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

* upstream/master: (79 commits) Update richtext and flowless (#3386) Source tab: hide notification pane when code is correct again (#3387) Titles are optional at crossref (#3378) Update entry for every change in the source panel (#3366) Rework AutoSetFileLinks (#3368) revert wrongly commited changes Refactorings (#3370) Fix freezing when running cleanup file operations like rename (#3315) This additional style setting for IDEA (#3355) Fix checkstyle Add proper equals to content selector Source tab entry duplication (#3360) Use CITE_COMMENT not only for external latex editors but also for cop… (#3351) Updating with new translations (#3348) Upgrade error-prone (#3350) Jabref_pt_BR partially updated (#3349) Delete unused code Extract difference finder from gui to logic Used late initialization for context menus (#3340) Fix NPE when calling with bib file as cmd argument (#3343) ...
JabRef · Nov 1, 2017 · 2296ea5 · 2296ea5
2 parents e099c2a + 84e9071
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diff --git a/.mailmap b/.mailmap
@@ -1,3 +1,4 @@
+
 # Generate AUTHORS: scripts/generate-authors.sh
 
 # Tip for finding duplicates (besides scanning the output of AUTHORS for name
@@ -124,5 +125,10 @@ Nadeem Mahmood <mahmoodn@purdue.edu>
 Foivos Christoulakis <halx4@users.noreply.github.com>
 Predrag Milanovic <pmilanovic@gmail.com>
 Karsten Hiekmann <sammann-fnordbedarf-de@users.noreply.github.com>
+Karsten Hiekmann <h.k.hiekmann@nanooq.org>
 Andrew Levit <dreyskiy@gmail.com>
-
+Berk Gureken <berkgureken@gmail.com>
+Abhishek Rai <abhisheksavitarai@gmail.com>
+Abhishek Rai <betheunique@users.noreply.github.com>
+Stéphane Curet <stephane.curet@orange.fr>
+Erdem Derebasoglu <erdemderebasoglu@hotmail.com>
diff --git a/AUTHORS b/AUTHORS
@@ -1,6 +1,7 @@
 # This file lists all individuals having contributed content to the repository.
 # For how it is generated, see `scripts/generate-authors.sh`.
 Aaron Chen
+Abhishek Rai
 Adam Rehn
 Admir Obralija
 Adrian Daerr
@@ -20,6 +21,8 @@ Anita Armbruster
 Antonio Ribeiro
 Arno Blouin
 Behrouz Javanmardi
+Benjamin Köhler
+Berk Gureken
 Bernd Kalbfuss
 Bernhard Tempel
 Brian Quistorff
@@ -47,6 +50,7 @@ Eduard Braun
 Eduardo Greco
 Egon Willighagen
 Ellen Reitmayr
+Erdem Derebasoglu
 Erik Putrycz
 Ervin Kolenovic
 Fabian Bauer
@@ -170,6 +174,7 @@ Stefan Robert
 Stefano Gariazzo
 Stephan Lau
 Stephan Rave
+Stéphane Curet
 Sven Jäger
 The Gitter Badger
 Thiago Toledo

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,41 +12,34 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We added bracketed expresion support for file search patterns, import file name patterns and file directory patters, in addition to bibtexkey patterns.
+- We added support for '[entrytype]' bracketed expression.
+- Updated French translation
+- We improved the handling of abstracts in the "Astrophysics Data System" fetcher. [#2471](https://github.com/JabRef/jabref/issues/2471)
+- We added support for pasting entries in different formats [#3143](https://github.com/JabRef/jabref/issues/3143)
+- In the annotation tab, PDF files are now monitored for new or changed annotation. A manual reload is no longer necessary. [#3292](https://github.com/JabRef/jabref/issues/3292)
+- We increased the relative size of the "abstract" field in the entry editor. [Feature request in the forum](http://discourse.jabref.org/t/entry-preview-in-version-4/827)
+- Crossreferenced entries are now used when a BibTex key is generated for an entry with empty fields. [#2811](https://github.com/JabRef/jabref/issues/2811)
+- We now set the WM_CLASS of the UI to org-jabref-JabRefMain to allow certain Un*x window managers to properly identify its windows
+- We changed the default paths for the OpenOffice/LibreOffice binaries to the default path for LibreOffice
+- We no longer create a new entry editor when selecting a new entry to increase performance. [#3187](https://github.com/JabRef/jabref/pull/3187)
+- We increased performance and decreased the memory footprint of the entry editor drastically. [#3331](https://github.com/JabRef/jabref/pull/3331)
+- Late initialization of the context menus in the entry editor. This improves performance and memory footprint further [#3340](https://github.com/JabRef/jabref/pull/3340)
 
