Merge remote-tracking branch 'upstream/master' into changemergesdialog

# By Tobias Diez (11) and others
# Via GitHub (1) and Tobias Diez (1)
* upstream/master: (29 commits)
  Improve things arround change detection (#5770)
  Revert "Update to most recent journal abbreviation list" (#5769)
  Various fixes to the dark theme (#5764)
  Bump mockito-core from 3.2.0 to 3.2.4 (#5760)
  Bump classgraph from 4.8.58 to 4.8.59 (#5761)
  Improve dependency update rules
  Update jpackage to build 27 (#5758)
  Persistent column sortorder (#5730)
  Fix medline fetcher/importer when using installer (#5752)
  New Crowdin translations (#5751)
  Bump byte-buddy-parent from 1.10.4 to 1.10.5 (#5750)
  Fix checkstyle
  Fix filename
  Update to most recent journal abbreviation list
  Remove obsolete string
  Revert "Switch back to development"
  Switch back to development
  Next development cycle
  Release 5.0-beta (#5684)
  Fix multiple entries allowed in crossref (issue #5284) (#5724)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/collab/ChangeDisplayDialog.java
#	src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java

Author: Siedlerchr

.gitattributes

@@ -16,4 +16,4 @@ AUTHORS text eol=lf
 *.bib text !eol
 
 # disable after a release
-# CHANGELOG.md merge=union
+CHANGELOG.md merge=union

.github/failure-csl-update .github/failure-csl-update.md

@@ -1,6 +1,6 @@
 name: Deployment
 
-on: [create, push]
+on: [push]
 
 jobs:
   deploy:
@@ -11,17 +11,17 @@ jobs:
         include:
          - os: ubuntu-latest
            displayName: linux
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_linux-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_linux-x64_bin.tar.gz
            jdk14Path: /jdk-14
            archivePortable: tar -czf build/distribution/JabRef-portable_linux.tar.gz -C build/distribution JabRef && rm -R build/distribution/JabRef
          - os: windows-latest
            displayName: windows
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_windows-x64_bin.zip
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_windows-x64_bin.zip
            jdk14Path: /jdk-14
            archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
          - os: macOS-latest
            displayName: macOS
-           jpackageDownload: https://download.java.net/java/early_access/jpackage/1/openjdk-14-jpackage+1-70_osx-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_osx-x64_bin.tar.gz
            jdk14Path: /jdk-14.jdk/Contents/Home
            archivePortable: tar -czf build/distribution/JabRef-portable_macos.tar.gz -C build/distribution JabRef.app && rm -R build/distribution/JabRef.app
 

.github/workflows/deployment.yml

@@ -13,18 +13,31 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
+### Fixed
+
+- We fixed an issue where the Medline fetcher was only working when JabRef was running from source [#5645](https://github.com/JabRef/jabref/issues/5645)
+- We fixed some visual issues in the dark theme [#5764](https://github.com/JabRef/jabref/pull/5764) [#5753](https://github.com/JabRef/jabref/issues/5753)
+
+### Removed
+
+
+## [5.0-beta] – 2019-12-15
+
+### Changed
+
 - We added a short DOI field formatter which shortens DOI to more human-readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
 - We improved the display of group memberships by adding multiple colored bars if the entry belongs to more than one group. [#4574](https://github.com/JabRef/jabref/issues/4574)
 - We added an option to show the preview as an extra tab in the entry editor (instead of in a split view). [#5244](https://github.com/JabRef/jabref/issues/5244)
 - A custom Open/LibreOffice jstyle file now requires a layout line for the entry type `default` [#5452](https://github.com/JabRef/jabref/issues/5452)
 - The entry editor is now open by default when JabRef starts up. [#5460](https://github.com/JabRef/jabref/issues/5460)
 - Customized entry types are now serialized in alphabetical order in the bib file.
-- We added a new ADS fetcher to use the new ADS API [#4949](https://github.com/JabRef/jabref/issues/4949)
+- We added a new ADS fetcher to use the new ADS API. [#4949](https://github.com/JabRef/jabref/issues/4949)
 - We added support of the [X11 primary selection](https://unix.stackexchange.com/a/139193/18033) [#2389](https://github.com/JabRef/jabref/issues/2389)
 - We added support to switch between biblatex and bibtex library types. [#5550](https://github.com/JabRef/jabref/issues/5550)
 - We changed the save action buttons to be easier to understand. [#5565](https://github.com/JabRef/jabref/issues/5565)
 - We made the columns for groups, files and uri in the main table reorderable and merged the clickable icon columns for uri, url, doi and eprint. [#5544](https://github.com/JabRef/jabref/pull/5544)
 - We reduced the number of write actions performed when autosave is enabled [#5679](https://github.com/JabRef/jabref/issues/5679)
+- We made the column sort order in the main table persistent [#5730](https://github.com/JabRef/jabref/pull/5730)
 
