Merge remote-tracking branch 'upstream/main' into 321-fjournal-refactor

* upstream/main: (40 commits) Update guidelines-for-setting-up-a-local-workspace.md Add link to good first issues (and fix link) Refine guidelines (and fix .md file linking) Extend ArXiv fetcher results by using data from related DOIs (#9170) New Crowdin updates (#9366) Fix token New translations JabRef_en.properties (Chinese Simplified) (#9364) Fix date field change causes an uncaught exception (#9365) Add date format and respective test case (#9310) Bump jackson-datatype-jsr310 from 2.13.4 to 2.14.0 (#9357) Bump jackson-dataformat-yaml from 2.13.4 to 2.14.0 (#9356) Bump tika-core from 2.5.0 to 2.6.0 (#9358) Refine guideline "Set up a local workspace" (#9355) Adds missing "requires" statement (#9354) Bind "Find unlinked files" default directory to the current library (#9290) Rename "Remote" to "Tele" (#9270) Fixed display of file field adjusting for the dark theme (#9343) Update sorting of entries in maintable by special fields immediately (#9338) New translations JabRef_en.properties (German) (#9336) Fix Abbreviation for Escaped Ampersand (#9288) ... # Conflicts: # CHANGELOG.md
JabRef · Nov 12, 2022 · dc80ea0 · dc80ea0
2 parents f198208 + a1f2d51
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diff --git a/.github/workflows/GreetingFirstTimeCodeContribution.yml b/.github/workflows/GreetingFirstTimeCodeContribution.yml
@@ -15,7 +15,6 @@ jobs:
     - name: GreetingFirstTimeCodeContribution
       uses: peter-evans/create-or-update-comment@v2
       with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
         issue-number: ${{ github.event.issue.number }}
         body: |
             As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -31,7 +31,6 @@ concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
-
 jobs:
   build:
     strategy:
@@ -51,45 +50,58 @@ jobs:
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.14
+        uses: gittools/actions/gitversion/setup@v0.9.15
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.14
+        uses: gittools/actions/gitversion/execute@v0.9.15
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
           java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Setup OSX key chain on OSX for app id cert
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
+        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
+        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         shell: bash
         run: |
           codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
@@ -100,7 +112,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/')
+        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
@@ -157,12 +169,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.14
+        uses: gittools/actions/gitversion/setup@v0.9.15
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.14
+        uses: gittools/actions/gitversion/execute@v0.9.15
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -1,6 +1,10 @@
 name: Deploy Jekyll site to Pages
 
 on:
+  pull_request:
+    paths:
+      - 'docs/**'
+      - '.github/workflows/pages.yml'
   push:
     paths:
       - 'docs/**'
@@ -27,19 +31,21 @@ jobs:
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '3.0' # Not needed with a .ruby-version file
+          ruby-version: '2.7' # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-          cache-version: 0 # Increment this number if you need to re-download cached gems
+          cache-version: 1 # Increment this number if you need to re-download cached gems
+          working-directory: docs/
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v2
       - name: Build with Jekyll
-        uses: actions/jekyll-build-pages@v1
-        with:
-          source: docs/
-          destination: ./_site
+        run: |
+          cd docs
+          bundle exec jekyll build
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/_site/
 
   deploy:
     if: github.ref == 'refs/heads/main'

diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - An SLR can now be started from the SLR itself. [#9131](https://github.com/JabRef/jabref/pull/9131), [koppor#601](https://github.com/koppor/jabref/issues/601)
 - Implement a new ISBN Fetcher ([doi-to-bibtex-converter.herokuapp.com](http://doi-to-bibtex-converter.herokuapp.com) as source). [#9145](https://github.com/JabRef/jabref/pull/9145)
 - We added support for the Ukrainian and Arabic languages. [#9236](https://github.com/JabRef/jabref/pull/9236), [#9243](https://github.com/JabRef/jabref/pull/9243)
+- The default file directory of a library is used as default directory for [unlinked file lookup](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [koppor#546](https://github.com/koppor/jabref/issues/546)
 - We added integrate `fjournal` support in article to abbreviation and unabbreviation functionalities. [#321](https://github.com/JabRef/jabref/pull/321) 
 
 ### Changed
@@ -46,11 +47,19 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
 - When adding or editing a subgroup it is placed w.r.t. to alphabetical ordering rather than at the end. [koppor#577](https://github.com/koppor/jabref/issues/577)
 - We modified the Directory of Open Access Books (DOAB) fetcher so that it will now also fetch the ISBN when possible. [#8708](https://github.com/JabRef/jabref/issues/8708)
+- ArXiv fetcher now retrieves additional data from related DOIs (both ArXiv and user-assigned). [#9170](https://github.com/JabRef/jabref/pull/9170)
+- Groups context menu now shows appropriate options depending on number of subgroups. [koppor#579](https://github.com/koppor/jabref/issues/579)
+- We changed the color of found text from red to high-contrast colors (background: yellow; font color: purple). [koppor#552](https://github.com/koppor/jabref/issues/552)
 - We modified the "Delete file" dialog and add the full file path to the dialog text. The file path in the title was changed to file name only. [koppor#534](https://github.com/koppor/jabref/issues/534)
 - Download from URL now automatically fills with URL from clipboard. [koppor#535](https://github.com/koppor/jabref/issues/535)
+- We added HTML and Markdown files to Find Unlinked Files and removed BibTeX.[koppor#547](https://github.com/koppor/jabref/issues/547)
+- We changed the messages after importing unlinked local files to past tense. [koppor#548](https://github.com/koppor/jabref/issues/548)
+- We fixed an issue where the wrong icon for a successful import of a bib entry was shown [#9308](https://github.com/JabRef/jabref/pull/9308)
 
