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

* upstream/main: (150 commits) fix unit test Add check for developer's documentation Merge GitBook view Fix zbMath fetcher (#8623) GitBook: [#56] No subject Add an extra dialog to ask the user whether they want to open the saved file folder when the export the entries (#8567) Bump checkstyle from 10.0 to 10.1 (#8620) Bump peter-evans/create-pull-request from 3 to 4 (#8619) Bump pascalgn/automerge-action from 0.14.3 to 0.15.2 (#8618) Bump flexmark from 0.62.2 to 0.64.0 (#8621) Bump classgraph from 4.8.141 to 4.8.143 (#8622) update test getPart (#8610) Add ControlHelper truncateString tests comments (#8612) Allow using custom SSL certificates (#8583) Fix protectedTerms not stored due to weaklistener (#8609) Fix changelog and version parsing (#8578) Creating more unit tests for NumericFieldComparatorTest (#8604) Fix merge entries dialog exceeding screen size (#8599) StringUtilTest new test for method GetPart (#8594) Use unkown entry type ... # Conflicts: # build.gradle # src/main/java/org/jabref/logic/pdf/search/retrieval/PdfSearcher.java
JabRef · Mar 30, 2022 · 81f08ef · 81f08ef
2 parents 33a826b + 2bf53cb
commit 81f08ef
Show file tree

Hide file tree

Showing 662 changed files with 42,695 additions and 9,432 deletions.
diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -1,6 +1,6 @@
 # These are supported funding model platforms
 
-github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
+github: JabRef
 patreon: # Patreon user account
 open_collective: # Replace with a single Open Collective username
 ko_fi: # Replace with a single Ko-fi username

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.4 (latest release)"
+        - "5.5 (latest release)"
         - "3.8.2"
         - Latest development branch build (please note build date below)
         - Other (please describe below)

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -15,4 +15,5 @@ The title of the PR must not reference an issue, because GitHub does not support
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
 - [ ] Screenshots added in PR description (for UI changes)
+- [ ] [Checked developer's documentation](https://devdocs.jabref.org/): Is the information available and up to date? If not, I outlined it in this pull request.
 - [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not, I created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, I submitted a pull request to the documentation repository.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,22 +1,27 @@
 version: 2
 updates:
-- package-ecosystem: gradle
-  directory: "/"
-  schedule:
-    interval: weekly
-  open-pull-requests-limit: 15
-  labels:
-  - "type: dependencies"
-  ignore:
-  - dependency-name: com.microsoft.azure:applicationinsights-core
-    versions:
-    - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
-  - dependency-name: com.microsoft.azure:applicationinsights-logging-log4j2
-    versions:
-    - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
-- package-ecosystem: "github-actions"
-  directory: "/"
-  schedule:
-    interval: weekly
-  labels:
-  - "type: dependencies"
+  - package-ecosystem: gradle
+    directory: "/"
+    schedule:
+      interval: weekly
+    labels:
+      - "type: dependencies"
+    ignore:
+      - dependency-name: com.microsoft.azure:applicationinsights-core
+        versions:
+          - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
+      - dependency-name: com.microsoft.azure:applicationinsights-logging-log4j2
+        versions:
+          - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
+  - package-ecosystem: gradle
+    directory: "buildSrc/"
+    schedule:
+      interval: weekly
+    labels:
+      - "type: dependencies"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: weekly
+    labels:
+      - "type: dependencies"
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -21,7 +21,7 @@ jobs:
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.14.3
+        uses: pascalgn/automerge-action@v0.15.2
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
@@ -13,7 +13,7 @@ jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:
           use-quiet-mode: 'yes'

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -51,21 +51,21 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].11
+        uses: gittools/actions/gitversion/[email protected].13
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].11
+        uses: gittools/actions/gitversion/[email protected].13
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
         if: matrix.os == 'macos-latest'
@@ -152,16 +152,16 @@ jobs:
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].11
+        uses: gittools/actions/gitversion/[email protected].13
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].11
+        uses: gittools/actions/gitversion/[email protected].13
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

diff --git a/.github/workflows/gource.yml b/.github/workflows/gource.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Determine dates

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -13,7 +13,7 @@ jobs:
     if: github.repository == 'JabRef/jabref'
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           fetch-depth: 0
@@ -42,7 +42,7 @@ jobs:
           cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
           git add .
           git commit -m"Refresh example styles" || true
-      - uses: peter-evans/create-pull-request@v3
+      - uses: peter-evans/create-pull-request@v4
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
           branch: refresh-csl

diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -10,16 +10,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           persist-credentials: false
           fetch-depth: 0
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Update journal lists
         run: |
@@ -46,7 +46,7 @@ jobs:
           # create .mv file
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
-      - uses: peter-evans/create-pull-request@v3
+      - uses: peter-evans/create-pull-request@v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           branch: update-journallist

diff --git a/.github/workflows/snap.yml b/.github/workflows/snap.yml
@@ -30,7 +30,7 @@ jobs:
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
       # See snap/snapcraft.yml for details
       - name: Run snapcraft build

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -37,12 +37,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run fetcher tests
         run: ./gradlew fetcherTest

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -26,12 +26,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
@@ -50,12 +50,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest
@@ -82,12 +82,12 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
@@ -116,12 +116,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Run GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
@@ -154,12 +154,12 @@ jobs:
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 16
-          distribution: 'adopt'
+          java-version: 17
+          distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics
         if: ${{ steps.checksecrets.outputs.secretspresent }}
@@ -174,5 +174,5 @@ jobs:
     name: "Validate Gradle Wrapper"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: gradle/wrapper-validation-action@v1
diff --git a/.github/workflows/update-gradle-wrapper.yml b/.github/workflows/update-gradle-wrapper.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Update Gradle Wrapper
         uses: gradle-update/update-gradle-wrapper-action@v1