-- We add a textArea to see versionInfo in the About JabRef Dialog.[#2942](https://github.com/JabRef/jabref/issues/2942)
-- We turned the validation feature in the entry editor off by default, because of a bug in the library we have been using [#3145](https://github.com/JabRef/jabref/issues/3145)
-- Added 'Filter All' and 'Filter None' buttons with corresponding functionality to Quality Check tool.
-- We increased the size of the keywords and file text areas in the entry editor
-- When the entry that is currently shown in the entry editor is deleted externally, the editor is now closed automatically [#2946](https://github.com/JabRef/jabref/issues/2946)
-- We added reordering of file and link entries in the `General`-Tab [3165, comment](https://github.com/JabRef/jabref/issues/3165#issuecomment-326269715)
-- We added autcompletion for the `crossref` field on basis of the BibTeX-key. To accept such an autcompleted key as new entry-link, you have to press <kbd>Enter</kbd> two times, otherwise the field data is not stored in the library file.[koppor#257](https://github.com/koppor/jabref/issues/257)
-- We added drag and drop support for adding files directly in the `General`-Tab. The dragged files are currently only linked from their existing directory. For more advanced features use the `Add files` dialog. [#koppor#244](https://github.com/koppor/jabref/issues/244)
-- We added the file description filed back to the list of files in the `General`-Tab [#2930, comment](https://github.com/JabRef/jabref/issues/2930#issuecomment-328328172)
 
 ### Fixed
+ - We fixed the translation of \textendash in the entry preview [#3307](https://github.com/JabRef/jabref/issues/3307)
+ - We fixed an issue where JabRef would not terminated after asking to collect anonymous statistics [#2955 comment](https://github.com/JabRef/jabref/issues/2955#issuecomment-334591123)
+ - We fixed an issue where JabRef would not shut down when started with the '-n' (No GUI) option. [#3247](https://github.com/JabRef/jabref/issues/3247)
+ - We improved the way metadata is updated in remote databases. [#3235](https://github.com/JabRef/jabref/issues/3235)
+ - We improved font rendering of the Entry Editor for Linux based systems [#3295](https://github.com/JabRef/jabref/issues/3295)
+ - We fixed an issue where JabRef would freeze when trying to replace the original entry after a merge with new information from identifiers like DOI/ISBN etc. [3294](https://github.com/JabRef/jabref/issues/3294)
+ - We fixed an issue where JabRef would not show the translated content at some points, although there existed a translation
+ - We fixed an issue where editing in the source tab would override content of other entries [#3352](https://github.com/JabRef/jabref/issues/3352#issue-268580818)
+ - We fixed several issues with the automatic linking of files in the entry editor where files were not found or not correctly saved in the bibtex source [#3346](https://github.com/JabRef/jabref/issues/3346)
+ - We fixed an issue where fetching entries from crossref that had no titles caused an error [#3376](https://github.com/JabRef/jabref/issues/3376)
 