 ### Fixed
 
@@ -64,6 +77,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an exception which occurred when an invalid jstyle was loaded. [#5452](https://github.com/JabRef/jabref/issues/5452)
 - We fixed an issue where the command line arguments `importBibtex` and `importToOpen` did not import into the currently open library, but opened a new one. [#5537](https://github.com/JabRef/jabref/issues/5537)
 - We fixed an error where the preview theme did not adapt to the "Dark" mode [#5463](https://github.com/JabRef/jabref/issues/5463)
+- We fixed an issue where multiple entries were allowed in the "crossref" field [#5284](https://github.com/JabRef/jabref/issues/5284)
 - We fixed an issue where the merge dialog showed the wrong text colour in "Dark" mode [#5516](https://github.com/JabRef/jabref/issues/5516)
 - We fixed visibility issues with the scrollbar and group selection highlight in "Dark" mode, and enabled "Dark" mode for the OpenOffice preview in the style selection window. [#5522](https://github.com/JabRef/jabref/issues/5522)
 - We fixed an issue where the author field was not correctly parsed during bibtex key-generation. [#5551](https://github.com/JabRef/jabref/issues/5551)
@@ -83,52 +97,6 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We removed the option to control the default drag and drop behaviour. You can use the modifier keys (like CtrL or Alt) instead.
 
 
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-
 ## [5.0-alpha] – 2019-08-25
 
 ### Changed
@@ -283,5 +251,6 @@ The changelog of JabRef 4.x is available at the [v4.x branch](https://github.com
 The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
 The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/v5.0-alpha...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v5.0-beta...HEAD
+[5.0-beta]: https://github.com/JabRef/jabref/compare/v5.0-alpha...v5.0-beta
 [5.0-alpha]: https://github.com/JabRef/jabref/compare/v4.3...v5.0-alpha

CHANGELOG.md

@@ -1,10 +1,9 @@
 assembly-versioning-format: '{major}.{minor}.{WeightedPreReleaseNumber}'
 assembly-informational-format: '{major}.{minor}{PreReleaseTagWithDash}--{CommitDate}--{ShortSha}'
+mode: ContinuousDeployment
 
 branches:
   master:
     regex: ^master
-    mode: ContinuousDelivery
     tag: beta
-    increment: Minor
     pre-release-weight: 30000 # 0 after stable release, 15000 before alpha release, 30000 before beta release, 50000 before stable release

GitVersion.yml

@@ -206,15 +206,15 @@ dependencies {
     }
 
 
-    testCompile 'io.github.classgraph:classgraph:4.8.58'
+    testCompile 'io.github.classgraph:classgraph:4.8.59'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.5.2'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.5.2'
     testCompile 'org.junit.platform:junit-platform-launcher:1.5.2'
 
