Merge remote-tracking branch 'upstream/master' into importerbackgroun…

…dtask

* upstream/master:
  Update guidelines-for-setting-up-a-local-workspace.md (#7339)
  Updates to colored group indicator for cited entries (#7173)
  Add some special fields as default columns (#7286)
  Add a more descriptive path when Directory cannot be found (#7232)
  Bump antlr4 from 4.9 to 4.9.1 (#7327)
  Bump unirest-java from 3.11.09 to 3.11.10 (#7329)
  Bump mockito-core from 3.6.28 to 3.7.0 (#7328)
  Bump antlr4-runtime from 4.9 to 4.9.1 (#7330)
  Bump gittools/actions from v0.9.7 to v0.9.8 (#7331)
  Update to gradle 6.8 (#7324)
  Link to GitHub contributors in about dialog (#7319)
  Fix snapcraft upload (#7263)

.gitattributes

@@ -5,9 +5,6 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# required for proper releasing
-AUTHORS text eol=lf
-
 # ensure that line endings of *.java, and *.properties are normalized
 *.java text
 *.properties text

.github/workflows/deployment.yml

@@ -50,12 +50,12 @@ jobs:
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.7
+        uses: gittools/actions/gitversion/setup@v0.9.8
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.7
+        uses: gittools/actions/gitversion/execute@v0.9.8
       - name: Set up JDK 15 for linux and mac
         uses: actions/setup-java@v1
         with:
@@ -162,12 +162,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.7
+        uses: gittools/actions/gitversion/setup@v0.9.8
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.7
+        uses: gittools/actions/gitversion/execute@v0.9.8
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.github/workflows/snap.yml

@@ -1,6 +1,7 @@
 name: Snap
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - snapcraft
@@ -28,12 +29,12 @@ jobs:
         uses: actions/checkout@v2
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
       # See snap/snapcraft.yml for details
-      - name: Build snap (1) Run build
+      - name: Run snapcraft build
         uses: snapcore/action-build@v1
         id: snapcraft
         with:
           snapcraft-args: "--debug"
-      - name: Build snap (2) Upload snap
+      - name: Upload snap
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: snapcore/action-publish@v1
         with:

.github/workflows/tests.yml

@@ -232,35 +232,3 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: gradle/wrapper-validation-action@v1
-  checkauthors:
-    name: "Validate AUTHORS"
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          # full checkout needed for authors generation
-          fetch-depth: 0
-      - name: "All authors of this PR listed in AUTHORS"
-        id: authors_check
-        shell: bash
-        run: |
-          git config user.name "JabRef Author Checker [bot]"
-          git config user.email "noreply@jabref.org"
-          ./scripts/generate-authors.sh
-          set +o pipefail
-          added=$(git diff HEAD --no-ext-diff --unified=0 -a --no-prefix | egrep "^\+[^+]" | sed "s/^\+//")
-          if [ -z "$added" ]; then
-            echo "No authors added"
-            exit 0
-          fi
-          echo "Authors found in this PR not listed in the AUTHORS file."
-          echo
-          echo "The JabRef maintainers will add the following name to the AUTHORS file"
-          echo
-          echo -e "$added"
-          echo
-          echo "In case you want to use a different one, please comment here and adjust your name in your git configuration for future commits"
-          echo
-          echo "Just adding yourself into the AUTHORS file does not help as it is overwritten by our script ./scripts/generate-authors."
-          echo "Read more on the AUTHORS file at found at https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits"
-          exit 1

CHANGELOG.md

@@ -103,6 +103,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the password for a shared SQL database was not remembered [#6869](https://github.com/JabRef/jabref/issues/6869)
 - We fixed an issue where newly added entires were not synced to a shared SQL database [#7176](https://github.com/JabRef/jabref/issues/7176)
 - We fixed an issue where the PDF-Content importer threw an exception when no DOI number is present at the first page of the PDF document [#7203](https://github.com/JabRef/jabref/issues/7203)
+- We fixed an issue where groups created from aux files did not update on file changes [#6394](https://github.com/JabRef/jabref/issues/6394)
 - We fixed an issue where authors that only have last names were incorrectly identified as institutes when generating citation keys [#7199](https://github.com/JabRef/jabref/issues/7199)
 - We fixed an issue where institutes were incorrectly identified as universities when generating citation keys [#6942](https://github.com/JabRef/jabref/issues/6942)
 

build.gradle

@@ -50,6 +50,10 @@ modularity.patchModule("test", "fastparse_2.12-1.0.0.jar")
 modularity.patchModule("test2", "fastparse-utils_2.12-1.0.0.jar")
 modularity.patchModule("test3", "sourcecode_2.12-0.1.4.jar")
 
+// Workaround for https://github.com/openjfx/javafx-gradle-plugin/issues/89
+// See also https://github.com/java9-modularity/gradle-modules-plugin/issues/165
+modularity.disableEffectiveArgumentsAdjustment()
+
 sourceSets {
     main {
         java {
@@ -119,8 +123,8 @@ dependencies {
     antlr3 'org.antlr:antlr:3.5.2'
     implementation 'org.antlr:antlr-runtime:3.5.2'
 
-    antlr4 'org.antlr:antlr4:4.9'
-    implementation 'org.antlr:antlr4-runtime:4.9'
+    antlr4 'org.antlr:antlr4:4.9.1'
+    implementation 'org.antlr:antlr4-runtime:4.9.1'
 
     implementation (group: 'org.apache.lucene', name: 'lucene-queryparser', version: '8.7.0') {
         exclude group: 'org.apache.lucene', module: 'lucene-sandbox'
@@ -157,7 +161,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.0.3'
 
     implementation 'org.jsoup:jsoup:1.13.1'
-    implementation 'com.konghq:unirest-java:3.11.09'
+    implementation 'com.konghq:unirest-java:3.11.10'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -194,7 +198,7 @@ dependencies {
     testImplementation 'net.bytebuddy:byte-buddy-parent:1.10.19'
     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'
-    testImplementation 'org.mockito:mockito-core:3.6.28'
+    testImplementation 'org.mockito:mockito-core:3.7.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.15.0'
@@ -269,8 +273,7 @@ processResources {
     filesMatching("build.properties") {
         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(", "),
+                "maintainers": new File('MAINTAINERS').readLines().findAll { !it.startsWith("#") }.join(", "),
                 "azureInstrumentationKey": System.getenv('AzureInstrumentationKey'),
                 "springerNatureAPIKey": System.getenv('SpringerNatureAPIKey'),
                 "astrophysicsDataSystemAPIKey": System.getenv('AstrophysicsDataSystemAPIKey'),

docs/contributing.md

@@ -47,17 +47,9 @@ In case you add keys to the changelog, please follow these rules:
 
 #### Author credits
 
-You will be given credit in the [`AUTHORS`](https://github.com/JabRef/jabref/blob/master/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`.
-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.
-Please make sure there are no duplicates or alternate spellings of your name listed.
-If you need to merge different Git usernames or email addresses you can do so by editing `.mailmap`.
-More information on this can be found via `man git-shortlog`.
-
 Please, **do not add yourself at JavaDoc's `@authors`**.
-The contribution information is tracked via the version control system.
+The contribution information is tracked via the version control system and shown at <https://github.com/JabRef/jabref/graphs/contributors>.
+We also link to the contributors page in our about dialog.
 
 Your contribution is considered being made under [MIT license](https://tldrlegal.com/license/mit-license).