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

CHANGELOG.md

@@ -12,21 +12,63 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
 
 ## [Unreleased]
 
+### Changed
+- Add options to close other/all databases in tab right-click menu
+- Implements #470: Show editor (as an alternative to author) and booktitle (as an alternative to journal) in the main table by default
+- Restore focus to last focused tab on start
+- Add ability to format/cleanup the date field
+- Add support for proxy authentication via VM args and GUI settings, this implements Feature Request #388
+- Move Bibtex and Biblatex mode switcher to File menu
+- Display active edit mode (BibTeX or Biblatex) at window title
+- Implements #444: The search is cleared by either clicking the clear-button or by pressing ESC with having focus in the search field. 
+
+### Fixed
+- Fixed #434: Revert to old 'JabRef' installation folder name instead of 'jabref'
+- Fixed #435: Retrieve non open access ScienceDirect PDFs via HTTP DOM
+- Fixed: Cleanup process aborts if linked file does not exists
+- Fixed #420: Reenable preference changes
+- Fixed #414: Rework BibLatex entry types with correct required and optional fields
+- Fixed #413: Help links in released jar version are not working
+- Fixes #412: Biblatex preserves capital letters, checking whether letters may be converted to lowercase within the Integrity Check action is obsolete.
+- Fixed #437: The toolbar after the search field is now correctly wrapped when using a small window size for JabRef
+- Fixed #438: Cut, Copy and Paste are now translated correctly in the menu
+
+### Removed
+- Removed file history size preference (never available from the UI)
+- Removed jstorImporter because it's hardly ever used, even Jstor.org doesn't support/export said format anymore
+
+
+
+
+## [3.0] - 2015-11-29
+
 ### Changed
  - Updated to support OpenOffice 4 and LibreOffice 5
+ - Add toolbar icon for deleting an entry, and move menu item for this action to BibTeX
  - Better support for IEEEtranBSTCTL entries
  - Quick selection of month in entry editor
  - Unknown entry types will be converted to 'Misc' (was 'Other' before).
  - EntryTypes are now clustered per group on the 'new entry' GUI screen.
  - Tab shows the minimal unique folder name substring if multiple database files share the same name
  - Added a page numbers integrity checker
  - Position and size of certain dialogs are stored and restored.
+ - Feature: Search Springer
  - 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
+ - Improvements to search:
+   - Search bar is now at the top
+   - A summary of the search result is shown in textual form in the search bar
+   - The search text field changes its color based on the search result (red if nothing is found, green if at least one entry is found)
+   - Autocompletion suggestions are shown in a popup
+   - Search options are available via a drop-down list, this implements Feature Request #853
+   - "Clear search" button also clears search field, this implements Feature Request #601
+   - Every search is done automatically (live) as soon as the search text is changed
+   - Search is local by default. To do a global search, one has to do a local search and then this search can be done globally as well, opening a new window. 
+   - The local search results can be shown in a new window. 
  - 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/))
@@ -63,6 +105,7 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
  - Show replaced journal abbreviations on console
  - Integrated [GVK-Plugin](http://www.gbv.de/wikis/cls/Jabref-GVK-Plugin)
  - The three options to manage file references are moved to their own separated group in the Tools menu. 
+ - Default preferences: Remote server (port 6050) always started on first JabRef instance. This prevents JabRef loaded twice when opening a bib file.
 
 ### Fixed
  - Fixed the bug that the file encoding was not correctly determined from the first (or second) line
@@ -99,6 +142,10 @@ to [sourceforge feature requests](https://sourceforge.net/p/jabref/features/) by
  - 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
+ - Remove incremental search
+ - Remove option to disable autocompleters for search and make this always one
+ - Remove option to highlight matches and make this always one when not using regex or grammar-based search
+ - Remove non-working web searches: JSTOR and Sciencedirect (planned to be fixed for the next release)
  - Remove option Tools -> Open PDF or PS which is replaced by Tools -> Open File
 
 ## 2.80 - never released
@@ -119,8 +166,9 @@ Since much functionality has changed during development, a release of this versi
 
 ## 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).
+The changelog of 2.11 and versions before is maintained as [text file](https://github.com/JabRef/jabref/blob/dev_2.11/CHANGELOG) in the [dev_2.11 branch](https://github.com/JabRef/jabref/tree/dev_2.11).
 