-- We re-added the "Normalize to BibTeX name format" context menu item [#3136](https://github.com/JabRef/jabref/issues/3136)
-- We fixed a memory leak in the source tab of the entry editor [#3113](https://github.com/JabRef/jabref/issues/3113)
-- We fixed a [java bug](https://bugs.openjdk.java.net/browse/JDK-8185792) where linux users could not enter accented characters in the entry editor and the search bar [#3028](https://github.com/JabRef/jabref/issues/3028)
-- We fixed a regression introduced in v4.0-beta2: A file can be dropped to the entry preview to attach it to the entry [koppor#245](https://github.com/koppor/jabref/issues/245)
-- We fixed an issue in the "Replace String" dialog (<kbd>Ctrl</kbd>+<kbd>R</kbd> where search and replace did not work for the `bibtexkey` field. [#3132](https://github.com/JabRef/jabref/issues/3132)
-- We fixed an issue in the entry editor where adding a term to a new protected terms list freezed JabRef completely. [#3157](https://github.com/JabRef/jabref/issues/3157)
-- We fixed an issue in the "Manage protected terms" dialog where an 'Open file' dialog instead of a 'Save file' dialog was shown when creating a new list. [#3157](https://github.com/JabRef/jabref/issues/3157)
-- We fixed an issue where unparseable dates of the FileAnnotations caused the FileAnnotationsTab to crash.
-- We fixed an issue where a new protected terms list was not available immediately after its addition. [#3161](https://github.com/JabRef/jabref/issues/3161)
-- We fixed an issue where an online file link could not be removed from an entry [#3165](https://github.com/JabRef/jabref/issues/3165)
-- We fixed an issue where an online file link did not open the browser and created an error [#3165](https://github.com/JabRef/jabref/issues/3165)
-- We fixed an issue where the arrow keys in the search bar did not work as expected [#3081](https://github.com/JabRef/jabref/issues/3081)
-- We fixed wrong hotkey being displayed at "automatically file links" in the entry editor
-- We fixed an issue where metadata syncing with local and shared database were unstable. It will also fix syncing groups and sub-groups in database. [#2284](https://github.com/JabRef/jabref/issues/2284)
-- We fixed an issue where renaming a linked file would fail silently if a file with the same name existed.  Added support for overriding existing file at user discretion. [#3172] (https://github.com/JabRef/jabref/issues/3172)
-- We fixed an issue where the "Remove group and subgroups" operation did not remove group information from entries in the group [#3190](https://github.com/JabRef/jabref/issues/3190)
-- We fixed an issue where it was possible to leave the entry editor with an imbalance of braces. [#3167](https://github.com/JabRef/jabref/issues/3167)
-- Renaming files now truncates the filename to not exceed the limit of 255 chars [#2622](https://github.com/JabRef/jabref/issues/2622)
-- We improved the handling of hyphens in names. [#2775](https://github.com/JabRef/jabref/issues/2775)
-- We fixed an issue where an entered file description was not written to the bib-file [#3208](https://github.com/JabRef/jabref/issues/3208)
-### Removed
-- We removed support for LatexEditor, as it is not under active development. [#3199](https://github.com/JabRef/jabref/issues/3199)
+ ### Removed
 
 
 
