Merge branch 'master' into copacimportertest

CHANGELOG.md

@@ -0,0 +1,94 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+This project **does not** adhere to [Semantic Versioning](http://semver.org/).
+This file tries to follow the conventions proposed by [keepachangelog.com](http://keepachangelog.com/).
+Here, the categories "Changed" for added and changed functionality,
+"Fixed" for fixed functionality, and
+"Removed" for removed functionality is used.
+
+We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#NUM`,
+to [sourceforge bugs](https://sourceforge.net/p/jabref/bugs/) by using `bug NUM`, and
+to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by using `feature NUM`.
+
+## [Unreleased]
+
+### Changed
+ - Feature: Search DOAJ, Directory of Open Access Journals
+ - Changes the old integrity check by improving the code base (+tests) and converting it to a simple issues table
+ - Added combo box in MassSetFieldAction to simplify selecting the correct field name
+ - Feature: Merge information from both entries on duplication detection
+ - Always use import inspection dialog on import from file
+ - All duplicate whitespaces / tabs / newlines are now removed from non-multiline fields
+ - Feature: Merge information from a DOI generated BibTex entry to an entry
+ - Added more characters to HTML/Unicode converter
+ - Feature: Push citations to Texmaker ([bug 318](https://sourceforge.net/p/jabref/bugs/318/), [bug 582](https://sourceforge.net/p/jabref/bugs/582/))
+ - Case changers improved to honor words (not yet more than single words) within {}
+ - Feature: Added converters from HTML and Unicode to LaTeX on right click in text fields (#191)
+ - Feature: Add an option to the FileList context menu to delete an associated file from the file system
+ - Feature: Field names "Doi", "Ee", and "Url" are now written as "DOI", "EE", and "URL"
+ - The default language is now automatically set to the system's locale.
+ - Use correct encoding names (#155) and replace old encoding names in bibtex files. This changes the file header.
+ - No longer write JabRef version to BibTex file header.
+ - No longer add blank lines inside a bibtex entry
+ - Feature: When pasting a Google search URL, meta data will be automatically stripped before insertion.
+ - Feature: PDF auto download from ACS, arXiv, ScienceDirect, SpringerLink, and Google Scholar
+ - List of authors is now auto generated `scripts/generate-authors.sh` and inserted into L10N About.html
+ - Streamline logging API: Replace usages of java.util.logging with commons.logging
+ - Remove support for custom icon themes. The user has to use the default one.
+ - Solved feature request #767: New subdatabase based on AUX file (biblatex)
+ - Feature: DOItoBibTeX fetcher now also handles HTTP URLs
+ - Feature: "Normalize to BibTeX name format" also removes newlines
+ - Tweak of preference defaults
+   - Autolink requires that the filename starts with the given BibTeX key and the default filename patterns is key followed by title
+   - Default sorting changed
+   - Default label pattern changed from [auth][year] to [authors3][year]
+ - Feature: case changers now leave protected areas (enclosed with curly brakets) alone
+ - BREAKING: The BibTeX key generator settings from previous versions are lost
+ - BREAKING: LabelPatterns `[auth.etal]`, `[authEtAl]`, `[authors]`, `[authorsN]`, `[authorLast]` and more to omit spaces and commas (and work as described at http://jabref.sourceforge.net/help/LabelPatterns.php)
+ - BREAKING: `[keywordN]` returns the Nth keyword (as described in the help) and not the first N keywords
+ - BREAKING: If field consists of blanks only or an emtpy string, it is not written at all
+ - Feature: new LabelPattern `[authFirstFull]` returning the last name of the first author and also a "van" or "von" if it exists
+ - Feature: all new lines when writing an entry are obeying the globally configured new line (File -> newline separator). Affects fields: abstract and review
+ - Feature: `[veryShortTitle]` and `[shortTitle]` also skip words like "in", "among", "before", ...
+ - Feature: New LabelPattern `[keywordsN]`, where N is optional. Returns the first N keywords. If no N is specified ("`[keywords]`"), all keywords are returned. Spaces are removed.
+ - Update supported LookAndFeels
+ - Show replaced journal abbreviations on console
+
+### Fixed
+ - Fixed #325: Deactivating AutoCompletion crashes EntryEditor
+ - Fixed bug when having added and then removed a personal journal list, an exception is always shown on startup
+ - Fixed a bug in the IEEEXploreFetcher
+ - Fixed [bug 1282](https://sourceforge.net/p/jabref/bugs/1282/) related to backslashes duplication.
+ - Fixed [bug 1285](https://sourceforge.net/p/jabref/bugs/1285/): Editing position is not lost on saving
+ - Fixed [bug 1297](https://sourceforge.net/p/jabref/bugs/1297/): No console message on closing
+ - Fixed #194: JabRef starts again on Win XP and Win Vista
+ - Fixed: Tooltips are now shown for the #-field when the bibtex entry is incomplete.
+ - Fixed #173: Personal journal abbreviation list is not loaded twice
+ - Bugfix: Preview of external journal abbreviation list now displays the correct list
+ - Fixed #223: Window is displayed in visible area even when having multiple screens
+ - Localization tweaks: "can not" -> "cannot" and "file name" -> "filename"
+ - Fixed: When reconfiguring the BibTeX key generator, changes are applied instantly without requiring a restart of JabRef
+ - Fixed #250: No hard line breaks after 70 chars in serialized JabRef meta data
+ - Fixed [bug 1296](https://sourceforge.net/p/jabref/bugs/1296/): External links in the help open in the standard browser
+
+### Removed
+ - BREAKING: Remove plugin functionality.
+ - The key bindings for searching specific databases are removed
+ - Remove option to toggle native file dialog on mac by making JabRef always use native file dialogs on mac
+ - Remove options to set PDF and PS directories per .bib database as the general options have also been deleted.
+ - Remove option to disable renaming in FileChooser dialogs.
+ - Remove option to hide the BibTeX Code tab in the entry editor.
+ - Remove option to set a custom icon for the external file types. This is not possible anymore with the new icon font.
+ - Remove legacy options to sync files in the "pdf" or "ps" field
+ - Remove button to merge entries and keep the old ones.
+ - Remove non-compact rank symbols in favor of compact rank
+ - Remove Mr.DLib support as MR.DLib will be shut down in 2015
+ - Remove support for key bindings per external application by allowing only the key binding "push to application" for the currently selected external application.
+ - Remove "edit preamble" from toolbar
+ - Remove support to the move-to-SysTray action
+
+## 2.11 - 2015-11-11
+
+The changelog of 2.11 and versions before is maintained as text file in the [dev_2.11 branch](https://github.com/JabRef/jabref/tree/dev_2.11).
+
+[Unreleased]: https://github.com/JabRef/jabref/compare/v2.11...HEAD

