Merge remote-tracking branch 'upstream/main' into fix-for-issue-8011

* upstream/main:
  Disable ResearchGateTest on CI (JabRef#8955)
  Bump checkstyle from 10.1 to 10.3.1 (JabRef#8950)
  Bump checkstyle from 10.1 to 10.3.1 (JabRef#8950)
  Bump mariadb-java-client from 2.7.5 to 2.7.6 (JabRef#8953)
  Add notification when adding previous entries to new group configuration (JabRef#8919)
  Remember Sidepane width after restart (JabRef#8936)
  move "Warn about duplicates on import" preferences option (JabRef#8937)
  Fix theme switching exception (JabRef#8939)
  fix merge conflict
  Squashed 'buildres/csl/csl-locales/' changes from 969d9567ac..55459cd79f
  Squashed 'buildres/csl/csl-styles/' changes from e740261..3d3573c
  Show pdf icon for mime type in maintable (JabRef#8935)
  Fix for Dark theme not readable (JabRef#8929)
  Find Unlinked files should ignore Thumbs.db, etc (JabRef#8800)
  Try to  make reproducible builds (JabRef#8925)
  Link to new board (and refine text)

CHANGELOG.md

@@ -13,11 +13,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
+- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
 - We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322)
 
 ### Changed
 
+- The file column in the main table now shows the corresponding defined icon for the linked file [8930](https://github.com/JabRef/jabref/issues/8930).
+- We improved the color of the selected entries and the color of the summary in the Import Entries Dialog in the dark theme. [#7927](https://github.com/JabRef/jabref/issues/7927)
 - We upgraded to Lucene 9.2 for the fulltext search.
   Thus, the now created search index cannot be read from older versions of JabRef anylonger.
   ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
@@ -31,10 +34,13 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We improved group expansion arrow that prevent it from activating group when expanding or collapsing. [#7982](https://github.com/JabRef/jabref/issues/7982), [#3176](https://github.com/JabRef/jabref/issues/3176)
 - When configured SSL certificates changed, JabRef warns the user to restart to apply the configuration.
 - We improved the appearances and logic of the "Manage field names & content" dialog, and renamed it to "Automatic field editor". [#6536](https://github.com/JabRef/jabref/issues/6536)
-- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
+- We improved the message explaining the options when modifying an automatic keyword group [#8911](https://github.com/JabRef/jabref/issues/8911)
+- We moved the preferences option "Warn about duplicates on import" option from the tab "File" to the tab "Import and Export". [kopper#570](https://github.com/koppor/jabref/issues/570)
 
 ### Fixed
 
+- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
+- We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930)
 - We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849)
 - We fixed an issue where the content of a big shared database library is not shown [#8788](https://github.com/JabRef/jabref/issues/8788)
 - We fixed the unnecessary horizontal scroll bar in group panel [#8467](https://github.com/JabRef/jabref/issues/8467)
@@ -46,6 +52,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the exception that there are invalid characters in filename. [#8786](https://github.com/JabRef/jabref/issues/8786)
 - When the proxy configuration removed the proxy user/password, this change is applied immediately.
 - We fixed an issue where removing several groups deletes only one of them. [#8390](https://github.com/JabRef/jabref/issues/8390)
+- We fixed an issue where the Sidepane (groups, web search and open office) width is not remembered after restarting JabRef. [#8907](https://github.com/JabRef/jabref/issues/8907)
+- We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939)
 
 ### Removed
 

build.gradle

@@ -81,7 +81,7 @@ repositories {
     mavenLocal()
     mavenCentral()
     maven { url 'https://oss.sonatype.org/content/groups/public' }
-    maven { url 'https://repository.apache.org/snapshots' }
+    maven { url 'https://jitpack.io' }
 }
 
 configurations {
@@ -95,6 +95,10 @@ configurations {
     }
 }
 
+dependencyLocking {
+    lockAllConfigurations()
+}
+
 javafx {
     version = "18"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
@@ -147,7 +151,7 @@ dependencies {
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.13.3'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.3'
 
-    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
     implementation 'org.postgresql:postgresql:42.4.0'
 
@@ -166,7 +170,7 @@ dependencies {
     // JavaFX stuff
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
-    implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT'
+    implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
     implementation 'org.fxmisc.flowless:flowless:0.6.10'
@@ -208,18 +212,16 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
-    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:4.6.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.23.1'
-    testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
-    testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
+    testImplementation "org.testfx:testfx-core:4.0.16-alpha"
+    testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.1'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'

buildres/csl/csl-locales/.github/workflows/merge.yaml

@@ -19,9 +19,9 @@ jobs:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       DISTRIBUTION_UPDATER_TOKEN: "${{ secrets.DISTRIBUTION_UPDATER_TOKEN }}"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'push'
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'workflow_dispatch'
       with:
         fetch-depth: 0
@@ -30,7 +30,7 @@ jobs:
       id: release
       run: echo ::set-output name=branch::v1.0.2
     - name: Checkout release branch
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ steps.release.outputs.branch }}
         path: './release'
@@ -63,7 +63,7 @@ jobs:
         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
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

buildres/csl/csl-locales/.github/workflows/sheldon.yaml

@@ -15,17 +15,17 @@ jobs:
     # labels to a PR
     # https://securitylab.github.com/research/github-actions-preventing-pwn-requests
     - name: Checkout repo for OWNER TEST
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: contains(github.event.pull_request.labels.*.name, 'safe to test')
       with:
         ref: ${{ github.event.pull_request.head.ref }}
 
