Merge branch 'main' into feat/11377

Author: Siedlerchr

.git-blame-ignore-revs

@@ -1,5 +1,8 @@
 # Automatic code reformatting
+f3cfa496e028dee1cafd0c47553f63cd1243bd8c
 c5bcad738fe6e8dfcb62442a426c2778241515a1
+10189bf2c1a6bc506f03461390f3cc46e5cc0651
+16fd6194b9a0b8282259c00b6fb0d4aa494e4b04
 
 # net.sf.jabref -> org.jabref
 b2ad6eb279f5def38fa21be12cb5dd4545c1ba1a
@@ -23,6 +26,6 @@ bf81b595a77f0f7f254872be6f05a063c44528d8
 
 # This commit should not exist
 185d7345946c29a2a4e2726c912be0c4db4810b9
-# Resulted in this problematic merge commits
+# ... and resulted in this problematic merge commits
 7e1645978b3028df5e65af19f0f819ddfd0f24aa
 a31f396765492ac12eaab228e33eb9d22487403b

.github/ghprcomment.yml

@@ -39,6 +39,16 @@
 
     You can then run these tests in IntelliJ to reproduce the failing tests locally.
     We offer a quick test running howto in the section [Final build system checks](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.html#final-build-system-checks) in our setup guide.
+- jobName: format
+  workflowName: 'Source Code Tests'
+  message: >
+    Your code currently does not meet JabRef's code guidelines.
+    IntelliJ auto format covers some cases.
+    There seem to be issues with your code style and autoformat configuration.
+    Please reformat your code (<kbd>Ctrl</kbd>+<kbd>Alt</kbd>+<kbd>L</kbd>) and commit, then push.
+
+
+    In special cases, consider using `// formatter:off` and `// formatter:on` annotations to allow deviation from the code style.
 - jobName: Checkstyle
   workflowName: 'Source Code Tests'
   message: >

.github/workflows/automerge.yml

@@ -14,22 +14,21 @@ jobs:
         id: shouldrun
         shell: bash
         run: |
-          actor='${{ github.actor }}'
-          title='${{ github.event.pull_request.title }}'
-
-          if [[ "$actor" == "renovate-bot" ]]; then
-            echo "✅ from renote-bot"
-            echo "shouldrun=true" >> "$GITHUB_OUTPUT"
-            exit 0
-          fi
-
           head_repo="${{ github.event.pull_request.head.repo.full_name }}"
           if [[ "$head_repo" != "JabRef/jabref" ]]; then
             echo "🚫 not from JabRef/jabref"
             echo "shouldrun=false" >> "$GITHUB_OUTPUT"
             exit 0
           fi
 
+          actor="${{ github.actor }}"
+          if [[ "$actor" == "renovate-bot" ]]; then
+            echo "✅ from renote-bot"
+            echo "shouldrun=true" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          title="${{ github.event.pull_request.title }}"
           if [[ "$actor" == "dependabot[bot]" ]] || \
             [[ "$title" == "[Bot] "* ]] || \
             [[ "$title" == "Bump "* ]] || \

.github/workflows/binaries.yml

@@ -343,6 +343,48 @@ jobs:
           comment-tag: download-link
           mode: recreate
 
+  comment-on-issue:
+    name: Comment on issue
+    # separate job, because it should wait until all binaries are available
+    needs: [conditions, build]
+    if: ${{ (github.event_name == 'pull_request') && (needs.conditions.outputs.upload-to-builds-jabref-org == 'true') }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: echo PR data
+        run: |
+          echo "PR Number: ${{ github.event.pull_request.number }}"
+          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          cat <<EOF
+          PR Body:
+          ${{ github.event.pull_request.body }}
+          EOF
+      - name: Determine issue number
+        id: get_issue_number
+        uses: koppor/ticket-check-action@add-output
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ticketLink: 'https://github.com/JabRef/jabref/issues/%ticketNumber%'
+          ticketPrefix: '#'
+          titleRegex: '^#(?<ticketNumber>\d+)'
+          branchRegex: '^(?<ticketNumber>\d+)'
+          # Matches GitHub's closes/fixes/resolves #{number}, but does not match our example `Closes #13109` in PULL_REQUEST_TEMPLATE
+          bodyRegex: '(?<action>fixes|closes|resolves)\s+(?:https?:\/\/github\.com\/JabRef\/jabref\/issues\/)?#?(?<ticketNumber>(?!13109\b)\d+)'
+          bodyRegexFlags: 'i'
+          outputOnly: true
+      - name: Comment on issue
+        if: ${{ steps.get_issue_number.outputs.ticketNumber != '-1' }}
+        uses: thollander/actions-comment-pull-request@v3
+        with:
+          pr-number: ${{ steps.get_issue_number.outputs.ticketNumber }}
+          message: >
+             A pull request addressing the issue has been created.
+             The build of this PR is available at <https://builds.jabref.org/pull/${{ github.event.pull_request.number }}/merge>.
+
+
+             For any feedback, add a comment to the pull request at ${{ github.event.pull_request.html_url }}.
+          comment-tag: download-link
+          mode: recreate
+
   notarize:
     # Outsourced in a separate job to be able to rerun if this fails for timeouts
     name: macOS notarization

.github/workflows/on-pr-opened-updated.yml

@@ -162,10 +162,11 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   remove_label:
     if: github.repository == 'JabRef/jabref'
-    name: Remove label "status: changes-required"
+    name: 'Remove label "status: changes-required"'
     runs-on: ubuntu-latest
     steps:
-      - run: gh issue --repo ${{ github.repository }} edit ${{ github.event.pull_request.number }} --remove-label "status: changes-required"
+      - run: |
+          gh issue --repo ${{ github.repository }} edit ${{ github.event.pull_request.number }} --remove-label "status: changes-required"
   upload-pr-number:
     if: github.repository == 'JabRef/jabref'
     runs-on: ubuntu-latest

.github/workflows/tests-code-fetchers.yml

@@ -32,7 +32,8 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
-  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS }}
+  MedlineApiKey: ${{ secrets.MedlineApiKey_FOR_TESTS }}
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"

.github/workflows/tests-code.yml

@@ -14,6 +14,7 @@ env:
   BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
   SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
+  MedlineAPiKey: ${{ secrets.MedlineApiKey_FOR_TESTS }}
   GRADLE_OPTS: -Xmx4g
   JAVA_OPTS: -Xmx4g
 
@@ -113,6 +114,18 @@ jobs:
         run: |
           ./gradlew --no-configuration-cache :rewriteDryRun
 
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: koppor/intellij-idea-format@update-to-latest-intellij
+        with:
+          file-mask: "*.java"
+          settings-file: "config/IntelliJ Code Style.xml"
+      # job should fail in case there are changes
+      - name: Check if any files changed
+        run: git diff --exit-code
+
   modernizer:
     name: Modernizer
     runs-on: ubuntu-latest

.gitignore

@@ -68,8 +68,22 @@ gradle.properties
 
 
 # IntelliJ IDEA
-.idea/*
-!.idea/runConfigurations/
+.idea/workspace.xml
+.idea/checkstyleidea-libs
+
+# only contains the reference name
+.idea/codeStyles/codeStyleConfig.xml
+
+# references JDK_24 and the JDK name - high risk for conflicts
+.idea/misc.xml
+
+# We don't modify these (and the defaults are good enough)
+.idea/.name
+.idea/IntelliLang.xml
+.idea/compiler.xml
+.idea/kotlinc.xml
+.idea/modules.xml
+
 *.ipr
 *.iml