CONTRIBUTING.md

@@ -25,10 +25,9 @@ When you use Eclipse, the required config is generated automatically by `gradlew
 You can also run `gradlew format` to let the [Gradle Format plugin](https://github.com/youribonnaffe/gradle-format-plugin) do the formatting.
 
 
-### Add your change to the CHANGELOG
-You should edit the [CHANGELOG](CHANGELOG) located in the root directory of the JabRef source.
-Add a line with your changes and your name.
-Nicknames are OK.
+### Add your change to CHANGELOG.md
+You should edit the [CHANGELOG.md](CHANGELOG.md) located in the root directory of the JabRef source.
+Add a line with your changes in the appropriate section.
 
 If you did internal refactorings or improvements not visible to the user (e.g., UI, .bib file), then you don't need to put an entry there.
 

DEVELOPERS

@@ -3,5 +3,6 @@
 Jörg Lenhard
 Matthias Geiger
 Oliver Kopp
+Oscar Gustafsson
 Simon Harrer
 Stefan Kolb

README.md

@@ -3,8 +3,8 @@
 [![CircleCI](https://img.shields.io/circleci/project/JabRef/jabref.svg)](https://circleci.com/gh/JabRef/jabref)
 [![Dependency Status](https://www.versioneye.com/user/projects/557f2723386664002000009c/badge.svg?style=flat)](https://www.versioneye.com/user/projects/557f2723386664002000009c)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
+[![Coverity Status](https://badges.ondemand.coverity.com/streams/tslj9m8e2149d8elggiskktgpc)](https://ondemand.coverity.com/streams/tslj9m8e2149d8elggiskktgpc)
 [![License](https://img.shields.io/badge/license-GPLv2-blue.svg)](http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt)
-[![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![Donation](https://img.shields.io/badge/donate-paypal-orange.svg)](https://www.paypal.com/cgi-bin/webscr?item_name=JabRef+Bibliography+Manager&cmd=_donations&lc=US&currency_code=EUR&business=jabrefmail%40gmail.com)
 [![Flattr this git repo](http://api.flattr.com/button/flattr-badge-large.png)](https://flattr.com/submit/auto?user_id=koppor&url=https%3A%2F%2Fgh.neting.cc%2FJabRef%2Fjabref&title=JabRef&language=Java&tags=github&category=software)
 [![Download JabRef](https://img.shields.io/sourceforge/dw/jabref.svg)](http://sourceforge.net/projects/jabref/files/jabref/)
@@ -13,7 +13,6 @@ This version is a development version. Features may not work as expected.
 
