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

calixtus · Oct 12, 2019 · 7a39096 · 7a39096
2 parents a844c5c + d4d3764
commit 7a39096
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diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -45,7 +45,7 @@ jobs:
     - name: Set up JDK
       uses: actions/setup-java@v1
       with:
-        java-version: 11.0.4
+        java-version: 12.0.2
     - name: Download jpackage
       # We need to download jpackage from https://jdk.java.net/jpackage/
       run: |
@@ -88,8 +88,8 @@ jobs:
       env:
         SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
       run: |
-          docker run -v $(pwd):$(pwd) -t lyzardking/snapcraft-bionic sh -c "apt update -qq && cd $(pwd) && snapcraft && mv jabref*.snap build/distribution/"
-          # cd build/distribution/ && mdkir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg && snapcraft push --release=beta *.snap
+          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: Upload to builds.jabref.org
       uses: garygrossgarten/github-action-scp@release

diff --git a/.travis.yml b/.travis.yml
@@ -1,6 +1,6 @@
 language: java
 jdk:
-  - openjdk11
+  - openjdk12
 
 # we test at Ubuntu Trusty (Ubuntu 14.04 LTS)
 # see https://docs.travis-ci.com/user/trusty-ci-environment/

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,13 +22,15 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where it was no longer possible to connect to LibreOffice. [#5261](https://github.com/JabRef/jabref/issues/5261)
 - The "All entries group" is no longer shown when no library is open.
 - We fixed an exception which occurred when closing JabRef. [#5348](https://github.com/JabRef/jabref/issues/5348)
+- We fixed a few problems that prevented JabFox to communicate with JabRef. [#4737](https://github.com/JabRef/jabref/issues/4737) [#4303](https://github.com/JabRef/jabref/issues/4303)
 - We fixed an error where the groups containing an entry loose their highlight color when scrolling. [#5022](https://github.com/JabRef/jabref/issues/5022) 
 - We fixed an error where an exception was thrown when merging entries. [#5169](https://github.com/JabRef/jabref/issues/5169)
 - After assigning an entry to a group, the item count is now properly colored to reflect the new membership of the entry. [#3112](https://github.com/JabRef/jabref/issues/3112)
 - The group panel is now properly updated when switching between libraries (or when closing/opening one). [#3142](https://github.com/JabRef/jabref/issues/3142)
 - We fixed an error where the number of matched entries shown in the group pane was not updated correctly. [#4441](https://github.com/JabRef/jabref/issues/4441)
 - We fixed an issue where empty keywords lead to a strange display of automatic keyword groups. [#5333](https://github.com/JabRef/jabref/issues/5333)
 - We fixed an error where the default color of a new group was white instead of dark gray. [#4868](https://github.com/JabRef/jabref/issues/4868)
+- We fixed an issue where the first field in the entry editor got the focus while performing a different action (like searching). [#5084](https://github.com/JabRef/jabref/issues/5084)
 - We fixed an error mentioning "javafx.controls/com.sun.javafx.scene.control" that was thrown when interacting with the toolbar.
 - We fixed an error where a cleared search was restored after switching libraries. [#4846](https://github.com/JabRef/jabref/issues/4846) 
 - We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,28 +1,37 @@
+# Contributing Guide
+
 After reading through this guide, check out some good first issues to contribute to by clicking here: [Good First Issues](https://github.com/JabRef/jabref/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22)
 
+
 ## Understanding the basics
+
 We welcome contributions to JabRef and encourage you to follow the GitHub workflow specified below. If you are not familiar with this type of workflow, take a look at GitHub's excellent overview on the [GitHub flow](https://guides.github.com/introduction/flow/index.html) and the explanation of [Feature Branch Workflow](https://atlassian.com/git/tutorials/comparing-workflows#feature-branch-workflow) for the idea behind this kind of development.
 1. Get the JabRef code on your local machine. Detailed instructions about this step can be found in our [guidelines for setting up a local workspace](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
     1. Fork the JabRef into your GitHub account.
     2. Clone your forked repository on your local machine.
-3. **Create a new branch** (such as `fix-for-issue-121`). Be sure to create a **separate branch** for each improvement you implement.
-4. Do your work on the **new branch - not the master branch.** Refer to our [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) if you have questions about your implementation.
-5. Create a pull request. For an overview of pull requests, take a look at GitHub's [pull request help documentation](https://help.github.com/articles/about-pull-requests/).
+2. **Create a new branch** (such as `fix-for-issue-121`). Be sure to create a **separate branch** for each improvement you implement.
+3. Do your work on the **new branch - not the master branch.** Refer to our [code howtos](https://github.com/JabRef/jabref/wiki/Code-Howtos) if you have questions about your implementation.
+4. Create a pull request. For an overview of pull requests, take a look at GitHub's [pull request help documentation](https://help.github.com/articles/about-pull-requests/).
+5. In case your pull request is not yet complete or not yet ready for review, consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) instead.
 
 In case you have any questions, do not hesitate to write one of our [JabRef developers](https://github.com/orgs/JabRef/teams/developers) an email. We should also be online at [gitter](https://gitter.im/JabRef/jabref).
 
 
 ## Formal requirements for a pull request
+
 The main goal of the formal requirements is to provide credit to you and to be able to understand the patch.
 
+
 ### 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.
 
 
 #### Key format
+
 Example: `<kbd>Ctrl</kbd> + <kbd>Enter</kbd>`
 
 In case you add keys to the changelog, please follow these rules:
@@ -34,8 +43,9 @@ In case you add keys to the changelog, please follow these rules:
 
 
 ### Author credits
-You will be given credit in the `AUTHORS` file in the root of the repository and the 'About' pages inside the main application.
-We will periodically update the contributors list inside `AUTHORS`.
+
+You will be given credit in the [`AUTHORS`](AUTHORS) file in the root of the repository and the 'About' pages inside the main application.
+We will periodically update the contributors list inside [`AUTHORS`](AUTHORS).
 This is done by an automatic shell script `scripts/generate-authors.sh`.
 
 If you want to add yourself directly with your pull request please run this script.
@@ -50,18 +60,21 @@ Your contribution is considered being made under [MIT license](https://tldrlegal
 
 
 ### Write a good commit message
+
 See [good commit message] or [commit guidelines section of Pro Git].
-The first line of your commit message is automatically taken as title for the pull-request.
+The first line of your commit message is automatically taken as the title for the pull-request.
 All other lines make up the body of the pull request. Add the words `fixes #xxx` to your PR to auto-close the corresponding issue.
 
 
 ### Test your code
-We know that writing test cases causes a lot of time.
+
+We know that writing test cases takes a lot of time.
 Nevertheless, we rely on our test cases to ensure that a bug fix or a feature implementation doesn't break anything.
-In case you do not have time to add a test case, we nevertheless ask you to run `gradlew check` to ensure that your change doesn't break anything else.
+In case you do not have time to add a test case, we nevertheless ask you to at least run `gradlew check` to ensure that your change doesn't break anything else.
 
 
 ### When adding a library
+
 Please try to use a version available at jCenter and add it to `build.gradle`.
 In any case, describe the library at [external-libraries.txt](external-libraries.txt).
 We need that information for our package maintainers (e.g., those of the [debian package](https://tracker.debian.org/pkg/jabref)).
@@ -71,6 +84,7 @@ You can see the result in `build\resources\main\help\en\About.html` or when clic
 
 
 ### When making an architectural decision
+
 In case you add a library or do major code rewrites, we ask you to document your decision.
 Recommended reading: <https://adr.github.io/>.
 
@@ -90,8 +104,9 @@ because <additional rationale>.
 
 
 ### When adding a new Localization.lang entry
-Add new `Localization.lang("KEY")` to Java file.
-Tests fail. In the test output a snippet is generated which must be added to the English translation file.
+
+Add new `Localization.lang("KEY")` to a Java file.
+The tests will fail. In the test output a snippet is generated, which must be added to the English translation file.
 
 Example:
 
