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

* upstream/master:
  Fix eclipse classpath build file
  New translations JabRef_en.properties (French) (#5709)
  Check for existing master branch
  Disable failing MathSciNet test due to missing subscription
  Try to force creating reflog
  Change travis to github in Readme
  Use GitVersion to increment build numbers (#5682)
  New Crowdin translations (#5687)
  Bump checkstyle from 8.26 to 8.27 (#5694)
  Bump byte-buddy-parent from 1.10.3 to 1.10.4
  Bump classgraph from 4.8.54 to 4.8.58
  Bump unirest-java from 3.1.04 to 3.2.00
  Bump richtextfx from 0.10.2 to 0.10.3
  Bump mockito-core from 3.1.0 to 3.2.0
  Update JavaFX (#5690)
  Run outdated dependency check after dpendabot
  Update outdatedDependencies.md

.github/outdatedDependencies.md

@@ -2,5 +2,4 @@
 title: Outdated dependencies
 labels: code-quality, dependencies
 ---
-There are outdated dependencies! 
-See https://github.com/JabRef/jabref/actions?query=is%3Afailure for details.
+[There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22) 

.github/workflows/check-outdated-dependencies.yml

@@ -2,7 +2,7 @@ name: Check dependencies
 
 on: 
  schedule:
- - cron: '0 0 * * 0' # Run every Sunday
+ - cron: '0 0 * * TUE' # Run every Tuesday (after dependabot, which runs Monday)
 
 jobs:
  checkDependencies:

.github/workflows/deployment.yml

@@ -30,18 +30,24 @@ jobs:
 
  steps:
  - name: Checkout source
- uses: actions/checkout@v1
+ uses: actions/checkout@v2-beta
  with:
- depth: 1
- submodules: false
- - name: Extract branch name
- shell: bash
+ fetch-depth: 0
+ - name: Fetch tags and master for GitVersion
  run: |
- ref=${GITHUB_REF#refs/heads/}
- ref=${ref#refs/pull/}
- ref=${ref%/merge}
- echo "##[set-output name=branch;]${ref}"
- id: extract_branch
+ git fetch --tags origin
+ git rev-parse --verify master
+ if (-not $?) {
+ git branch --force --create-reflog master origin/master
+ }
+ shell: pwsh
+ - name: Install GitVersion
+ uses: gittools/actions/setup-gitversion@v0.3
+ with:
+ versionSpec: '5.1.2'
+ - name: Run GitVersion
+ id: gitversion
+ uses: gittools/actions/execute-gitversion@v0.3
  - name: Set up JDK
  uses: actions/setup-java@v1
  with:
@@ -82,11 +88,11 @@ jobs:
  zip.close()
  shell: python
  - name: Build runtime image
- run: ./gradlew -Pdev=true jlinkZip
+ run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
  - name: Build installer
  run: |
  export BADASS_JLINK_JPACKAGE_HOME="${GITHUB_WORKSPACE}${{ matrix.jdk14Path }}"
- ./gradlew -Pdev=true jpackage
+ ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
  shell: bash
  - name: Add installer as artifact
  uses: actions/upload-artifact@master
@@ -97,18 +103,23 @@ jobs:
  run: ${{ matrix.archivePortable }}
  shell: bash
  - name: Build and publish snap
- if: matrix.os == 'ubuntu-latest' && steps.extract_branch.outputs.branch == 'master'
+ if: matrix.os == 'ubuntu-latest' && steps.gitversion.outputs.branchName == 'master'
  env:
  SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
  run: |
  mkdir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg
  docker run -v $(pwd):$(pwd) -t lyzardking/snapcraft-bionic sh -c "apt update -qq && cd $(pwd) && snapcraft && mv jabref*.snap build/distribution/ && snapcraft push build/distribution/jabref*.snap --release edge || true"
  shell: bash
+ - name: Rename files
+ run: |
+ get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
+ get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
+ shell: pwsh
  - name: Upload to builds.jabref.org
  uses: garygrossgarten/github-action-scp@release
  with:
  local: build/distribution
- remote: www/${{ steps.extract_branch.outputs.branch }}
+ remote: www/${{ steps.gitversion.outputs.branchName }}
  host: builds.jabref.org
  username: builds_jabref_org
  privateKey: ${{ secrets.buildJabRefPrivateKey }}