-    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.4'
+    testCompile 'net.bytebuddy:byte-buddy-parent:1.10.5'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testCompile 'org.mockito:mockito-core:3.2.0'
+    testCompile 'org.mockito:mockito-core:3.2.4'
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
@@ -249,20 +249,29 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject('Release candidate')
             }
         }
-        rules.withModule("com.github.tomtung:latex2unicode_2.12") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /0.2.*/) {
-                // Reject version higher than 2.0.2. see https://github.com/JabRef/jabref/pull/3781
-                selection.reject("Cannot be updated to 0.2.4 until JabRef is prepared for it")
+        rules.withModule("org.python:jython-standalone") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.7.2b2/) {
+                selection.reject('Release candidate')
+            }
+        }
+        rules.withModule("de.jensd:fontawesomefx-materialdesignfont") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.0.26-9.1.2/) {
+                selection.reject('1.7.22-11 is actually newer (strange version system)')
+            }
+        }
+        rules.withModule("org.javamodularity.moduleplugin:org.javamodularity.moduleplugin.gradle.plugin") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /1.6.0/) {
+                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5270")
             }
         }
-        rules.withModule("com.github.johnrengelman.shadow:com.github.johnrengelman.shadow.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /4.*/) {
-                selection.reject("Version 4.X breaks the release process.")
+        rules.withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.5.1/) {
+                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
             }
         }
-        rules.withModule("com.google.errorprone:error_prone_core") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.3.3/) {
-                selection.reject("Does not work due to bug https://github.com/google/error-prone/issues/1240")
+        rules.withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
+            if (selection.candidate.version ==~ /2.5.1/) {
+                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
             }
         }
     }
@@ -597,6 +606,7 @@ jlink {
         uses 'com.airhacks.afterburner.injection.PresenterFactory'
         uses 'org.controlsfx.glyphfont.GlyphFont'
         uses 'com.airhacks.afterburner.views.ResourceLocator'
+        uses 'javax.xml.bind.JAXBContextFactory'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         provides 'org.apache.commons.logging.LogFactory' with 'org.apache.logging.log4j.jcl.LogFactoryImpl'

build.gradle

@@ -211,6 +211,7 @@
 
     /* The small thin light "shadow" for mark-like objects. Typically used in
      * conjunction with -fx-mark-color with an insets of 1 0 -1 0. */
+    -fx-mark-color: -fx-text-base-color;
     -fx-mark-highlight-color: transparent;
     /*-fx-mark-highlight-color: derive(-fx-color,80%);*/
 
@@ -235,12 +236,16 @@
     /** Focus line for keyboard focus traversal on cell based controls */
     -fx-cell-focus-inner-border: derive(-fx-selection-bar,30%);
 
-    -fx-focused-mark-color : -fx-focused-text-base-color;
+    -fx-focused-mark-color: -fx-focused-text-base-color;
 
     /* Consistent size for headers of tab-pane and side-panels*/
     -jr-header-height: 3em;
 }
 
+#frame {
+    -fx-background-color: -jr-background-alt;
+}
+
 /*
  * The base css file defining the style that is valid for every pane and dialog.
  */
@@ -262,6 +267,9 @@
        the text is always vertically centered within the bounds. Based on
        the cap height of the text. */
     -fx-bounds-type: logical_vertical_center;
+
+    /* The base color of icons should always be the same as the text. */
+    -fx-fill: -fx-text-base-color;
 }
 
 .tooltip {
@@ -385,7 +393,7 @@
 }
 
 .check-box > .box {
-    -fx-border-color: rgba(0, 0, 0, 0.54);
+    -fx-border-color: -fx-outer-border; /* rgba(0, 0, 0, 0.54); */
     -fx-border-width: 2px;
     -fx-border-radius: 1px;
     -fx-padding: 0.1em 0.1em 0.2em 0.2em;
@@ -564,6 +572,10 @@
     -fx-background-insets: 0;
 }
 
