Merge branch 'upstream-main' into gsoc-ocr-tess4j-initial-implementation

Author: Kaan0029

.devcontainer/devcontainer.json

@@ -31,9 +31,9 @@
         // Install java.
         // See https://github.com/devcontainers/features/tree/main/src/java#options for details.
         "ghcr.io/devcontainers/features/java:1": {
-            "version": "24.0.1-tem",
+            "version": "24.0.1-amzn",
             "installGradle": false,
-            "jdkDistro": "Temurin"
+            "jdkDistro": "Corretto"
         }
     }
 }

.dockerignore

@@ -1,22 +1,27 @@
+.git
 .gitignore
 .dockerignore
 
 Dockerfile
 Dockerfile.*
 .github/
 
+.devcontainer/
+
+*/bin
+*/build
+*/out
+
+docs/
+
+gg.cmd
+gradlew.bat
+
 # no generated files in version control
 src/main/gen/
 src/main/generated/
 src-gen/
 
-src/main/resources/csl-styles
-src/main/resources/csl-locales
-buildres/abbrv.jabref.org
-
-jablib/src/main/resources/csl-styles
-jablib/src/main/resources/csl-locales
-
 .lycheecache
 
 .kotlin

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,16 +1,17 @@
-Closes #_____
+Closes _____
+<!-- LINK THE ISSUE WITH THE "Closes" KEYWORD. Example: Closes https://github.com/JabRef/jabref/issues/13109 OR Closes #13109 -->
 
-In about one to three sentences, describe the changes you have made: what, where, why, ...
+<!-- In about one to three sentences, describe the changes you have made: what, where, why, ... (REPLACE THIS LINE) -->
 
 <!-- NOTE: If your work is not yet complete, please open a draft pull request. In that case, outline your intended next steps. Do you need feedback? Will you continue in parallel? ... -->
 
 ### Steps to test
 
-Describe how reviewers can test this fix/feature. Ideally, think of how you would guide a beginner user of Jabef to try out your change.
-You can add screenshots or videos (using [Loom](https://www.loom.com/) or by just adding .mp4 files).
+<!-- Describe how reviewers can test this fix/feature. Ideally, think of how you would guide a beginner user of Jabef to try out your change. -->
+<!-- You can add screenshots or videos (using Loom - https://www.loom.com or by just adding .mp4 files). -->
+<!-- (REPLACE THIS PARAGRAPH) -->
 
 <!-- YOU HAVE TO MODIFY THE ABOVE TEXT FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT. -->
-<!-- LINK THE ISSUE WITH THE "Closes" KEYWORD. Example: Closes (link) OR Closes #12345 -->
 
 ### Mandatory checks
 

.github/dependabot.yml

@@ -2,13 +2,9 @@ version: 2
 updates:
   - package-ecosystem: gradle
     directories:
-      - "/build-logic"   # Build-related logic for gradle
-      - "/jabgui"        # JabRef's GUI
-      - "/jabkit"        # JabRef's CLI ("JabKit")
-      - "/jablib"        # Core library
-      - "/jabsrv"        # Server-related module
-      - "/jabsrv-cli"    # CLI for the server
-      - "/test-support"  # Module for test utilities
+      - "/build-logic"   # versions of 3rd party gradle plugins
+      - "/versions"      # versions of 3rd party dependencies of all JabRef modules
+      - "/"              # plugins
     schedule:
       interval: weekly
     labels:

.github/ghprcomment.yml

@@ -1,6 +1,7 @@
 # Compilation, tests, and code style
 
 - jobName: windows installer and portable version
+  workflowName: 'Source Code Tests'
   message: >
     Your code does not compile.
     Please ensure your changes compile successfully before pushing changes.
@@ -9,6 +10,7 @@
     To verify compilation locally, run `./gradlew build` or try running JabRef.
 
