if: github.repository_owner == 'JabRef'
     strategy:
       fail-fast: false
       matrix:

.github/workflows/gource.yml

@@ -15,6 +15,7 @@ concurrency:
 
 jobs:
   action:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'

.github/workflows/on-labeled-issue.yml

@@ -6,8 +6,36 @@ on:
        - labeled
 
 jobs:
+  Assigned:
+    # Triggered when manually assigned the label "📍 Assigned" to trigger the automatic unassignment after 30 days
+    name: "📍 Assigned"
+    if: ${{ github.event.label.name == '📍 Assigned' && github.repository_owner == 'JabRef' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Move Issue to "Free to take" Column in "Candidates for University Projects"
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
+        with:
+          github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/3"
+          target-labels: "📍 Assigned"
+          target-column: "Free to take"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true
+      - name: Move Issue to "Free to take" Column in "Good First Issues"
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
+        with:
+          github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/5"
+          target-labels: "📍 Assigned"
+          target-column: "Free to take"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true
   FirstTimeCodeContribution:
-    if: ${{ github.event.label.name == 'FirstTimeCodeContribution' }}
+    if: ${{ github.event.label.name == 'FirstTimeCodeContribution' && github.repository_owner == 'JabRef' }}
     runs-on: ubuntu-latest
     permissions:
       issues: write
@@ -35,7 +63,7 @@ jobs:
       with:
         github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
         project-url: "https://github.com/orgs/JabRef/projects/3"
-        target-labels: "📍 Assigned"
+        target-labels: "FirstTimeCodeContribution"
         target-column: "Assigned"
         ignored-columns: ""
         default-column: "Free to take"
@@ -45,14 +73,14 @@ jobs:
       with:
         github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
         project-url: "https://github.com/orgs/JabRef/projects/5"
-        target-labels: "📍 Assigned"
+        target-labels: "FirstTimeCodeContribution"
         target-column: "Assigned"
         ignored-columns: ""
         default-column: "Free to take"
         skip-if-not-in-project: true
   good-first-issue:
     name: "good first issue"
-    if: "${{ github.event.label.name == 'good first issue' }}"
+    if: "${{ github.event.label.name == 'good first issue' && github.repository_owner == 'JabRef' }}"
     runs-on: ubuntu-latest
     steps:
       - name: "good first issue"
@@ -62,7 +90,7 @@ jobs:
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
           gh project item-add 5 --owner JabRef --url $ISSUE_URL
   needs-refinement:
-    if: github.event.label.name == 'needs-refinement'
+    if: github.event.label.name == 'needs-refinement' && github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
     steps:
       - name: needs-refinement
@@ -73,7 +101,7 @@ jobs:
           gh project item-add 15 --owner JabRef --url $ISSUE_URL
   status-freeze:
     name: "status: freeze"
-    if: "${{ github.event.label.name == 'status: freeze' }}"
+    if: "${{ github.event.label.name == 'status: freeze' && github.repository_owner == 'JabRef' }}"
     runs-on: ubuntu-latest
     steps:
       - name: "status: freeze"
@@ -83,7 +111,7 @@ jobs:
           ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
           gh project item-add 9 --owner JabRef --url $ISSUE_URL
   ui:
-    if: "${{ github.event.label.name == 'ui' }}"
+    if: "${{ github.event.label.name == 'ui' && github.repository_owner == 'JabRef' }}"
     runs-on: ubuntu-latest
     steps:
       - name: ui

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

@@ -8,7 +8,7 @@ on:
 jobs:
   automerge:
     name: Auto Merge
-    if: "${{ github.event.label.name == 'automerge' }}"
+    if: "${{ github.event.label.name == 'automerge' && github.repository_owner == 'JabRef' }}"
     runs-on: ubuntu-latest
     steps:
       - name: Approve PR

.github/workflows/on-unlabeled-issue.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   FirstTimeCodeContribution_or_Assigned:
-    if: ${{ (github.event.label.name == 'FirstTimeCodeContribution') || (github.event.label.name == '📍 Assigned') }}
+    if: ${{ ((github.event.label.name == 'FirstTimeCodeContribution') || (github.event.label.name == '📍 Assigned')) && github.repository_owner == 'JabRef' }}
     runs-on: ubuntu-latest
     permissions:
       issues: write

.github/workflows/pr-comment.yml

@@ -14,7 +14,7 @@ on:
 jobs:
   comment:
     # https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#running-a-workflow-based-on-the-conclusion-of-another-workflow
-    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    if: ${{ github.event.workflow_run.conclusion == 'failure' && (github.repository_owner == 'JabRef') }}
     runs-on: ubuntu-latest
     permissions:
       actions: read
@@ -37,22 +37,23 @@ jobs:
       - uses: actions/checkout@v4
       - name: Determine owner
         if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
-        id: owner
+        id: isCrossRepository
         run: |
-          owner=$(gh pr view $pr_number --json headRepositoryOwner --jq '.headRepositoryOwner')
-          echo "Got owner $owner"
-          echo owner=$owner >> $GITHUB_OUTPUT
+          isCrossRepository=$(gh pr view $pr_number --json isCrossRepository --jq '.isCrossRepository')
+          echo "Got isCrossRepository $isCrossRepository"
+          echo isCrossRepository=$isCrossRepository >> $GITHUB_OUTPUT
         env:
           GH_TOKEN: ${{ github.token }}
+          pr_number: ${{ steps.read-pr_number.outputs.pr_number }}
       - name: Checkout
-        if: ${{ (steps.read-pr_number.outputs.pr_number != '') && (steps.owner.owner != 'JabRef') }}
+        if: ${{ (steps.read-pr_number.outputs.pr_number != '') && (steps.isCrossRepository.isCrossRepository == 'true') }}
         uses: actions/checkout@v4
         with:
           fetch-depth: '0'
           show-progress: 'false'
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: jbang
-        if: ${{ (steps.read-pr_number.outputs.pr_number != '') && (steps.owner.owner != 'JabRef') }}
+        if: ${{ (steps.read-pr_number.outputs.pr_number != '') && (steps.isCrossRepository.isCrossRepository == 'true') }}
         uses: jbangdev/[email protected]
         with:
           script: ghprcomment@koppor/ghprcomment

.github/workflows/update-gradle-wrapper.yml

@@ -7,6 +7,7 @@ on:
 
 jobs:
   update-gradle-wrapper:
+    if: github.repository_owner == 'JabRef'
     runs-on: ubuntu-latest
 
     steps:

CHANGELOG.md

@@ -40,6 +40,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
 - We added a search bar for filtering keyboard shortcuts. [#11686](https://github.com/JabRef/jabref/issues/11686)
 - By double clicking on a local citation in the Citation Relations Tab you can now jump the linked entry. [#11955](https://github.com/JabRef/jabref/pull/11955)
+- We use the menu icon for background tasks as a progress indicator to visualise an import's progress when dragging and dropping several PDF files into the main table. [#12072](https://github.com/JabRef/jabref/pull/12072)
 
 ### Changed
 
@@ -104,6 +105,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where it was not possible to select selecting content of other user's comments.[#11106](https://github.com/JabRef/jabref/issues/11106)
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
 - We fixed an issue where trying to open a library from a failed mounted directory on Mac would cause an error. [#10548](https://github.com/JabRef/jabref/issues/10548)
+- We fixed an issue where identifier paste couldn't work with Unicode REPLACEMENT CHARACTER. [#11986](https://github.com/JabRef/jabref/issues/11986)
 
 ### Removed
 

src/main/java/org/jabref/gui/externalfiles/ImportHandler.java

@@ -102,6 +102,7 @@ public BackgroundTask<List<ImportFilesResultItemViewModel>> importFilesInBackgro
         return new BackgroundTask<>() {
             private int counter;
             private final List<ImportFilesResultItemViewModel> results = new ArrayList<>();
+            private final List<BibEntry> allEntriesToAdd = new ArrayList<>();
 