GitVersion.yml

@@ -0,0 +1,2 @@
+assembly-versioning-format: '{major}.{minor}.{buildmetadata}'
+assembly-informational-format: '{major}.{minor}{PreReleaseTagWithDash}--{CommitDate}--{ShortSha}'

README.md

@@ -1,6 +1,7 @@
 # JabRef Bibliography Management
 
-[![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
+[![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
+[![Build Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
 [![Crowdin](https://d322cqt584bo4o.cloudfront.net/jabref/localized.svg)](https://crowdin.com/project/jabref)
@@ -94,7 +95,7 @@ When you want to develop, it is necessary to generate additional sources using `
 and then generate the Eclipse `gradlew eclipse`.
 For IntelliJ IDEA, just import the project via a Gradle Import by pointing at the `build.gradle`.
 
-`gradlew test` executes all tests. We use [Travis CI](https://travis-ci.org/) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Travis will report any other failure.
+`gradlew test` executes all tests. We use [Github Actions](https://github.com/JabRef/jabref/actions) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Github will report any other failure.
 
  [BibTeX]: https://www.ctan.org/pkg/bibtex
  [Biblatex]: https://www.ctan.org/pkg/biblatex

build.gradle

@@ -44,7 +44,7 @@ apply plugin: LocalizationPlugin
 apply from: 'eclipse.gradle'
 
 group = "org.jabref"
-version = "5.0.0"
+version = project.findProperty('projVersion') ?: '100.0.0'
 
 sourceCompatibility = 13
 targetCompatibility = 13
@@ -102,7 +102,7 @@ configurations {
 }
 
 javafx {
- version = "13"
+ version = "13.0.1"
  modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -163,13 +163,13 @@ dependencies {
  compile 'de.saxsys:mvvmfx:1.8.0'
  compile 'org.fxmisc.easybind:easybind:1.0.3'
  compile 'org.fxmisc.flowless:flowless:0.6.1'
- compile 'org.fxmisc.richtext:richtextfx:0.10.2'
+ compile 'org.fxmisc.richtext:richtextfx:0.10.3'
  compile group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
  compile 'com.jfoenix:jfoenix:9.0.9'
  compile 'org.controlsfx:controlsfx:11.0.0'
 
  compile 'org.jsoup:jsoup:1.12.1'
- compile 'com.konghq:unirest-java:3.1.04'
+ compile 'com.konghq:unirest-java:3.2.00'
 
  compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
  compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -206,15 +206,15 @@ dependencies {
  }
 
 
- testCompile 'io.github.classgraph:classgraph:4.8.54'
+ testCompile 'io.github.classgraph:classgraph:4.8.58'
  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:1.10.3'
+ testCompile 'net.bytebuddy:byte-buddy-parent:1.10.4'
  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:3.1.0'
+ testCompile 'org.mockito:mockito-core:3.2.0'
  //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
  testCompile 'org.xmlunit:xmlunit-core:2.6.3'
  testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
@@ -225,7 +225,7 @@ dependencies {
  testCompile "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
  testCompile "org.hamcrest:hamcrest-library:2.2"
 
- checkstyle 'com.puppycrawl.tools:checkstyle:8.26'
+ checkstyle 'com.puppycrawl.tools:checkstyle:8.27'
  xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.2'
  jython 'org.python:jython-standalone:2.7.1'
 }
@@ -283,7 +283,7 @@ processResources {
  filteringCharset = 'UTF-8'
 
