Merge remote-tracking branch 'origin/auto-relativize-file-paths'

Author: u7676493

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,7 +9,7 @@ Link the issue that will be closed, e.g., "Closes #333". If your PR closes a kop
 -->
 
 - [x] I own the copyright of the code submitted and I licence it under the [MIT license](https://github.com/JabRef/jabref/blob/main/LICENSE)
-- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
+- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if change is visible to the user)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
 - [ ] Screenshots added in PR description (for UI changes)

.github/ghprcomment.yml

@@ -34,3 +34,8 @@
   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: 'Unit tests'
+  message: |
+    JUnit tests are failing. In the area "Some checks were not successful", locate "Tests / Unit tests (pull_request)" and click on "Details". This brings you to the test output.
+
+    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.

.github/workflows/on-labeled-issue.yml

@@ -6,6 +6,34 @@ on:
        - labeled
 
 jobs:
+  Assigned:
+    # Triggered when manually assigned the label "📍 Assigned" to trigger the automatic unassignment after 30 days
+    name: "📍 Assigned"
+    if: ${{ github.event.label.name == '📍 Assigned' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Move Issue to "Free to take" Column in "Candidates for University Projects"
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
+        with:
+          github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/3"
+          target-labels: "📍 Assigned"
+          target-column: "Free to take"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true
+      - name: Move Issue to "Free to take" Column in "Good First Issues"
+        uses: m7kvqbe1/github-action-move-issues@feat/skip-if-not-in-project-flag
+        with:
+          github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
+          project-url: "https://github.com/orgs/JabRef/projects/5"
+          target-labels: "📍 Assigned"
+          target-column: "Free to take"
+          ignored-columns: ""
+          default-column: "Free to take"
+          skip-if-not-in-project: true
   FirstTimeCodeContribution:
     if: ${{ github.event.label.name == 'FirstTimeCodeContribution' }}
     runs-on: ubuntu-latest
@@ -35,7 +63,7 @@ jobs:
       with:
         github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
         project-url: "https://github.com/orgs/JabRef/projects/3"
-        target-labels: "📍 Assigned"
+        target-labels: "FirstTimeCodeContribution"
         target-column: "Assigned"
         ignored-columns: ""
         default-column: "Free to take"
@@ -45,7 +73,7 @@ jobs:
       with:
         github-token: ${{ secrets.GH_TOKEN_ACTION_MOVE_ISSUE }}
         project-url: "https://github.com/orgs/JabRef/projects/5"
-        target-labels: "📍 Assigned"
+        target-labels: "FirstTimeCodeContribution"
         target-column: "Assigned"
         ignored-columns: ""
         default-column: "Free to take"

.github/workflows/on-review-submitted.yml

@@ -6,6 +6,8 @@ on:
       - 'docs/**'
       - '.github/workflows/pages.yml'
   push:
+    branches:
+      main
     paths:
       - 'docs/**'
       - '.github/workflows/pages.yml'
@@ -17,9 +19,8 @@ permissions:
   pages: write
   id-token: write
 
-# Allow one concurrent deployment
 concurrency:
-  group: "pages"
+  group: "${{ github.workflow }}-${{ github.head_ref || github.ref }}"
   cancel-in-progress: true
 
 jobs:
@@ -33,9 +34,9 @@ jobs:
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '2.7' # Not needed with a .ruby-version file
+          ruby-version: '3.3' # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-          cache-version: 1 # Increment this number if you need to re-download cached gems
+          cache-version: 0 # Increment this number if you need to re-download cached gems
           working-directory: docs/
       - name: Setup Pages
         id: pages

.github/workflows/pages.yml

@@ -34,15 +34,25 @@ jobs:
           PR_NUMBER=$(cat pr_number.txt)
           echo "Read PR number $PR_NUMBER"
           echo "pr_number=$PR_NUMBER" >> $GITHUB_OUTPUT
-      - name: Checkout
+      - uses: actions/checkout@v4
+      - name: Determine owner
         if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
+        id: isCrossRepository
+        run: |
+          isCrossRepository=$(gh pr view $pr_number --json isCrossRepository --jq '.isCrossRepository')
+          echo "Got isCrossRepository $isCrossRepository"
+          echo isCrossRepository=$isCrossRepository >> $GITHUB_OUTPUT
+        env:
+          GH_TOKEN: ${{ github.token }}
+      - name: Checkout
+        if: ${{ (steps.read-pr_number.outputs.pr_number != '') && (steps.isCrossRepository.isCrossRepository == 'true') }}
         uses: actions/checkout@v4
         with:
           fetch-depth: '0'
           show-progress: 'false'
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: jbang
-        if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
+        if: ${{ (steps.read-pr_number.outputs.pr_number != '') && (steps.isCrossRepository.isCrossRepository == 'true') }}
         uses: jbangdev/[email protected]
         with:
           script: ghprcomment@koppor/ghprcomment

.github/workflows/pr-comment.yml

@@ -131,7 +131,7 @@ jobs:
           export PATH=$PATH:$HOME/.jbang/bin
 
           # run heylogs verification
-          jbang com.github.nbbrd.heylogs:heylogs-cli:0.7.2:bin check CHANGELOG.md > heylogs.txt || true
+          jbang com.github.nbbrd.heylogs:heylogs-cli:0.9.2:bin check CHANGELOG.md > heylogs.txt || true
 
