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

* upstream/main: (109 commits)
  Fix right clicking a group and choosing "remove selected entries from this group" leads to error when Bibtex source tab is selected (JabRef#8821)
  Fix single identifier cannot be opened on click (JabRef#8838)
  Add Pubmed/Medline Query Transformer (JabRef#8818)
  adjust and add testcases for FileAnnotationViewModel (JabRef#8830)
  Append config instead of replacing (JabRef#8834)
  Fix eclipse config (JabRef#8835)
  Add Nemo file manager (JabRef#8831)
  Fix missing clear action on pressing esc within the "Filter groups" field (JabRef#8829)
  Update bouncycalse to new base version (JabRef#8827)
  add: add test cases for FileUtil (JabRef#8810)
  Restrict use of standard streams (JabRef#8816)
  updated 8802 (JabRef#8817)
  Bump pascalgn/automerge-action from 0.15.2 to 0.15.3 (JabRef#8803)
  Bump jackson-dataformat-yaml from 2.13.2 to 2.13.3 (JabRef#8804)
  Bump icu4j-charset from 70.1 to 71.1 (JabRef#8805)
  Fix notifications that overlap task bar (JabRef#8775)
  checkstye
  Default path for ssl key store is nested inside "JabRef" directory (JabRef#8796)
  Add log on disk (JabRef#8791)
  Fix for JabRef#8788 JabRef not showing contents of shared database library (JabRef#8793)
  ...

.editorconfig

@@ -6,5 +6,8 @@ indent_style = space
 insert_final_newline = true
 trim_trailing_whitespace = true
 
+[*.{fxml,java,properties,sh}]
+end_of_line = lf
+
 [*.md]
 trim_trailing_whitespace = false

.gitattributes

@@ -5,9 +5,10 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# ensure that line endings of *.java, and *.properties are normalized
-*.java text
-*.properties text
+# ensure that line endings of *.fxml, *.java, and *.properties are normalized
+*.fxml text eol=lf
+*.java text eol=lf
+*.properties text eol=lf
 
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.5 (latest release)"
+        - "5.6 (latest release)"
         - "3.8.2"
         - Latest development branch build (please note build date below)
         - Other (please describe below)

.github/workflows/automerge.yml

@@ -9,19 +9,19 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.4"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.6"
         with:
           ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/[email protected].0
+        uses: hmarr/[email protected].1
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/[email protected].2
+        uses: pascalgn/[email protected].3
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

.github/workflows/deployment.yml

@@ -22,6 +22,7 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
   OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
   GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
   JAVA_OPTS: -Xmx4g
@@ -62,9 +63,9 @@ jobs:
         id: gitversion
         uses: gittools/actions/gitversion/[email protected]
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX

.github/workflows/refresh-csl-subtrees.yml

@@ -6,6 +6,9 @@ on:
     - cron: '1 2 1,15 * *'
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   publish:
     name: Refresh Citation Style Language Files

.github/workflows/refresh-journal-lists.yml

@@ -4,8 +4,14 @@ on:
   workflow_dispatch:
     # Allow to run manually
 
+permissions:
+  contents: read
+
 jobs:
   publish:
+    permissions:
+      contents: write  # for peter-evans/create-pull-request to create branch
+      pull-requests: write  # for peter-evans/create-pull-request to create a PR
     name: Refresh Journal List Files
     runs-on: ubuntu-latest
     steps:
@@ -16,9 +22,9 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update journal lists

.github/workflows/tests-fetchers.yml

@@ -26,11 +26,15 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
 
 concurrency:
   group: fetcher-tests-${{ github.head_ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   fetchertests:
     name: Fetcher tests
@@ -39,9 +43,9 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v3
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run fetcher tests

.github/workflows/tests.yml

@@ -13,6 +13,7 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
   GRADLE_OPTS: -Xmx4g
   JAVA_OPTS: -Xmx4g
 
@@ -28,16 +29,17 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v3
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
           reporter: github-pr-check
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
+          checkstyle_version: '10.1'
       - name: Run checkstyle gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
       - name: Run markdown-lint
@@ -52,9 +54,9 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v3
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests
@@ -84,9 +86,9 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v3
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests on PostgreSQL
@@ -118,9 +120,9 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v3
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run GUI tests
@@ -156,9 +158,9 @@ jobs:
       - name: Checkout source
         uses: actions/checkout@v3
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics