Merge remote-tracking branch 'upstream/main' into jabrefonline

* upstream/main: (181 commits) Add of ADRs 22 and 23 (#8256) [Bot] Update CSL styles (#8245) Replace styfle/[email protected] by GitHub's "concurrency" feature (#8243) Bump gittools/actions from 0.9.10 to 0.9.11 (#8248) Bump commons-cli from 1.4 to 1.5.0 (#8250) Bump byte-buddy-parent from 1.12.0 to 1.12.1 (#8249) Bump antlr4 from 4.9.2 to 4.9.3 (#8251) Bump archunit-junit5-api from 0.21.0 to 0.22.0 (#8252) Fix search: NOT binds more than AND (#8241) New Crowdin updates (#8240) Make PdfGrobiImporterTest as FetcherTest Oobranch g : add actions (#7792) Fix mixed CRLF / CR (#8238) Fix "Library has changed externally" with CRLF markers (#8239) Fix for issue 8198, 8133 (#8229) Added more unit tests in AuthorTest (#8214) Add confirmation dialog for empty entries in JabRef (#8218) Fix entry editor column visibility (#8232) Use regexp to remove non-ASCII characters from DOI and inform user when data for valid DOI does not exist #8127 (#8228) Fix exception for search flags (#8237) ...
JabRef · Nov 19, 2021 · 6aad7f2 · 6aad7f2
2 parents 567a378 + 578c106
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -27,7 +27,7 @@ body:
       options:
         - Windows
         - GNU / Linux
-        - mac OS
+        - macOS
         - Other (please describe below)
     validations:
       required: true
@@ -36,7 +36,7 @@ body:
     attributes:
       label: Details on version and operating system
       description: OS Version, distribution, desktop environment, older JabRef version etc.
-      placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / Mac OS 10.14
+      placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / macOS 10.14
     validations:
       required: false
 
@@ -70,10 +70,13 @@ body:
       value: |
         ...
         <details>
+
         <summary>Log File</summary>
+
         ```
         Paste an excerpt of your log file here
         ```
+
         </details>
     validations:
       required: false
diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
@@ -7,6 +7,7 @@ on:
   schedule:
     # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
     - cron: "0 9 1 * *"
+  workflow_dispatch:
 
 jobs:
   markdown-link-check:

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -26,6 +26,10 @@ env:
   GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
   JAVA_OPTS: -Xmx4g
 
+concurrency:
+  group: ${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     strategy:
@@ -45,21 +49,17 @@ jobs:
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v2
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -155,12 +155,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

diff --git a/.github/workflows/gource.yml b/.github/workflows/gource.yml
@@ -6,6 +6,7 @@ on:
       - gource
   schedule:
     - cron:  '15 3 1 1,4,7,10 *'
+  workflow_dispatch:
 
 jobs:
   action:

diff --git a/.github/workflows/snap.yml b/.github/workflows/snap.yml
@@ -9,6 +9,10 @@ on:
    # run on each day
   - cron: "33 4 * * *"
 
+concurrency:
+  group: snap-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -20,12 +20,17 @@ on:
   schedule:
     # run on each Wednesday
     - cron: '2 3 * * 3'
+  workflow_dispatch:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
 
+concurrency:
+  group: fetcher-tests-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   fetchertests:
     name: Fetcher tests

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -3,9 +3,11 @@ name: Tests
 on:
   push:
     branches:
-      - master
+      - main
+      - main-release
   pull_request:
     # always run on pull requests
+  workflow_dispatch:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
@@ -14,15 +16,15 @@ env:
   GRADLE_OPTS: -Xmx4g
   JAVA_OPTS: -Xmx4g
 
+concurrency:
+  group: tests-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   checkstyle:
     name: Checkstyle
     runs-on: ubuntu-latest
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
@@ -41,7 +43,7 @@ jobs:
       - name: Run markdown-lint
         uses: avto-dev/markdown-lint@v1
         with:
-          args: CHANGELOG.md CONTRIBUTING.md README.md docs/
+          args: CHANGELOG.md CONTRIBUTING.md README.md
           config: '.markdownlint.yml'
   tests:
     name: Unit tests

diff --git a/.markdownlint.yml b/.markdownlint.yml
@@ -1,24 +1,8 @@
 default: true
 
-# Using h2 has side effects in GitBook's toc. Thus, we sometimes switch from h1 to h3
-MD001: false
-
-MD012:
-  # 2 are required, because GitBook adss two blank lines at the end of a file
-  maximum: 2
-
+# allow arbitrary line length
 MD013: false
 
-# The FAQs state questions - we allow them
-MD026:
-  punctuation: ".,;:!"
-
-# not supported by gitbook
-MD031: false
-
 MD033:
   # we have <a> tags with ids and superscript
   allowed_elements: ['a', 'kbd', 'sup']
-
-# seems to be unsupported by gitbook anymore
-MD045: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added confirmation dialog when user wants to close a library where any empty entires are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
 - We added import support for CFF files. [#7945](https://github.com/JabRef/jabref/issues/7945)
 - We added the option to copy the DOI of an entry directly from the context menu copy submenu. [#7826](https://github.com/JabRef/jabref/issues/7826)
 - We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)
@@ -23,9 +24,13 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We readded the possibility to keep the search string when switching tabs. It is implemented by a toggle button. [#4096](https://github.com/JabRef/jabref/issues/4096#issuecomment-575986882)
 - We allowed the user to also preview the available citation styles in the preferences besides the selected ones [#8108](https://github.com/JabRef/jabref/issues/8108)
 - We added an option to search the available citation styles by name in the preferences [#8108](https://github.com/JabRef/jabref/issues/8108)
+- We added an option to generate bib-entries from ID through a popover in the toolbar. [#4183](https://github.com/JabRef/jabref/issues/4183)
 
 ### Changed
 
+- Local library settings may overwrite the setting "Search and store files relative to library file location" [#8179](https://github.com/JabRef/jabref/issues/8179)
+- The option "Fit table horizontally on screen" in the "Entry table" preferences is now disabled by default [#8148](https://github.com/JabRef/jabref/pull/8148)
+- We improved the preferences and descriptions in the "Linked files" preferences tab [#8148](https://github.com/JabRef/jabref/pull/8148)
 - We slightly changed the layout of the Journal tab in the preferences for ui consistency. [#7937](https://github.com/JabRef/jabref/pull/7937)
 - The JabRefHost on Windows now writes a temporary file and calls `-importToOpen` instead of passing the bibtex via `-importBibtex`. [#7374](https://github.com/JabRef/jabref/issues/7374), [JabRef Browser Ext #274](https://github.com/JabRef/JabRef-Browser-Extension/issues/274)
 - We reordered some entries in the right-click menu of the main table. [#6099](https://github.com/JabRef/jabref/issues/6099)
@@ -35,10 +40,19 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The metadata-to-pdf actions now also embeds the bibfile to the PDF. [#8037](https://github.com/JabRef/jabref/pull/8037)
 - The snap was updated to use the core20 base and to use lzo compression for better startup performance [#8109](https://github.com/JabRef/jabref/pull/8109)
 - We improved the Drag and Drop behavior in the "Customize Entry Types" Dialog [#6338](https://github.com/JabRef/jabref/issues/6338)
+- When determining the URL of an ArXiV eprint, the URL now points to the version [#8149](https://github.com/JabRef/jabref/pull/8149)
+- We Included all standard fields with citation key when exporting to Old OpenOffice/LibreOffice Calc Format [#8176](https://github.com/JabRef/jabref/pull/8176)
+- In case the database is encoded with `UTF8`, the `% Encoding` marker is not written anymore
+- The written `.bib` file has the same line endings [#390](https://github.com/koppor/jabref/issues/390)
+- The written `.bib` file always has a final line break
+- The written `.bib` file keeps the newline separator of the loaded `.bib` file
+- We present options to manually enter an article or return to the New Entry menu when the fetcher DOI fails to find an entry for an ID [#7870](https://github.com/JabRef/jabref/issues/7870)
+- We trim white space and non-ASCII characters from DOI [#8127](https://github.com/JabRef/jabref/issues/8127)
+- The duplicate checker now inspects other fields in case no difference in the required and optional fields are found.
 
 ### Fixed
 
-- We fixed an issue where an exception ocurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
+- We fixed an issue where an exception occurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
 - We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
 - We fixed some icons that were drawn in the wrong color when JabRef used a custom theme. [#7853](https://github.com/JabRef/jabref/issues/7853)
 - We fixed an issue where the `Aux file` on `Edit group` doesn't support relative sub-directories path to import. [#7719](https://github.com/JabRef/jabref/issues/7719).