 - jobName: 'Unit tests – jablib'
+  workflowName: 'Source Code Tests'
   message: >
     JUnit tests of `jablib` are failing.
     You can see which checks are failing by locating the box "Some checks were not successful" on the pull request page.
@@ -18,6 +20,7 @@
     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: 'Unit tests – jabkit'
+  workflowName: 'Source Code Tests'
   message: >
     JUnit tests of `jabkit` are failing.
     You can see which checks are failing by locating the box "Some checks were not successful" on the pull request page.
@@ -27,6 +30,7 @@
     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: 'Unit tests – jabsrv'
+  workflowName: 'Source Code Tests'
   message: >
     JUnit tests of `jabsrv` are failing.
     You can see which checks are failing by locating the box "Some checks were not successful" on the pull request page.
@@ -36,6 +40,7 @@
     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: Checkstyle
+  workflowName: 'Source Code Tests'
   message: >
     Your code currently does not meet [JabRef's code guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
     We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
@@ -50,6 +55,7 @@
     Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
     Afterwards, please [run checkstyle locally](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#run-checkstyle) and fix the issues, commit, and push.
 - jobName: OpenRewrite
+  workflowName: 'Source Code Tests'
   message: >
     Your code currently does not meet JabRef's code guidelines.
     We use [OpenRewrite](https://docs.openrewrite.org/) to ensure "modern" Java coding practices.
@@ -60,6 +66,7 @@
     The issues found can be **automatically fixed**.
     Please execute the gradle task *`rewriteRun`* from the [`rewrite` group of the Gradle Tool window](https://devdocs.jabref.org/code-howtos/faq.html#failing-openrewrite-tests) in IntelliJ, then check the results, commit, and push.
 - jobName: Modernizer
+  workflowName: 'Source Code Tests'
   message: >
     Your code currently does not meet JabRef's code guidelines.
     We use [Gradle Modernizer Plugin](https://github.com/andygoossens/gradle-modernizer-plugin#gradle-modernizer-plugin) to ensure "modern" Java coding practices.
@@ -72,20 +79,32 @@
 # CHANGELOG.md and *.md
 
 - jobName: 'CHANGELOG.md needs to be modified'
+  workflowName: 'PR Tests'
   message: >
     You ticked that you modified `CHANGELOG.md`, but no new entry was found there.
 
 
     If you made changes that are visible to the user, please add a brief description along with the issue number to the `CHANGELOG.md` file.
     If you did not, please replace the cross (`[x]`) by a slash (`[/]`) to indicate that no `CHANGELOG.md` entry is necessary.
     More details can be found in our [Developer Documentation about the changelog](https://devdocs.jabref.org/decisions/0007-human-readable-changelog.html).
-- jobName: CHANGELOG.md
+- jobName: 'CHANGELOG.md - only unreleased touched'
+  workflowName: 'Source Code Tests'
   message: >
     While the PR was in progress, a new version of JabRef has been released.
 
 
     You have to merge `upstream/main` and move your entry in `CHANGELOG.md` up to the section `## [Unreleased]`.
+- jobName: CHANGELOG.md
+  workflowName: 'Source Code Tests'
+  message: >
+    You modified `CHANGELOG.md` and did not meet JabRef's rules for consistently formatted Markdown files.
+    To ensure consistent styling, we have [markdown-lint](https://github.com/DavidAnson/markdownlint) in place.
+    [Markdown lint's rules](https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#rules) help to keep our Markdown files consistent within this repository and consistent with the Markdown files outside here.
+
+
+    You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "CHANGELOG.md".
 - jobName: Markdown
+  workflowName: 'Source Code Tests'
   message: >
     You modified Markdown (`*.md`) files and did not meet JabRef's rules for consistently formatted Markdown files.
     To ensure consistent styling, we have [markdown-lint](https://github.com/DavidAnson/markdownlint) in place.
@@ -98,12 +117,14 @@
 # Submodules and branches
 
 - jobName: 'Submodules not modified'
+  workflowName: 'PR Tests'
   message: >
     Your pull request modified git submodules.
 
 
     Please follow our [FAQ on submodules](https://devdocs.jabref.org/code-howtos/faq.html#submodules) to fix.
 - jobName: no-force-push
+  workflowName: 'PR Tests'
   always: true
   message: >
     Hey, we noticed that you **force-pushed** your changes.
@@ -114,13 +135,15 @@
 
     In future, **please avoid that**. For now, you can continue working.
 - jobName: 'Conflicts with target branch'
+  workflowName: 'On PR opened/updated'
   message: >
     Your pull request conflicts with the target branch.
 
