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

* upstream/main: (25 commits) Update Gradle Wrapper from 7.4.2 to 7.5. (JabRef#8986) New translations JabRef_en.properties (Russian) (JabRef#8985) [Bot] Update CSL styles (JabRef#8978) New Crowdin updates (JabRef#8972) New Crowdin updates (JabRef#8969) Fix .bat errorlevel handling with pwsh.exe check (JabRef#8965) revert jsoup version upgrade Fix charset detection with utf16 and others (JabRef#8947) Bump classgraph from 4.8.147 to 4.8.149 (JabRef#8968) Bump jsoup from 1.15.1 to 1.15.2 (JabRef#8967) Keep UTF-8 encoding header if present (JabRef#8964) Cleanup index when opening a library (JabRef#8962) Refactor context menu entry types changing (JabRef#8957) Improvement on check for missing commas when importing or opening a .bib file (JabRef#8840) 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) ...
Ognimalf · Jul 18, 2022 · 658cbea · 658cbea
2 parents cc8dc5c + baf8499
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -34,10 +34,14 @@ 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". [koppor#570](https://github.com/koppor/jabref/issues/570)
+- When JabRef encounters `% Encoding: UTF-8` header, it is kept during writing (and not removed). [#8964](https://github.com/JabRef/jabref/pull/8964)
+- We replace characters which cannot be decoded using the specified encoding by a (probably another) valid character. This happens if JabRef detects the wrong charset (e.g., UTF-8 instead of Windows 1252). One can use the [Integrity Check](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity) to find those characters.
 
 ### 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)
@@ -50,6 +54,10 @@ 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)
+- We fixed a bug where files that were deleted in the source bibtex file were kept in the index. [#8962](https://github.com/JabRef/jabref/pull/8962)
+- We fixed "Error while sending to JabRef" when the browser extension interacts with JabRef. [JabRef-Browser-Extension#479](https://github.com/JabRef/JabRef-Browser-Extension/issues/479)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -100,7 +100,7 @@ dependencyLocking {
 }
 
 javafx {
-    version = "18"
+    version = "18.0.1"
     modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
 }
 
@@ -127,7 +127,6 @@ dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.214'
 
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
-    implementation 'com.ibm.icu:icu4j-charset:71.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.71'
@@ -151,7 +150,7 @@ 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'
 
@@ -208,7 +207,7 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.147'
+    testImplementation 'io.github.classgraph:classgraph:4.8.149'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
@@ -221,7 +220,7 @@ dependencies {
     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'

diff --git a/buildres/csl/csl-locales/.github/workflows/merge.yaml b/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'
@@ -48,6 +48,10 @@ jobs:
             - deleted: [ '*.csl', 'dependent/*.csl', '*.xml' ]
           workflows:
             - added|modified: .github/workflows/*.yaml
+          updated_composer:
+            - added|modified: composer.json
+          deleted_composer:
+            - deleted: composer.json
 
     - name: Changed files
       if: github.event_name == 'push'
@@ -63,7 +67,7 @@ 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') }}
@@ -87,11 +91,24 @@ jobs:
       run: cd release && git rm ${{ steps.update.outputs.deleted_files }}
       if: github.event_name == 'push' && steps.update.outputs.deleted == 'true'
 
+    - name: Update composer.json
+      if: steps.update.outputs.updated_composer == 'true'
+      run: |
+        cp composer.json release/composer.json
+        cd release
+        git add composer.json
+  
+    - name: Delete composer.json
+      if: steps.update.outputs.deleted_composer == 'true'
+      run: |
+        cd release
+        git rm composer.json
+    
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         repository: 'release'
-        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }}
-      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true' || steps.update.outputs.updated_composer == 'true' || steps.update.outputs.deleted_composer == 'true')
 
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
@@ -116,3 +133,21 @@ jobs:
         git-user: "csl-bot"
         git-user-email: github@citationstyles.org
         git-commit-message: copied ${{ steps.update.outputs.workflows_files }} from styles
+
+    - name: Bump version and push tag
+      id: tag_version
+      uses: mathieudutour/github-tag-action@v5.6
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        default_bump: patch
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+
+    - name: Create a GitHub release
+      uses: softprops/action-gh-release@v0.1.14
+      env:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.tag_version.outputs.new_tag }}
+        name: Release ${{ steps.tag_version.outputs.new_tag }}
+        body: Released ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
diff --git a/buildres/csl/csl-locales/.github/workflows/sheldon.yaml b/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') }}

diff --git a/buildres/csl/csl-locales/Gemfile.lock b/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)

diff --git a/buildres/csl/csl-styles/.github/dependabot.yml b/buildres/csl/csl-styles/.github/dependabot.yml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/buildres/csl/csl-styles/.github/workflows/merge.yaml b/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'
@@ -48,6 +48,10 @@ jobs:
             - deleted: [ '*.csl', 'dependent/*.csl', '*.xml' ]
           workflows:
             - added|modified: .github/workflows/*.yaml
+          updated_composer:
+            - added|modified: composer.json
+          deleted_composer:
+            - deleted: composer.json
 
     - name: Changed files
       if: github.event_name == 'push'
@@ -63,7 +67,7 @@ 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') }}
@@ -87,11 +91,24 @@ jobs:
       run: cd release && git rm ${{ steps.update.outputs.deleted_files }}
       if: github.event_name == 'push' && steps.update.outputs.deleted == 'true'
 
+    - name: Update composer.json
+      if: steps.update.outputs.updated_composer == 'true'
+      run: |
+        cp composer.json release/composer.json
+        cd release
+        git add composer.json
+  
+    - name: Delete composer.json
+      if: steps.update.outputs.deleted_composer == 'true'
+      run: |
+        cd release
+        git rm composer.json
+    
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
         repository: 'release'
-        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }}
-      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+        commit_message: Releasing ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true' || steps.update.outputs.updated_composer == 'true' || steps.update.outputs.deleted_composer == 'true')
 
     - uses: stefanzweifel/git-auto-commit-action@v4
       with:
@@ -116,3 +133,21 @@ jobs:
         git-user: "csl-bot"
         git-user-email: github@citationstyles.org
         git-commit-message: copied ${{ steps.update.outputs.workflows_files }} from styles
+
+    - name: Bump version and push tag
+      id: tag_version
+      uses: mathieudutour/github-tag-action@v5.6
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        default_bump: patch
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
+
+    - name: Create a GitHub release
+      uses: softprops/action-gh-release@v0.1.14
+      env:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        tag_name: ${{ steps.tag_version.outputs.new_tag }}
+        name: Release ${{ steps.tag_version.outputs.new_tag }}
+        body: Released ${{ steps.update.outputs.updated_files }} ${{ steps.update.outputs.deleted_files }} ${{ steps.update.outputs.updated_composer_files }} ${{ steps.update.outputs.deleted_composer_files }}
+      if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
diff --git a/buildres/csl/csl-styles/.github/workflows/sheldon.yaml b/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') }}

diff --git a/buildres/csl/csl-styles/Gemfile.lock b/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)

diff --git a/buildres/csl/csl-styles/advanced-materials.csl b/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"/>