 The branch of this README file is `master`.
 The intention of this branch is to move JabRef forward to modern technologies such as Java8 and JavaFX.
-The development version will be called `v2.80` and is meant as preparation to the `v3.0` release.
 
 The last version with Java6 support is `v2.11` being developed at the [dev_2.11 branch](https://github.com/JabRef/jabref/tree/dev_2.11).
 

build.gradle

@@ -3,9 +3,10 @@ import org.gradle.internal.os.OperatingSystem
 plugins {
     id 'com.github.johnrengelman.shadow' version '1.2.2'
     id "edu.sc.seis.launch4j" version "1.1.4"
-    id "com.github.kt3k.coveralls" version "2.4.0"
+    id "com.github.kt3k.coveralls" version "2.4.0x"
     id "edu.sc.seis.macAppBundle" version "2.1.1"
     id "com.github.youribonnaffe.gradle.format" version "1.2"
+    id "com.coverity.ondemand" version "1.3.708"
 }
 
 apply plugin: "java"
@@ -15,6 +16,17 @@ apply plugin: 'jacoco'
 apply plugin: 'com.github.kt3k.coveralls'
 apply from: 'eclipse.gradle'
 
+// HACK to disable coverityCheck task when not on CI server
+// necessary as coverity automatically adds check.dependsOn coverityCheck
+gradle.taskGraph.whenReady { taskGraph ->
+    def tasks = taskGraph.getAllTasks()
+    if (System.env.CI == null) {
+        tasks.findAll {it.name.startsWith('coverityCheck')}.each { task ->
+                task.enabled = false
+        }
+    }
+}
+
 group = "net.sf.jabref"
 version = "2.80dev"
 project.ext.threeDotVersion = "2.80.0.0"
@@ -27,6 +39,7 @@ task wrapper(type: Wrapper) {
     gradleVersion = '2.8'
 }
 
+
 repositories {
     jcenter()
 }
@@ -61,7 +74,7 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.5.1-1'
 
     compile 'mysql:mysql-connector-java:5.1.37'
-    compile 'org.postgresql:postgresql:9.4-1204-jdbc42'
+    compile 'org.postgresql:postgresql:9.4-1205-jdbc42'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
     compile fileTree(dir: 'lib', includes: ['*.jar'])

circle.yml

@@ -18,6 +18,7 @@ test:
   override:
     - TERM=dumb ./gradlew test
   post:
+    - TERM=dumb [[ -z "$COVERITY_ACCESS_TOKEN" ]] || ./gradlew coverityCheck || exit 0
     - mkdir -p $CIRCLE_TEST_REPORTS/junit/
     - find . -type f -regex ".*/build/test-results/.*xml" -exec cp {} $CIRCLE_TEST_REPORTS/junit/ \;
     - TERM=dumb ./gradlew jacocoTestReport coveralls

eclipse.gradle

@@ -1,5 +1,8 @@
 apply plugin: "eclipse"
 
+// ensure that source code is generated, otherwise class `BstLexer` cannot be found
+tasks.eclipseClasspath.dependsOn "generateSource"
+
 // workaround until https://issues.gradle.org/browse/GRADLE-2274 is resolved
 eclipseJdt << {
     File f = file('.settings/org.eclipse.core.resources.prefs')
@@ -18,7 +21,7 @@ tasks.cleanEclipse.doLast {
 
 tasks.eclipse.doFirst {
     File jdt_core_prefs = file("${project.projectDir}/.settings/org.eclipse.jdt.core.prefs")
-    // existance check doesn't work as gradle generates the file on its own
+    // existence check doesn't work as gradle generates the file on its own
     /* following entries are not written as they are generated by gradle:
             org.eclipse.jdt.core.compiler.debug.lineNumber=generate
             org.eclipse.jdt.core.compiler.debug.localVariable=generate