Merge branch 'main' into jabrefonline

.github/workflows/check-links.yaml

@@ -4,6 +4,8 @@ on:
   push:
     paths:
       - '**.md'
+    paths-ignore:
+      - 'CHANGELOG.md'
   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 * *"

.github/workflows/cleanup_pr.yml

@@ -13,21 +13,21 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ -z "$BUILDJABREFPRIVATEKEY" ]; then
-            echo ::set-output name=secretspresent::false
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Extract branch name
         id: extract_branch
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: |
-          echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
+          echo "branch=${{ github.event.pull_request.head.ref }}" >> $GITHUB_OUTPUT
       - name: Delete folder on builds.jabref.org
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/[email protected].5
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: appleboy/[email protected].6
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

.github/workflows/deployment.yml

@@ -36,15 +36,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macOS-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         include:
           - os: ubuntu-latest
             displayName: linux
             archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
           - os: windows-latest
             displayName: windows
             archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
-          - os: macOS-latest
+          - os: macos-latest
             displayName: macOS
             archivePortable: brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app
     runs-on: ${{ matrix.os }}
@@ -55,9 +55,9 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo ::set-output name=secretspresent::false
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -79,29 +79,29 @@ jobs:
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         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') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
-        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
-        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
-        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
@@ -112,7 +112,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
+        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(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 $3}')
@@ -133,15 +133,17 @@ jobs:
           rm "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
           mv "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg"
       - name: Package application image
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: ${{ matrix.archivePortable }}
       - name: Rename files
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: pwsh
         run: |
-          get-childitem -Path build/distribution/*
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Upload to GitHub workflow artifacts store
+        if: (matrix.os != 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'YES')
         uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
@@ -158,42 +160,49 @@ jobs:
         shell: bash
         run: |
           if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
-            echo ::set-output name=secretspresent::false
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Checkout source
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/checkout@v3
       - name: Fetch all history for all tags and branches
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         run: git fetch --prune --unshallow
       - name: Install GitVersion
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: gittools/actions/gitversion/[email protected]
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         id: gitversion
         uses: gittools/actions/gitversion/[email protected]
       - name: Get linux binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-linux
           path: build/distribution
       - name: Get windows binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-windows
           path: build/distribution
       - name: Get macOS binaries
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: actions/download-artifact@master
         with:
           name: JabRef-macOS
           path: build/distribution/
       - name: Deploy to builds.jabref.org
         id: deploy
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: Pendect/action-rsyncer@v1.1.0
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: Pendect/action-rsyncer@v2.0.0
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
           BRANCH: ${{ steps.gitversion.outputs.branchName }}

.github/workflows/gource.yml

@@ -19,9 +19,9 @@ jobs:
       - name: Determine dates
         id: dates
         run: |
-          echo ::set-output name=start_date::`date -d "$(date +%Y-%m-01) -3 months" +%Y-%m-%d`
-          echo ::set-output name=stop_date::`date -d "$(date +%Y-%m-01) -1 day" +%Y-%m-%d`
-          echo ::set-output name=quarter::`date -d "$(date +%Y-%m-01) -1 day" +%Y`-Q$(( ((`date -d "$(date +%Y-%m-01) -1 day" +%m`)-1)/3+1 ))
+          echo "start_date=`date -d "$(date +%Y-%m-01) -3 months" +%Y-%m-%d`" >> $GITHUB_STATE
+          echo "stop_date=`date -d "$(date +%Y-%m-01) -1 day" +%Y-%m-%d`" >> $GITHUB_STATE
+          echo "quarter=`date -d "$(date +%Y-%m-01) -1 day" +%Y`-Q$(( ((`date -d "$(date +%Y-%m-01) -1 day" +%m`)-1)/3+1 ))" >> $GITHUB_STATE
       - name: 'Development history of last quarter'
         uses: nbprojekt/gource-action@v1
         with:

.github/workflows/snap.yml

@@ -22,10 +22,10 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ "SNAPCRAFT_LOGIN_FILE" == "" ]; then
-            echo ::set-output name=secretspresent::false
+          if [ "$SNAPCRAFT_LOGIN_FILE" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
@@ -39,7 +39,7 @@ jobs:
         with:
           snapcraft-args: "--debug"
       - name: Upload snap
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         uses: snapcore/action-publish@v1
         with:
           store_login: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}

.github/workflows/tests.yml

@@ -149,10 +149,10 @@ jobs:
         id: checksecrets
         shell: bash
         run: |
-          if [ "CODECOV_TOKEN" == "" ]; then
-            echo ::set-output name=secretspresent::false
+          if [ "$CODECOV_TOKEN" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
           else
-            echo ::set-output name=secretspresent::true
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
           fi
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
@@ -165,7 +165,7 @@ jobs:
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics
-        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);
         env:
           CI: "true"

CHANGELOG.md

@@ -21,6 +21,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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 support for the field `fjournal` (in `@article`) for abbreviation and unabbreviation functionalities. [#321](https://github.com/JabRef/jabref/pull/321)
 
 ### Changed
 
@@ -53,11 +54,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- In the context of the [Cleanup dialog](https://docs.jabref.org/finding-sorting-and-cleaning-entries/cleanupentries) we changed the text of the conversion of BibTeX to biblatex (and vice versa) to make it more clear. [koppor#545](https://github.com/koppor/jabref/issues/545)
 - 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)
+- We modified the Change case sub-menus and their corresponding tips (displayed when you stay long over the menu) to properly reflect exemplified cases. [#9339](https://github.com/Jabref/jabref/issues/9339)
 
 ### Fixed
 
-- We fixed the readability of the file field in the dark dark theme [#9340](https://github.com/JabRef/jabref/issues/9340)
+- We fixed an issue where importing from XMP would fail for certain PDFs [#9383](https://github.com/JabRef/jabref/issues/9383)
+- We fixed the readability of the file field in the 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)
@@ -82,12 +87,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue with the message that is displayed when fetcher returns an empty list of entries for given query. [#9195](https://github.com/JabRef/jabref/issues/9195)
 - We fixed an issue where an exception was not logged correctly. [koppor#627](https://github.com/JabRef/koppor/issues/627)
 - 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 an issue where a user could not open an attached file in a new unsaved library. [#9386](https://github.com/JabRef/jabref/issues/9386)
 - 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 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 the behavior of "Discard changes" when reopening a modified library. [#9361](https://github.com/JabRef/jabref/issues/9361)
+- We fixed an issue that JabRef displayed the wrong group tree after loading. [koppor#637](https://github.com/koppor/jabref/issues/637)
 - 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)
+- We fixed an issue where a known journal's medline/dot-less abbreviation does not switch to the full name. [#9370](https://github.com/JabRef/jabref/issues/9370)
 
 ### Removed
 

MAINTAINERS

@@ -8,3 +8,4 @@ Carl Christian Snethlage (since 2020)
 Dominik Voigt (since 2020)
 Jonatan Askertop (since 2021)
 Benedikt Tutzer (since 2021)
+Thilo Ertel (since 2021)