 ### Fixed
 
+- We fixed the readability of the file field in the dark dark theme [#9340](https://github.com/JabRef/jabref/issues/9340)
+- We fixed that sorting of entries in the maintable by special fields is updated immediately [#9334](https://github.com/JabRef/jabref/issues/9334)
 - We fixed the Cleanup entries dialog is partially visible [#9223](https://github.com/JabRef/jabref/issues/9223)
 - We fixed the display of the "Customize Entry Types" dialogue title [#9198](https://github.com/JabRef/jabref/issues/9198)
 - We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
@@ -61,6 +70,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
 - We fixed a bug where spaces are trimmed when highlighting differences in the Entries merge dialog. [koppor#371](https://github.com/koppor/jabref/issues/371)
 - We fixed some visual glitches with the linked files editor field in the entry editor and increased its height. [#8823](https://github.com/JabRef/jabref/issues/8823)
+- We fixed some visual inconsistencies (round corners of highlighted buttons). [#8806](https://github.com/JabRef/jabref/issues/8806)
 - We fixed several bugs regarding the manual and the autosave of library files that sometimes lead to exceptions or data loss. [#9067](https://github.com/JabRef/jabref/pull/9067), [#8448](https://github.com/JabRef/jabref/issues/8484), [#8746](https://github.com/JabRef/jabref/issues/8746), [#6684](https://github.com/JabRef/jabref/issues/6684), [#6644](https://github.com/JabRef/jabref/issues/6644), [#6102](https://github.com/JabRef/jabref/issues/6102), [#6002](https://github.com/JabRef/jabref/issues/6000)
 - We fixed an issue where applied save actions on saving the library file would lead to the dialog "The library has been modified by another program" popping up [#4877](https://github.com/JabRef/jabref/issues/4877)
 - We fixed issues with save actions not correctly loaded when opening the library. [#9122](https://github.com/JabRef/jabref/pull/9122)
@@ -75,6 +85,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where hitting enter on the search field within the preferences dialog closed the dialog. [koppor#630](https://github.com/koppor/jabref/issues/630)
 - We fixed a typo within a connection error message. [koppor#625](https://github.com/koppor/jabref/issues/625)
 - We fixed an issue where the 'close dialog' key binding was not closing the Preferences dialog. [#8888](https://github.com/jabref/jabref/issues/8888)
+- We fixed an issue where editing entry's "date" field in library mode "biblatex" causes an uncaught exception. [#8747][https://github.com/JabRef/jabref/issues/8747]
+- We fixed an issue where journal abbreviations would not abbreviate journal titles with escaped ampersands (\\&). [#8948](https://github.com/JabRef/jabref/issues/8948)
+- We fixed an issue where font size preferences did not apply correctly to preference dialog window and the menu bar. [#8386](https://github.com/JabRef/jabref/issues/8386) and [#9279](https://github.com/JabRef/jabref/issues/9279)
+- We fixed an issue when using an unsafe character in the citation key, the auto-linking feature fails to link files. [#9267](https://github.com/JabRef/jabref/issues/9267)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -125,7 +125,7 @@ dependencies {
     implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0'
     implementation 'com.h2database:h2-mvstore:2.1.214'
 
-    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.5.0'
+    implementation group: 'org.apache.tika', name: 'tika-core', version: '2.6.0'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.71.1'
@@ -143,8 +143,8 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.3.0.202209071007-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.13.4'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.4'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.14.0'
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.14.0'
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
@@ -176,7 +176,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.1.2'
 
     implementation 'org.jsoup:jsoup:1.15.3'
-    implementation 'com.konghq:unirest-java:3.13.11'
+    implementation 'com.konghq:unirest-java:3.13.12'
 
     implementation 'org.slf4j:slf4j-api:2.0.3'
     implementation "org.tinylog:tinylog-api:2.5.0"
@@ -217,7 +217,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.4'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.4'
     // 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-styles/Gemfile.lock b/buildres/csl/csl-styles/Gemfile.lock
@@ -65,10 +65,10 @@ GEM
     mini_portile2 (2.8.0)
     multipart-post (2.1.1)
     namae (1.1.1)
-    nokogiri (1.13.6)
+    nokogiri (1.13.9)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
-    nokogiri (1.13.6-x64-mingw32)
+    nokogiri (1.13.9-x64-mingw32)
       racc (~> 1.4)
     octokit (4.21.0)
       faraday (>= 0.9)