             @Override
             public List<ImportFilesResultItemViewModel> call() {
@@ -115,8 +116,13 @@ public List<ImportFilesResultItemViewModel> call() {
                     }
 
                     UiTaskExecutor.runInJavaFXThread(() -> {
-                        updateMessage(Localization.lang("Processing file %0", file.getFileName()));
-                        updateProgress(counter, files.size() - 1d);
+                        setTitle(Localization.lang("Importing files into %1 | %2 of %0 file(s) processed.",
+                                files.size(),
+                                bibDatabaseContext.getDatabasePath().map(path -> path.getFileName().toString()).orElse(Localization.lang("untitled")),
+                                counter));
+                        updateMessage(Localization.lang("Processing %0", FileUtil.shortenFileName(file.getFileName().toString(), 68)));
+                        updateProgress(counter, files.size());
+                        showToUser(true);
                     });
 
                     try {
@@ -168,10 +174,7 @@ public List<ImportFilesResultItemViewModel> call() {
 
                         UiTaskExecutor.runInJavaFXThread(() -> updateMessage(Localization.lang("Error")));
                     }
-
-                    // We need to run the actual import on the FX Thread, otherwise we will get some deadlocks with the UIThreadList
-                    // That method does a clone() on each entry
-                    UiTaskExecutor.runInJavaFXThread(() -> importEntries(entriesToAdd));
+                    allEntriesToAdd.addAll(entriesToAdd);
 
                     ce.addEdit(new UndoableInsertEntries(bibDatabaseContext.getDatabase(), entriesToAdd));
                     ce.end();
@@ -180,6 +183,9 @@ public List<ImportFilesResultItemViewModel> call() {
 
                     counter++;
                 }
+                // We need to run the actual import on the FX Thread, otherwise we will get some deadlocks with the UIThreadList
+                // That method does a clone() on each entry
+                UiTaskExecutor.runInJavaFXThread(() -> importEntries(allEntriesToAdd));
                 return results;
             }
 

src/main/java/org/jabref/gui/icon/IconTheme.java

@@ -283,6 +283,7 @@ public enum JabRefIcons implements JabRefIcon {
         APPLICATION_SUBLIMETEXT(JabRefMaterialDesignIcon.SUBLIME_TEXT),
         APPLICATION_TEXSHOP(JabRefMaterialDesignIcon.TEXSHOP),
         APPLICATION_TEXWORS(JabRefMaterialDesignIcon.TEXWORKS),
+        APPLICATION_VSCODE(JabRefMaterialDesignIcon.VSCODE),
         KEY_BINDINGS(MaterialDesignK.KEYBOARD),
         FIND_DUPLICATES(MaterialDesignC.CODE_EQUAL),
         CONNECT_DB(MaterialDesignC.CLOUD_UPLOAD),

src/main/java/org/jabref/gui/maintable/SmartConstrainedResizePolicy.java

@@ -17,6 +17,7 @@
  * This resize policy is almost the same as {@link TableView#CONSTRAINED_RESIZE_POLICY}
  * We make sure that the width of all columns sums up to the total width of the table.
  * However, in contrast to {@link TableView#CONSTRAINED_RESIZE_POLICY} we size the columns initially by their preferred width.
+ * Although {@link TableView#CONSTRAINED_RESIZE_POLICY} is deprecated, this policy maintains a similar resizing behavior.
  */
 public class SmartConstrainedResizePolicy implements Callback<TableView.ResizeFeatures, Boolean> {
 

src/main/java/org/jabref/gui/preferences/JabRefGuiPreferences.java

@@ -139,6 +139,7 @@ public class JabRefGuiPreferences extends JabRefCliPreferences implements GuiPre
     private static final String PUSH_VIM_SERVER = "vimServer";
     private static final String PUSH_VIM = "vim";
     private static final String PUSH_SUBLIME_TEXT_PATH = "sublimeTextPath";
+    private static final String PUSH_VSCODE_PATH = "VScodePath";
     // endregion
 