+.table-view .groupColumnBackground {
+    -fx-stroke: -jr-gray-2;
+}
+
 .scroll-pane:focused,
 .split-pane:focused,
 .list-view:focused,
@@ -1071,3 +1083,41 @@ We want to have a look that matches our icons in the tool-bar */
 .dialog-pane {
     -fx-background-color: -fx-control-inner-background;
 }
+
+.code-area .text {
+    -fx-fill: -fx-text-background-color;
+}
+
+.code-area .selection {
+    -fx-fill: -jr-accent;
+}
+
+.code-area .caret {
+    -fx-stroke: -fx-text-background-color;
+}
+
+.code-area .context-menu {
+    -fx-font-family: sans-serif;
+}
+
+.citationsList {
+    -fx-text-fill: -fx-text-base-color;
+}
+
+.citationsList .contextBox {
+    -fx-border-color: -fx-outer-border;
+    -fx-border-insets: 5;
+    -fx-border-style: dashed;
+    -fx-border-width: 2;
+    -fx-padding: 12;
+}
+
+.citationsList .contextBox * {
+    -fx-fill: -fx-text-base-color;
+}
+
+.citationsList .label {
+    -fx-font-family: monospace;
+    -fx-font-weight: bold;
+    -fx-label-padding: 5 0 10 10;
+}

src/main/java/org/jabref/gui/Base.css

@@ -991,10 +991,6 @@ public BibDatabaseContext getBibDatabaseContext() {
         return this.bibDatabaseContext;
     }
 
-    public void markExternalChangesAsResolved() {
-        changeMonitor.ifPresent(DatabaseChangeMonitor::markExternalChangesAsResolved);
-    }
-
     public SidePaneManager getSidePaneManager() {
         return sidePaneManager;
     }
@@ -1059,10 +1055,6 @@ public void resetChangeMonitorAndChangePane() {
         this.getChildren().setAll(changePane);
     }
 
-    public void updateTimeStamp() {
-        changeMonitor.ifPresent(DatabaseChangeMonitor::markAsSaved);
-    }
-
     public void copy() {
         mainTable.copy();
     }

src/main/java/org/jabref/gui/BasePanel.java

@@ -47,7 +47,7 @@
     -jr-menu-forground-active: derive(-fx-light-text-color, 50%);
 
     -jr-scrollbar-thumb: derive(-fx-outer-border, -30%);
-    -jr-scrollbar-track: derive(-fx-control-inner-background, -90%); 
+    -jr-scrollbar-track: derive(-fx-control-inner-background, -90%);
 
     -fx-focused-text-base-color: -fx-dark-text-color;
 
@@ -59,6 +59,15 @@
     color : #7d8591; /* -fx-mid-text-color*/
 }
 
+.table-view .groupColumnBackground {
+    -fx-stroke: -jr-gray-4;
+}
+
+.code-area .lineno {
+    -fx-background-color: -jr-background-alt;
+    -fx-text-fill: -fx-mid-text-color;
+}
+
 .text-unchanged {
     -fx-fill: -fx-light-text-color;
 }
@@ -73,4 +82,8 @@
 
 .numberColumn > .hits:all-selected {
     -fx-background-color: -jr-gray-3;
-}
+}
+
+#preferencesContainer .tab-pane > .tab-header-area > .tab-header-background {
+    -fx-background-color: -jr-background;
+}

src/main/java/org/jabref/gui/Dark.css

@@ -40,6 +40,7 @@
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
 import javafx.scene.layout.Priority;
+import javafx.scene.layout.VBox;
 import javafx.stage.Stage;
 
 import org.jabref.Globals;
@@ -405,9 +406,10 @@ public boolean quit() {
     private void initLayout() {
         setProgressBarVisible(false);
 
-        BorderPane head = new BorderPane();
-        head.setTop(createMenu());
-        head.setCenter(createToolbar());
+        setId("frame");
+
+        VBox head = new VBox(createMenu(),createToolbar());
+        head.setSpacing(0d);
         setTop(head);
 
         splitPane.getItems().addAll(sidePane, tabbedPane);