 
     Please [merge `upstream/main`](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork#syncing-a-fork-branch-from-the-command-line) with your code.
     For a step-by-step guide to resolve merge conflicts, see <https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line>.
 - jobName: 'Source branch is other than "main"'
+  workflowName: 'PR Tests'
   message: >
     You committed your code on the `main` brach of your fork. This is a bad practice.
     The right way is to branch out from `main`, work on your patch/feature in that new branch, and then get that branch merged via the pull request (see [GitHub flow](https://docs.github.com/en/get-started/using-github/github-flow)).
@@ -131,17 +154,36 @@
     See [CONTRIBUTING.md](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md#pull-request-process) for more details.
 
 
-# PR text
+# PR hygiene
 
+- jobName: 'Ensure that contributor is assigned (fails if not commented on issue)'
+  workflowName: 'On PR opened/updated'
+  message: >
+    You did not assign yourself to the issue.
+    Thus, it looks like you skipped reading our [CONTRIBUTING.md](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md), which explains exactly how to participate. No worries, it happens to the best of us.
+
+
+    Give it a read, and you’ll discover the ancient wisdom of assigning issues to yourself. Trust me, it’s worth it. 🚀
+
+- jobName: 'PR title must not start with "Fix for issue <number>"'
+  workflowName: 'PR Tests'
+  always: true
+  message: >
+    The title of the pull request must not start with "Fix for issue xyz".
+    Please use a concise one-line summary that explains what the fix or change actually does.
+    Example of a good title: "Prevent crash when importing malformed BibTeX entries".
 - jobName: 'Mandatory Checks present'
+  workflowName: 'PR Tests'
   always: true
   message: >
     You have removed the "Mandatory Checks" section from your pull request description. Please adhere to our [pull request template](https://github.com/JabRef/jabref/blob/main/.github/PULL_REQUEST_TEMPLATE.md?plain=1#L10).
 - jobName: 'PR checklist OK'
+  workflowName: 'PR Tests'
   always: true
   message: >
     Note that your PR will not be reviewed/accepted until you have gone through the mandatory checks in the description and marked each of them them exactly in the format of `[x]` (done), `[ ]` (not done yet) or `[/]` (not applicable).
 - jobName: 'Determine issue number'
+  workflowName: 'PR Tests'
   always: true
   message: |
     Your pull request needs to link an issue correctly.

.github/workflows/automerge.yml

@@ -8,31 +8,57 @@ permissions:
 jobs:
   automerge:
     runs-on: ubuntu-latest
-    # Run only if PR is inside JabRef's main repository and created by dependabot or by an update workflow
-    if: >
-      (github.repository == 'JabRef/jabref') &&
-      (
-        (github.actor == 'renovate-bot' && startsWith(github.event.pull_request.title, 'chore(deps):')) ||
-        (
-          (github.event.pull_request.head.repo.full_name == 'JabRef/jabref') &&
-          (
-            (github.actor == 'dependabot[bot]') ||
-            (
-              startsWith(github.event.pull_request.title, '[Bot] ') ||
-              startsWith(github.event.pull_request.title, 'Bump ') ||
-              startsWith(github.event.pull_request.title, 'New Crowdin updates') ||
-              startsWith(github.event.pull_request.title, 'Update Gradle Wrapper from')
-            )
-          )
-        )
-      )
+    if: github.repository == 'JabRef/jabref'
     steps:
+      - name: Determine if job should run
+        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" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          if [[ "$actor" == "dependabot[bot]" ]] || \
+            [[ "$title" == "[Bot] "* ]] || \
+            [[ "$title" == "Bump "* ]] || \
+            [[ "$title" == "New Crowdin updates"* ]] || \
+            [[ "$title" == "Update Gradle Wrapper from"* ]]; then
+            echo "✅ title OK"
+            echo "shouldrun=true" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          LABELS=$(gh api repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/labels --jq '.[].name')
+          if echo "$LABELS" | grep -q "^automerge"; then
+            echo "✅ label automerge"
+            echo "shouldrun=true" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          echo "🚫 no automerge"
+          echo "shouldrun=false" >> "$GITHUB_OUTPUT"
+        env:
+          GH_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
       - name: Approve PR
+        if: steps.shouldrun.outputs.shouldrun == 'true'
         run: gh pr review --approve "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
           GH_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
       - name: Merge PR
+        if: steps.shouldrun.outputs.shouldrun == 'true'
         run: gh pr merge --auto --squash "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}