  filesMatching("build.properties") {
- expand(version: createVersionString(),
+ expand(version: project.findProperty('projVersionInfo') ?: '100.0.0',
  "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
  "authors": new File('AUTHORS').readLines().findAll { !it.startsWith("#") }.join(", "),
  "developers": new File('DEVELOPERS').readLines().findAll { !it.startsWith("#") }.join(", "),
@@ -723,35 +723,3 @@ task bundleLibreOffice(type: Jar) {
  destinationDir = file('lib')
  archiveName = 'libreoffice.jar'
 }
-
-// Returns the value of project.version in production and a string of the format VERSION-dev--DATE--BRANCH--GIT_HASH for development versions
-def createVersionString() {
- if (hasProperty('dev')) {
- String command = "git log --pretty=format:%cd--%h -n 1 --date=short"
- String commitInfo
- if (OperatingSystem.current().isWindows()) {
- commitInfo = "cmd /c $command".execute().in.text
- } else {
- commitInfo = command.execute().in.text
- }
-
- // determine branch
- command = "git symbolic-ref -q --short HEAD"
- String branchName
- if (OperatingSystem.current().isWindows()) {
- branchName = "cmd /c $command".execute().in.text
- } else {
- branchName = command.execute().in.text
- }
- // A newline is returned. Remove it. (trim())
- // In the context of github, the branch name could be something like "pull/277"
- // "/" is an illegal character. To be safe, all illegal filename characters are replaced by "_"
- // http://stackoverflow.com/a/15075907/873282 describes the used pattern.
- branchName = branchName.trim().replaceAll("[^a-zA-Z0-9.-]", "_")
-
- // first the date (%cd), then the branch name, and finally the commit id (%h)
- return project.version + "-dev--" + commitInfo.substring(0, 10) + "--" + branchName + "--" + commitInfo.substring(12)
- } else {
- return project.version
- }
-}

eclipse.gradle

@@ -28,6 +28,9 @@ eclipse {
  javafxcontrols.entryAttributes['add-exports'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref';
  javafxcontrols.entryAttributes['add-opens'] = 'javafx.controls/com.sun.javafx.scene.control=org.jabref:javafx.controls/com.sun.javafx.scene.control.behavior=org.jabref:javafx.controls/javafx.scene.control=org.jabref';
 
+ def javafxgraphics = entries.find { isJavafxGraphics(it) };
+ javafxgraphics.entryAttributes['add-opens'] = 'javafx.graphics/javafx.scene=org.controlsfx.controls';
+
  def graaltruffle = entries.find{ isTruffleGraal(it) } ;
  graaltruffle.entryAttributes['add-exports'] = 'com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle';
 
@@ -56,6 +59,8 @@ boolean isControlsfx(entry) { return entry.properties.path.contains('controlsfx'
 
 boolean isJavafxControls(entry) { return entry.properties.path.contains('javafx-controls'); }
 
+boolean isJavafxGraphics(entry) { return entry.properties.path.contains('javafx-graphics'); }
+
 boolean isTruffleGraal(entry) {return entry.properties.path.contains('org.graalvm.regex'); }
 
 // add formatter and cleanup settings to Eclipse settings

src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java

@@ -49,9 +49,6 @@ public BracketedPattern() {
  this.pattern = null;
  }
 
- /**
- * @param bibentry
- */
  public BracketedPattern(String pattern) {
  this.pattern = pattern;
  }

src/main/java/org/jabref/logic/bst/BibtexTextPrefix.java

@@ -20,14 +20,9 @@ private BibtexTextPrefix() {
  }
 
  /**
- *
- * @param numOfChars
- * @param toPrefix
  * @param warn may-be-null
- * @return
  */
  public static String textPrefix(int inNumOfChars, String toPrefix, Warn warn) {
-
  int numOfChars = inNumOfChars;
  StringBuilder sb = new StringBuilder();
 

src/main/java/org/jabref/logic/openoffice/OOBibStyle.java

@@ -343,7 +343,6 @@ public boolean isValid() {
  * Parse a line providing bibliography structure information for an entry type.
  *
  * @param line The string containing the structure description.
- * @throws IOException
  */
  private void handleStructureLine(String line) {
  int index = line.indexOf('=');
@@ -369,7 +368,6 @@ private void handleStructureLine(String line) {
  * Parse a line providing a property name and value.
  *
  * @param line The line containing the formatter names.
- * @throws IOException
  */
  private void handlePropertiesLine(String line, Map<String, Object> map) {
  int index = line.indexOf('=');
@@ -393,9 +391,6 @@ private void handlePropertiesLine(String line, Map<String, Object> map) {
 
  /**
  * Parse a line providing a journal name for which this style is valid.
- *
- * @param line
- * @throws IOException
  */
  private void handleJournalsLine(String line) {
  if (!line.trim().isEmpty()) {