     # otherwise, checkout the current master, and the pr to the subdirectory 'pull-request'
     - name: Checkout base repo for pull-request test
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
     - name: Checkout pull-request
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -54,7 +54,7 @@ jobs:
       with:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

buildres/csl/csl-locales/Gemfile.lock

@@ -33,7 +33,7 @@ GEM
     csl-styles (2.0.0)
       csl (~> 2.0)
     diff-lcs (1.5.0)
-    diffy (3.4.0)
+    diffy (3.4.2)
     dotenv (2.7.6)
     erubis (2.7.0)
     faraday (1.8.0)

buildres/csl/csl-styles/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

buildres/csl/csl-styles/.github/workflows/merge.yaml

@@ -19,9 +19,9 @@ jobs:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       DISTRIBUTION_UPDATER_TOKEN: "${{ secrets.DISTRIBUTION_UPDATER_TOKEN }}"
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'push'
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       if: github.event_name == 'workflow_dispatch'
       with:
         fetch-depth: 0
@@ -30,7 +30,7 @@ jobs:
       id: release
       run: echo ::set-output name=branch::v1.0.2
     - name: Checkout release branch
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ steps.release.outputs.branch }}
         path: './release'
@@ -63,7 +63,7 @@ jobs:
         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
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

buildres/csl/csl-styles/.github/workflows/sheldon.yaml

@@ -15,17 +15,17 @@ jobs:
     # labels to a PR
     # https://securitylab.github.com/research/github-actions-preventing-pwn-requests
     - name: Checkout repo for OWNER TEST
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: contains(github.event.pull_request.labels.*.name, 'safe to test')
       with:
         ref: ${{ github.event.pull_request.head.ref }}
 
     # otherwise, checkout the current master, and the pr to the subdirectory 'pull-request'
     - name: Checkout base repo for pull-request test
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
     - name: Checkout pull-request
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       if: "! contains(github.event.pull_request.labels.*.name, 'safe to test')"
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -54,7 +54,7 @@ jobs:
       with:
         ruby-version: 3.0.2
     - name: but use cache to speed that up
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

buildres/csl/csl-styles/Gemfile.lock

@@ -33,7 +33,7 @@ GEM
     csl-styles (2.0.0)
       csl (~> 2.0)
     diff-lcs (1.5.0)
-    diffy (3.4.0)
+    diffy (3.4.2)
     dotenv (2.7.6)
     erubis (2.7.0)
     faraday (1.8.0)

buildres/csl/csl-styles/advanced-materials.csl

@@ -5,7 +5,7 @@
     <id>http://www.zotero.org/styles/advanced-materials</id>
     <link href="http://www.zotero.org/styles/advanced-materials" rel="self"/>
     <link href="http://www.zotero.org/styles/small" rel="template"/>
-    <link href="http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291521-4095/homepage/2089_authorresources.html" rel="documentation"/>
+    <link href="https://onlinelibrary.wiley.com/page/journal/15214095/homepage/author-guidelines" rel="documentation"/>
     <author>
       <name>Jimmy Lawrence</name>
       <email>jimmymisc@gmail.com</email>
@@ -16,13 +16,13 @@
     <issn>0935-9648</issn>
     <eissn>1521-4095</eissn>
     <summary>A style for Wiley's Advanced Materials</summary>
-    <updated>2012-09-27T22:06:38+00:00</updated>
+    <updated>2022-06-22T14:43:19+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <macro name="author">
     <names variable="author">
       <name initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-      <label form="short" prefix=", " text-case="capitalize-first" suffix=" "/>
+      <label form="short" text-case="capitalize-first" prefix=", "/>
       <substitute>
         <names variable="editor"/>
         <names variable="translator"/>
@@ -32,7 +32,7 @@
   <macro name="editor">
     <names variable="editor">
       <label form="short" text-case="capitalize-first" suffix=".: " strip-periods="true"/>
-      <name initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
+      <name delimiter-precedes-last="always" initialize-with=". "/>
     </names>
   </macro>
   <macro name="year-date">
@@ -124,7 +124,7 @@
             <text macro="year-date"/>
           </group>
         </else-if>
-        <else-if type="webpage">
+        <else-if type="webpage post post-weblog" match="any">
           <group delimiter=", ">
             <text variable="title" quotes="true"/>
             <text macro="access"/>