@@ -105,7 +120,7 @@ Expected :[]
 Actual   :[Opens\ JabRef's\ Twitter\ page (src\main\java\org\jabref\gui\JabRefFrame.java LANG)]
 ```
 
-Add snippet to English translation file located at `src/main/resources/l10n/JabRef_en.properties`.
+Add the above snippet to the English translation file located at `src/main/resources/l10n/JabRef_en.properties`.
 [Crowdin](http://translate.jabref.org/) will automatically pick up the new string and add it to the other translations.
 
 You can also directly run the specific test in your IDE.
@@ -114,10 +129,12 @@ Find more information in the [JabRef Wiki](https://github.com/JabRef/jabref/wiki
 
 
 ### Create a pull request
+
 Create a pull request on GitHub.
 For text inspirations, consider [How to write the perfect pull request](https://github.com/blog/1943-how-to-write-the-perfect-pull-request).
 
-You can add the prefix `[WIP]` to indicate that the pull request is not yet complete, but you want to discuss something or inform about the current state of affairs.
+If you want to indicate that a pull request is not yet complete **before** creating the pull request, you may consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+Alternatively, once the PR has been created, you can add the prefix `[WIP]` (which stands for "Work in Progress") to indicate that the pull request is not yet complete, but you want to discuss something or inform about the current state of affairs.
 
 
 [commit guidelines section of Pro Git]: http://git-scm.com/book/en/Distributed-Git-Contributing-to-a-Project#Commit-Guidelines

diff --git a/build.gradle b/build.gradle
@@ -21,7 +21,7 @@ plugins {
     id "com.simonharrer.modernizer" version '1.8.0-1'
     id 'me.champeau.gradle.jmh' version '0.4.8'
     //id 'net.ltgt.errorprone' version '0.8.1'
-    id 'com.github.ben-manes.versions' version '0.25.0'
+    id 'com.github.ben-manes.versions' version '0.26.0'
     id 'org.javamodularity.moduleplugin' version '1.5.0'
     id 'org.openjfx.javafxplugin' version '0.0.8'
     id 'org.beryx.jlink' version '2.16.0'
@@ -47,8 +47,8 @@ apply from: 'eclipse.gradle'
 
 group = "org.jabref"
 version = "5.0.0"
-sourceCompatibility = 11
-targetCompatibility = 11
+sourceCompatibility = 12
+targetCompatibility = 12
 mainClassName = "$moduleName/org.jabref.JabRefLauncher"
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode
@@ -102,7 +102,7 @@ configurations {
 }
 
 javafx {
-    version = "11.0.2"
+    version = "13"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -165,12 +165,12 @@ dependencies {
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-20190915.182410-364'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-20190915.182922-250'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-20190915.182837-57'
-    implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '3.0.0-20190915.182113-372'
-    compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
-    annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
+    compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
+    compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-SNAPSHOT'
+    compile group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-SNAPSHOT'
+    implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '3.0.0-SNAPSHOT'
+    compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
+    annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
 
     compile 'de.undercouch:citeproc-java:1.0.1'
 
@@ -198,19 +198,18 @@ dependencies {
         exclude module: "log4j-core"
     }
 
+
+    testCompile 'io.github.classgraph:classgraph:4.8.47'
     testCompile 'junit:junit:4.12'
     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:1.10.1'
-    testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
-    testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-20190915.182552-364'
+    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 'com.github.tomakehurst:wiremock:2.24.1'
-    testCompile ('org.reflections:reflections:0.9.11') {
-        exclude module: "jsr305"
-    }
     testCompile 'org.xmlunit:xmlunit-core:2.6.3'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.3'
     testCompile 'com.tngtech.archunit:archunit-junit5-api:0.11.0'
@@ -507,14 +506,11 @@ modernizer {
 }
 
 // Release tasks
-task generateFinalJabRefPS1File(type: Copy) {
-    from('buildres') {
-        include 'JabRef.ps1'
-    }
-    into 'build'
-    filter(org.apache.tools.ant.filters.ReplaceTokens, tokens: [jabRefJarFileName: jar.archiveName])
+task deleteInstallerTemp(type: Delete) {
+    delete "$buildDir/installer"
 }
 
+jpackage.dependsOn deleteInstallerTemp
 jlink {
     options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages']
     launcher {
@@ -585,7 +581,9 @@ jlink {
                     '--app-version', "${project.version}",
                     '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
                     '--win-dir-chooser',
-                    '--win-shortcut'
+                    '--win-shortcut',
+                    '--temp', "$buildDir/installer",
+                    '--resource-dir', "${projectDir}/buildres/windows"
             ]
         }
 
@@ -595,7 +593,9 @@ jlink {
             ]
             installerOptions = [
                     '--vendor', 'JabRef',
-                    '--app-version', "${project.version}"
+                    '--app-version', "${project.version}",
+                    //'--temp', "$buildDir/installer",
+                    '--resource-dir', "${projectDir}/buildres/linux"
             ]
         }
 
@@ -611,6 +611,35 @@ jlink {
     }
 }
 
+if (OperatingSystem.current().isWindows()) {
+    tasks.jpackageImage.doLast {
+        copy {
+            from("${projectDir}/buildres/windows") {
+                include "jabref.json", "JabRefHost.bat", "JabRefHost.ps1"
+            }
+            into "$buildDir/distribution/JabRef"
+        }
+    }
+}
+
+if (OperatingSystem.current().isLinux()) {
+    tasks.jpackageImage.doLast {
+        copy {
+            from("${projectDir}/buildres/linux") {
+                include "org.jabref.jabref.json", "jabrefHost.py"
+            }
+            into "$buildDir/distribution/JabRef/lib"
+        }
+    }
+}
+
+// Delete unnecessary folder in application image
+// TODO: Remove this workaround as soon as https://github.com/beryx/badass-jlink-plugin/issues/51 is fixed
+task deleteModsFolder(type: Delete) {
+    delete "$buildDir/distribution/JabRef/app/mods"
+}
+deleteModsFolder.shouldRunAfter jpackageImage
+
 jmh {
     warmupIterations = 5
     iterations = 10