     // region NameDisplayPreferences
@@ -360,6 +361,7 @@ private JabRefGuiPreferences() {
         defaults.put(PUSH_VIM, "vim");
         defaults.put(PUSH_VIM_SERVER, "vim");
         defaults.put(PUSH_EMACS_ADDITIONAL_PARAMETERS, "-n -e");
+        defaults.put(PUSH_VSCODE_PATH, OS.detectProgramPath("Code", "Microsoft VS Code"));
 
         if (OS.OS_X) {
             defaults.put(PUSH_EMACS_PATH, "emacsclient");
@@ -937,6 +939,7 @@ public PushToApplicationPreferences getPushToApplicationPreferences() {
         applicationCommands.put(PushToApplications.VIM, getEmptyIsDefault(PUSH_VIM));
         applicationCommands.put(PushToApplications.WIN_EDT, getEmptyIsDefault(PUSH_WINEDT_PATH));
         applicationCommands.put(PushToApplications.SUBLIME_TEXT, getEmptyIsDefault(PUSH_SUBLIME_TEXT_PATH));
+        applicationCommands.put(PushToApplications.VSCODE, getEmptyIsDefault(PUSH_VSCODE_PATH));
 
         pushToApplicationPreferences = new PushToApplicationPreferences(
                 get(PUSH_TO_APPLICATION),
@@ -971,6 +974,8 @@ private void storePushToApplicationPath(Map<String, String> commandPair) {
                         put(PUSH_WINEDT_PATH, value);
                 case PushToApplications.SUBLIME_TEXT ->
                         put(PUSH_SUBLIME_TEXT_PATH, value);
+                case PushToApplications.VSCODE ->
+                        put(PUSH_VSCODE_PATH, value);
             }
         });
     }

src/main/java/org/jabref/gui/push/PushToApplications.java

@@ -18,6 +18,7 @@ public class PushToApplications {
     public static final String WIN_EDT = "WinEdt";
     public static final String SUBLIME_TEXT = "Sublime Text";
     public static final String TEXSHOP = "TeXShop";
+    public static final String VSCODE = "VScode";
 
     private static final List<PushToApplication> APPLICATIONS = new ArrayList<>();
 
@@ -38,7 +39,8 @@ public static List<PushToApplication> getAllApplications(DialogService dialogSer
                 new PushToTeXworks(dialogService, preferences),
                 new PushToVim(dialogService, preferences),
                 new PushToWinEdt(dialogService, preferences),
-                new PushToTexShop(dialogService, preferences)));
+                new PushToTexShop(dialogService, preferences),
+                new PushToVScode(dialogService, preferences)));
 
         return APPLICATIONS;
     }

src/main/java/org/jabref/gui/push/PushToVScode.java

@@ -0,0 +1,38 @@
+package org.jabref.gui.push;
+
+import java.nio.file.Path;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.icon.JabRefIcon;
+import org.jabref.gui.preferences.GuiPreferences;
+
+public class PushToVScode extends AbstractPushToApplication {
+
+    public static final String NAME = PushToApplications.VSCODE;
+
+    public PushToVScode(DialogService dialogService, GuiPreferences preferences) {
+        super(dialogService, preferences);
+    }
+
+    @Override
+    public String getDisplayName() {
+        return NAME;
+    }
+
+    @Override
+    public JabRefIcon getApplicationIcon() {
+        return IconTheme.JabRefIcons.APPLICATION_VSCODE;
+    }
+
+    @Override
+    protected String[] getCommandLine(String keyString) {
+        // TODO - Implementing this will fix https://github.com/JabRef/jabref/issues/6775
+        return new String[] {commandPath};
+    }
+
+    @Override
+    public String[] jumpToLineCommandlineArguments(Path fileName, int line, int column) {
+        return new String[] {commandPath, "--g", "%s:%s:%s".formatted(fileName.toString(), line, column)};
+    }
+}