-[Unreleased]: https://github.com/JabRef/jabref/compare/dev_2.11...HEAD
+[Unreleased]: https://github.com/JabRef/jabref/compare/v3.0...HEAD
+[3.0]: https://github.com/JabRef/jabref/compare/v2.11.1...v3.0
 [dev_2.11]: https://github.com/JabRef/jabref/compare/v2.11.1...dev_2.11
 [2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 ## Understanding the basics
-We welcome contributions to JabRef and encourage to create a fork, make a patch, and create a pull request.
-Be sure to create a separate branch for each improvement you implement.
+We welcome contributions to JabRef and encourage to create a fork, clone, **create a new branch** (such as `fix-for-issue-121`), **work on the new branch - not master**, and create a pull request.
+Be sure to create a **separate branch** for each improvement you implement.
 Take a look at GitHub's excellent [help documentation] for a detailed explanation.
 
 We also have [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).

README.md

@@ -1,13 +1,13 @@
 # JabRef Development Version
 
-[![CircleCI](https://img.shields.io/circleci/project/JabRef/jabref.svg)](https://circleci.com/gh/JabRef/jabref)
+[![CircleCI](https://img.shields.io/circleci/project/JabRef/jabref/master.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)
 [![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%2Fgithub.com%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/)
+[![Download JabRef](https://img.shields.io/sourceforge/dw/jabref.svg)](http://sourceforge.net/projects/jabref/files/)
 [![Issue Stats](http://www.issuestats.com/github/jabref/jabref/badge/pr)](http://www.issuestats.com/github/jabref/jabref)
 [![Issue Stats](http://www.issuestats.com/github/jabref/jabref/badge/issue)](http://www.issuestats.com/github/jabref/jabref)
 
@@ -18,7 +18,9 @@ The intention of this branch is to move JabRef forward to modern technologies su
 
 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).
 
-The development builds are available at [builds.jabref.org](http://builds.jabref.org/)
+Development builds are available at [builds.jabref.org](http://builds.jabref.org/master/), the [latest release is available via GitHub](https://github.com/JabRef/jabref/releases/latest).
+
+Explanation of donation possibilities and usage of donations is available at our [donations page](https://github.com/JabRef/jabref/wiki/Donations).
 
 We use [install4j], the multi-platform installer builder.
 
@@ -108,19 +110,12 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 Requires [install4j].
 We've got an [Open Source License](https://www.ej-technologies.com/buy/install4j/openSource).
 
-We switched from [launch4j](http://launch4j.sourceforge.net/) and [NSIS](http://nsis.sourceforge.net), because install4j allows for JRE bundling and the taskbar pinning just works.
-
 To get a list of all targets, use `gradlew tasks`.
 ```
 releaseJar - Creates a Jar release.
 media - Creates executables and installers.
 ```
 
-To set the path to your local NSIS executable pass it via a Gradle property:
-
-`gradlew -PnsisExec=PATH ANY_RELEASE_TASK`
-Typically, this is `"C:\Program Files (x86)\NSIS\makensis.exe"` resulting in the command line `gradlew -PnsisExec="C:\Program Files (x86)\NSIS\makensis.exe" release`.
-
 All binaries are created inside the directory `build/releases`.
 
 ### Releasing Developer Releases
@@ -142,4 +137,4 @@ See the [LICENSE](LICENSE) for full details.
 JabRef also uses libraries distributed by other parties.
 See [external libraries](external-libraries.txt) for details.
 
-  [install4j]: https://www.ej-technologies.com/products/install4j/overview.html
+  [install4j]: https://www.ej-technologies.com/products/install4j/overview.html

build.gradle

@@ -14,7 +14,6 @@ buildscript {
 plugins {
     id 'com.github.johnrengelman.shadow' version '1.2.2'
     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 "1.4.742"
 }
@@ -40,8 +39,8 @@ gradle.taskGraph.whenReady { taskGraph ->
 }
 
 group = "net.sf.jabref"
-version = "3.0dev"
-project.ext.threeDotVersion = "3.0.0.0"
+version = "3.1dev"
+project.ext.threeDotVersion = "3.0.0.1"
 project.ext.install4jDir = hasProperty("install4jDir") ? getProperty("install4jDir") : (OperatingSystem.current().isWindows() ? 'C:/Program Files/install4j6' : 'install4j6')
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
@@ -90,16 +89,17 @@ dependencies {
     compile 'org.antlr:antlr4-runtime:4.5.1-1'
 
     compile 'mysql:mysql-connector-java:5.1.37'
-    compile 'org.postgresql:postgresql:9.4-1205-jdbc42'
+    compile 'org.postgresql:postgresql:9.4-1206-jdbc42'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
     compile fileTree(dir: 'lib', includes: ['*.jar'])
 