@@ -47,10 +61,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the icons in the search bar had the same color, toggled as well as untoggled. [#8014](https://github.com/JabRef/jabref/pull/8014)
 - We fixed an issue where typing an invalid UNC path into the "Main file directory" text field caused an error. [#8107](https://github.com/JabRef/jabref/issues/8107)
 - We fixed an issue where "Open Folder" didn't select the file on macOS in Finder [#8130](https://github.com/JabRef/jabref/issues/8130)
+- We fixed an issue where importing PDFs resulted in an uncaught exception [#8143](https://github.com/JabRef/jabref/issues/8143)
+- We fixed "The library has been modified by another program" showing up when line breaks change [#4877](https://github.com/JabRef/jabref/issues/4877)
+- The default directory of the "LaTeX Citations" tab is now the directory of the currently opened database (and not the directory chosen at the last open file dialog or the last database save) [koppor#538](https://github.com/koppor/jabref/issues/538)
+- We fixed an issue where right-clicking on a tab and selecting close will close the focused tab even if it is not the tab we right-clicked [#8193](https://github.com/JabRef/jabref/pull/8193)
+- We fixed an issue where selecting a citation style in the preferences would sometimes produce an exception [#7860](https://github.com/JabRef/jabref/issues/7860)
 
 ### Removed
 
-
+- We removed two orphaned preferences options [#8164](https://github.com/JabRef/jabref/pull/8164)
 
 
 

diff --git a/README.md b/README.md
@@ -100,5 +100,4 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 
 JabRef development is powered by YourKit Java Profiler [![YourKit Java Profiler](https://www.yourkit.com/images/yk_logo.png)](https://www.yourkit.com/java/profiler/)
 
-
 [JabRef]: https://www.jabref.org
diff --git a/build.gradle b/build.gradle
@@ -20,11 +20,11 @@ plugins {
 
     id 'org.openjfx.javafxplugin' version '0.0.10'
 
-    id 'org.beryx.jlink' version '2.24.2'
+    id 'org.beryx.jlink' version '2.24.4'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
-    id 'com.adarshr.test-logger' version '3.0.0'
+    id 'com.adarshr.test-logger' version '3.1.0'
 
     id 'jacoco'
 
@@ -110,7 +110,7 @@ configurations {
 }
 
 javafx {
-    version = "17.0.0.1"
+    version = "17.0.1"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -130,19 +130,19 @@ dependencies {
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk15on:1.69'
 
-    implementation 'commons-cli:commons-cli:1.4'
+    implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.2.1'
-    implementation 'org.libreoffice:unoloader:7.2.0'
+    implementation 'org.libreoffice:libreoffice:7.2.2'
+    implementation 'org.libreoffice:unoloader:7.2.2'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
     implementation 'info.debatty:java-string-similarity:2.0.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
     implementation 'org.antlr:antlr-runtime:3.5.2'
 
-    antlr4 'org.antlr:antlr4:4.9.2'
-    implementation 'org.antlr:antlr4-runtime:4.9.2'
+    antlr4 'org.antlr:antlr4:4.9.3'
+    implementation 'org.antlr:antlr4-runtime:4.9.3'
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.13.0.202109080827-r'
 
@@ -158,7 +158,7 @@ dependencies {
         exclude module: 'oraclepki'
     }
 
-    implementation ('com.google.guava:guava:31.0-jre') {
+    implementation ('com.google.guava:guava:31.0.1-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -171,14 +171,14 @@ dependencies {
     implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
-    implementation 'org.fxmisc.flowless:flowless:0.6.6'
-    implementation 'org.fxmisc.richtext:richtextfx:0.10.6'
+    implementation 'org.fxmisc.flowless:flowless:0.6.7'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.1.0'
 
-    implementation 'org.jsoup:jsoup:1.14.2'
-    implementation 'com.konghq:unirest-java:3.13.0'
+    implementation 'org.jsoup:jsoup:1.14.3'
+    implementation 'com.konghq:unirest-java:3.13.3'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha5'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -209,18 +209,18 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.121'
+    testImplementation 'io.github.classgraph:classgraph:4.8.130'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.1'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.11.18'
+    testImplementation 'net.bytebuddy:byte-buddy-parent:1.12.1'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:3.12.4'
-    testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
-    testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
-    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.21.0'
-    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.21.0'
+    testImplementation 'org.mockito:mockito-core:4.0.0'
+    testImplementation 'org.xmlunit:xmlunit-core:2.8.3'
+    testImplementation 'org.xmlunit:xmlunit-matchers:2.8.3'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.22.0'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"

diff --git a/buildres/csl/csl-locales/.github/workflows/merge.yaml b/buildres/csl/csl-locales/.github/workflows/merge.yaml
@@ -58,7 +58,7 @@ jobs:
       if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
       uses: ruby/setup-ruby@v1
       with:
-        ruby-version: 3.0.0
+        ruby-version: 3.0.2
     - name: but use cache to speed that up
       if: github.event_name == 'workflow_dispatch' || (github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true'))
       uses: actions/cache@v2

diff --git a/buildres/csl/csl-locales/.github/workflows/sheldon.yaml b/buildres/csl/csl-locales/.github/workflows/sheldon.yaml
@@ -50,7 +50,7 @@ jobs:
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:
-        ruby-version: 3.0.0
+        ruby-version: 3.0.2
     - name: but use cache to speed that up
       uses: actions/cache@v2
       with:

diff --git a/buildres/csl/csl-locales/Gemfile b/buildres/csl/csl-locales/Gemfile
@@ -1,4 +1,4 @@
-ruby '3.0.0'
+ruby '3.0.2'
 source 'https://rubygems.org'
 
 gem 'rake'