@@ -93,8 +86,49 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 
 
+## [4.0] - 2017-10-04
 
+### Changed
 
+- We add a textArea to see versionInfo in the About JabRef Dialog.[#2942](https://github.com/JabRef/jabref/issues/2942)
+- We turned the validation feature in the entry editor off by default, because of a bug in the library we have been using [#3145](https://github.com/JabRef/jabref/issues/3145)
+- Added 'Filter All' and 'Filter None' buttons with corresponding functionality to Quality Check tool.
+- We increased the size of the keywords and file text areas in the entry editor
+- When the entry that is currently shown in the entry editor is deleted externally, the editor is now closed automatically [#2946](https://github.com/JabRef/jabref/issues/2946)
+- We added reordering of file and link entries in the `General`-Tab [3165, comment](https://github.com/JabRef/jabref/issues/3165#issuecomment-326269715)
+- We added autcompletion for the `crossref` field on basis of the BibTeX-key. To accept such an autcompleted key as new entry-link, you have to press <kbd>Enter</kbd> two times, otherwise the field data is not stored in the library file.[koppor#257](https://github.com/koppor/jabref/issues/257)
+- We added drag and drop support for adding files directly in the `General`-Tab. The dragged files are currently only linked from their existing directory. For more advanced features use the `Add files` dialog. [#koppor#244](https://github.com/koppor/jabref/issues/244)
+- We added the file description filed back to the list of files in the `General`-Tab [#2930, comment](https://github.com/JabRef/jabref/issues/2930#issuecomment-328328172)
+- Added an error dialog if the file is open in another process and cannot be renamed. [#3229]
+- On Windows, the `JabRef.exe` executable can now be used to start JabRef from the command line. By default, no output is shown unless the new "-console" option is specified.
+
+### Fixed
+
+- We re-added the "Normalize to BibTeX name format" context menu item [#3136](https://github.com/JabRef/jabref/issues/3136)
+- We fixed a memory leak in the source tab of the entry editor [#3113](https://github.com/JabRef/jabref/issues/3113)
+- We fixed a [java bug](https://bugs.openjdk.java.net/browse/JDK-8185792) where linux users could not enter accented characters in the entry editor and the search bar [#3028](https://github.com/JabRef/jabref/issues/3028)
+- We fixed a regression introduced in v4.0-beta2: A file can be dropped to the entry preview to attach it to the entry [koppor#245](https://github.com/koppor/jabref/issues/245)
+- We fixed an issue in the "Replace String" dialog (<kbd>Ctrl</kbd>+<kbd>R</kbd> where search and replace did not work for the `bibtexkey` field. [#3132](https://github.com/JabRef/jabref/issues/3132)
+- We fixed an issue in the entry editor where adding a term to a new protected terms list freezed JabRef completely. [#3157](https://github.com/JabRef/jabref/issues/3157)
+- We fixed an issue in the "Manage protected terms" dialog where an 'Open file' dialog instead of a 'Save file' dialog was shown when creating a new list. [#3157](https://github.com/JabRef/jabref/issues/3157)
+- We fixed an issue where unparseable dates of the FileAnnotations caused the FileAnnotationsTab to crash.
+- We fixed an issue where a new protected terms list was not available immediately after its addition. [#3161](https://github.com/JabRef/jabref/issues/3161)
+- We fixed an issue where an online file link could not be removed from an entry [#3165](https://github.com/JabRef/jabref/issues/3165)
+- We fixed an issue where an online file link did not open the browser and created an error [#3165](https://github.com/JabRef/jabref/issues/3165)
+- We fixed an issue where the arrow keys in the search bar did not work as expected [#3081](https://github.com/JabRef/jabref/issues/3081)
+- We fixed wrong hotkey being displayed at "automatically file links" in the entry editor
+- We fixed an issue where metadata syncing with local and shared database were unstable. It will also fix syncing groups and sub-groups in database. [#2284](https://github.com/JabRef/jabref/issues/2284)
+- We fixed an issue where renaming a linked file would fail silently if a file with the same name existed.  Added support for overriding existing file at user discretion. [#3172] (https://github.com/JabRef/jabref/issues/3172)
+- We fixed an issue where the "Remove group and subgroups" operation did not remove group information from entries in the group [#3190](https://github.com/JabRef/jabref/issues/3190)
+- We fixed an issue where it was possible to leave the entry editor with an imbalance of braces. [#3167](https://github.com/JabRef/jabref/issues/3167)
+- Renaming files now truncates the filename to not exceed the limit of 255 chars [#2622](https://github.com/JabRef/jabref/issues/2622)
+- We improved the handling of hyphens in names. [#2775](https://github.com/JabRef/jabref/issues/2775)
+- We fixed an issue where an entered file description was not written to the bib-file [#3208](https://github.com/JabRef/jabref/issues/3208)
+- We improved the auto completion in the search bar. [koppor#253](https://github.com/koppor/jabref/issues/253)
+- We fixed renaming files which are not in the main directory. [#3230](https://github.com/JabRef/jabref/issues/3230)
+
+### Removed
+- We removed support for LatexEditor, as it is not under active development. [#3199](https://github.com/JabRef/jabref/issues/3199)
 
 
 ## [4.0-beta3] – 2017-08-16
@@ -956,7 +990,8 @@ Since much functionality has changed during development, a release of this versi
 
 The changelog of 2.11 and versions before is maintained as [text file](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG) in the [v2.11.1 tag](https://github.com/JabRef/jabref/tree/v2.11.1).
 