-    compile 'com.google.guava:guava:18.0'
+    compile 'com.google.guava:guava:19.0'
 
     compile 'commons-logging:commons-logging:1.2'
 
-    compile 'junit:junit:4.12'
+    testCompile 'junit:junit:4.12'
+    testCompile 'org.mockito:mockito-core:1.10.19'
 
     compile 'org.jsoup:jsoup:1.8.3'
     compile 'com.mashape.unirest:unirest-java:1.4.7'
@@ -348,7 +348,7 @@ task releaseJar(dependsOn: "shadowJar") {
 // see http://stackoverflow.com/a/27455099/873282 for an inspiration of this task
 // better solution: https://discuss.gradle.org/t/how-to-download-maven-dependencies-into-project-local-directory-and-set-eclipse-classpath/9851
 task getdeps(type: Copy) {
-    from (configurations.compile+configurations.testCompile) {
+    from (configurations.compile+configurations.antlr3+configurations.antlr4+configurations.testCompile) {
         include "*.jar"
     }
     into 'build/tmp/alldeps/'

circle.yml

@@ -7,6 +7,7 @@ dependencies:
     - scripts/prepare-install4j.sh
     - install4j6/bin/install4jc --verbose --license=$INSTALL4J_KEY
   override:
+    # We do this to decrease build time by using CircleCI's cache. See https://discuss.circleci.com/t/effective-caching-for-gradle/540 for a longer motivation.
     - TERM=dumb ./gradlew getdeps
   cache_directories:
     - "~/.install4j6"
@@ -21,9 +22,18 @@ test:
     - find . -type f -regex ".*/build/test-results/.*xml" -exec cp {} $CIRCLE_TEST_REPORTS/junit/ \;
     - TERM=dumb ./gradlew jacocoTestReport coveralls
     - bash <(curl -s https://codecov.io/bash)
+    # if you change something here, please also adapt deployment->release->commands
     - TERM=dumb ./gradlew -Pdev=true -Pinstall4jDir="install4j6" release --stacktrace || exit 0
     - timeout 580 scripts/upload-to-builds.jabref.org.sh || exit 0
 
+deployment:
+  release:
+    # we only do a simple check for SemVer and do not use a sophisticated check as presented at https://github.com/sindresorhus/semver-regex/blob/master/index.js
+    tag: /v[0-9]+(\.[0-9]+)*(-.+)?/
+    commands:
+      # we have to do a clean build as changing gradle's "procect.version" does not lead to a rebuild of resources (mirroring project.version)
+      - TERM=dumb ./gradlew -Pinstall4jDir="install4j6" clean release --stacktrace || exit 0
+
 general:
   artifacts:
     - "build/releases"

jabref.install4j

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <install4j version="6.0.4" transformSequenceNumber="5">
   <directoryPresets config="./buildres/JabRef.VisualElementsManifest.xml" />
-  <application name="JabRef" distributionSourceDir="" applicationId="0034-7691-1464-4754" mediaDir="build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="jabref" publisher="JabRef Community" publisherWeb="http://www.jabref.org/" version="3.0dev" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="true" macSignature="????" macVolumeId="780dfea2d33a0244" javaMinVersion="1.8" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
+  <application name="JabRef" distributionSourceDir="" applicationId="0034-7691-1464-4754" mediaDir="build/install4j" mediaFilePattern="${compiler:sys.shortName}_${compiler:sys.platform}_${compiler:sys.version}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="true" shortName="JabRef" publisher="JabRef Community" publisherWeb="http://www.jabref.org/" version="3.0dev" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="true" macSignature="????" macVolumeId="780dfea2d33a0244" javaMinVersion="1.8" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
     <languages skipLanguageSelection="true" languageSelectionInPrincipalLanguage="false">
       <principalLanguage id="en" customLocalizationFile="" />
       <additionalLanguages>