-[unreleased]: https://github.com/JabRef/jabref/compare/v4.0-beta3...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v4.0...HEAD
+[4.0]: https://github.com/JabRef/jabref/compare/v4.0-beta3...v4.0
 [4.0-beta3]: https://github.com/JabRef/jabref/compare/v4.0-beta2...v4.0-beta3
 [4.0-beta2]: https://github.com/JabRef/jabref/compare/v4.0-beta...v4.0-beta2
 [4.0-beta]: https://github.com/JabRef/jabref/compare/v3.8.2...v4.0-beta

diff --git a/build.gradle b/build.gradle
@@ -9,7 +9,7 @@ plugins {
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
     id "com.simonharrer.modernizer" version '1.5.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.3'
-    id 'net.ltgt.errorprone' version '0.0.11'
+    id 'net.ltgt.errorprone' version '0.0.13'
 }
 
 // use the gradle build scan feature: https://scans.gradle.com/get-started
@@ -31,8 +31,8 @@ apply from: 'localization.gradle'
 apply from: 'xjc.gradle'
 
 group = "org.jabref"
-version = "4.0-dev"
-project.ext.threeDotVersion = "4.0.2.1"
+version = "4.1-dev"
+project.ext.threeDotVersion = "4.0.3.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
@@ -91,44 +91,46 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.7'
 
     // VersionEye states that 6.0.5 is the most recent version, but http://dev.mysql.com/downloads/connector/j/ shows that as "Development Release"
-    compile 'mysql:mysql-connector-java:5.1.43'
+    compile 'mysql:mysql-connector-java:5.1.44'
 
     compile 'com.impossibl.pgjdbc-ng:pgjdbc-ng:0.7.1'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:23.0'
+    compile 'com.google.guava:guava:23.2-jre'
 
     // JavaFX stuff
     compile 'com.airhacks:afterburner.fx:1.7.0'
     compile 'de.codecentric.centerdevice:javafxsvg:1.2.1'
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
-    compile 'de.saxsys:mvvmfx-validation:1.6.0'
-    compile 'org.controlsfx:controlsfx:8.40.13'
+    compile 'de.saxsys:mvvmfx-validation:1.7.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
-    compile 'org.fxmisc.flowless:flowless:0.5.2'
-    compile 'org.fxmisc.richtext:richtextfx:0.7-M5'
+    compile 'org.fxmisc.flowless:flowless:0.6'
+    compile 'org.fxmisc.richtext:richtextfx:0.8.1'
+
+    // Cannot be updated to 9.*.* until Jabref works with Java 9
+    compile 'org.controlsfx:controlsfx:8.40.14'
 
     compile 'org.jsoup:jsoup:1.10.3'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     compile 'commons-logging:commons-logging:1.2'
-    compile 'org.apache.logging.log4j:log4j-jcl:2.9.0'
-    compile 'org.apache.logging.log4j:log4j-api:2.9.0'
-    compile 'org.apache.logging.log4j:log4j-core:2.9.0'
+    compile 'org.apache.logging.log4j:log4j-jcl:2.9.1'
+    compile 'org.apache.logging.log4j:log4j-api:2.9.1'
+    compile 'org.apache.logging.log4j:log4j-core:2.9.1'
 
     // need to use snapshots as the stable version is from 2013 and doesn't support v1.0.1 CitationStyles
     compile 'org.citationstyles:styles:1.0.1-SNAPSHOT'
     compile 'org.citationstyles:locales:1.0.1-SNAPSHOT'
     compile 'de.undercouch:citeproc-java:1.0.1'
 
-    compile 'com.github.tomtung:latex2unicode_2.12:0.2.1'
+    compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.+'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.+'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '1.0.9'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '1.0.9'
 
     testCompile 'junit:junit:4.12'
-    testCompile 'org.mockito:mockito-core:2.10.0'
+    testCompile 'org.mockito:mockito-core:2.11.0'
     testCompile 'com.github.tomakehurst:wiremock:2.8.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
@@ -353,7 +355,7 @@ task media(type: com.install4j.gradle.Install4jTask, dependsOn: "releaseJar") {
 checkstyle {
     // do not use other packages for checkstyle, excluding gen(erated) sources
     checkstyleMain.source = "src/main/java"
-    toolVersion = '8.0'
+    toolVersion = '8.3'
 }
 
 checkstyleMain.shouldRunAfter test