           # improve output
           sed -i 's/all-h2-contain-a-version/all-h2-contain-a-version (ignored)/' heylogs.txt
@@ -380,7 +380,7 @@ jobs:
         uses: actions/github-script@v7
         with:
           script: |
-              core.setFailed('Pull requests should come from a branch other than "main"\n\n👉 Please read https://devdocs.jabref.org/contributing again carefully. 👈')
+              core.setFailed('Pull requests should come from a branch other than "main"\n\n👉 Please read [the CONTRIBUTING guide](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md#contributing) carefully again. 👈')
 
   upload-pr-number:
     runs-on: ubuntu-latest

.github/workflows/tests.yml

@@ -12,7 +12,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 - We added a "view as BibTeX" option before importing an entry from the citation relation tab. [#11826](https://github.com/JabRef/jabref/issues/11826)
-- We added probable search hits instead of exact matches. Sorting by hit score can be done by the new score table column. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We added support finding LaTeX-encoded special characters based on plain Unicode and vice versa. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - When a search hits a file, the file icon of that entry is changed accordingly. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We added an AI-based chat for entries with linked PDF files. [#11430](https://github.com/JabRef/jabref/pull/11430)
@@ -31,9 +30,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a switch not to store the linked file URL, because it caused troubles at other apps. [#11735](https://github.com/JabRef/jabref/pull/11735)
 - When starting a new SLR, the selected catalogs now persist within and across JabRef sessions. [koppor#614](https://github.com/koppor/jabref/issues/614)
 - We added support for drag'n'drop on an entry in the maintable to an external application to get the entry preview dropped. [#11846](https://github.com/JabRef/jabref/pull/11846)
+- We added the functionality to double click on a [LaTeX citation](https://docs.jabref.org/advanced/entryeditor/latex-citations) to jump to the respective line in the LaTeX editor. [#11996](https://github.com/JabRef/jabref/issues/11996)
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 - We added a setting which always adds the literal "Cited on pages" text before each JStyle citation. [#11691](https://github.com/JabRef/jabref/pull/11732)
 - We added a new plain citation parser that uses LLMs. [#11825](https://github.com/JabRef/jabref/issues/11825)
+- We added support for modifier keys when dropping a file on an entry in the main table. [#12001](https://github.com/JabRef/jabref/pull/12001)
 - We added an importer for SSRN URLs. [#12021](https://github.com/JabRef/jabref/pull/12021)
 - We added a compare button to the duplicates in the citation relations tab to open the "Possible duplicate entries" window. [#11192](https://github.com/JabRef/jabref/issues/11192)
 - We added automatic browser extension install on Windows for Chrome and Edge. [#6076](https://github.com/JabRef/jabref/issues/6076)
@@ -42,15 +43,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
-- The search syntax is changed to [Apache Lucene syntax](https://lucene.apache.org/core/9_11_1/queryparser/org/apache/lucene/queryparser/classic/package-summary.html#Overview) (also to be similar to the [online search syntax](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax)). [#11542](https://github.com/JabRef/jabref/pull/11542/)
-- When searching using a regular expression, one needs to enclose the search string in `/`. [#11542](https://github.com/JabRef/jabref/pull/11542/)
 - A search in "any" fields ignores the [groups](https://docs.jabref.org/finding-sorting-and-cleaning-entries/groups). [#7996](https://github.com/JabRef/jabref/issues/7996)
 - When a communication error with an [online service](https://docs.jabref.org/collect/import-using-online-bibliographic-database) occurs, JabRef displays the HTTP error. [#11223](https://github.com/JabRef/jabref/issues/11223)
 - The Pubmed/Medline Plain importer now imports the PMID field as well [#11488](https://github.com/JabRef/jabref/issues/11488)
 - The 'Check for updates' menu bar button is now always enabled. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
 - JabRef does not show finished background tasks in the status bar popup. [#11821](https://github.com/JabRef/jabref/pull/11821)
 - We enhanced the indexing speed. [#11502](https://github.com/JabRef/jabref/pull/11502)
+- When dropping a file into the main table, after copy or move, the file is now put in the [configured directory and renamed according to the configured patterns](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#filename-format-and-file-directory-pattern). [#12001](https://github.com/JabRef/jabref/pull/12001)
 - ⚠️ Renamed command line parameters `embeddBibfileInPdf` to `embedBibFileInPdf`, `writeMetadatatoPdf` to `writeMetadataToPdf`, and `writeXMPtoPdf` to `writeXmpToPdf`. [#11575](https://github.com/JabRef/jabref/pull/11575)
 - The browse button for a Custom theme now opens in the directory of the current used CSS file. [#11597](https://github.com/JabRef/jabref/pull/11597)
 - The browse button for a Custom exporter now opens in the directory of the current used exporter file. [#11717](https://github.com/JabRef/jabref/pull/11717)
@@ -66,6 +66,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new CSS style class `main-table` for the main table. [#11881](https://github.com/JabRef/jabref/pull/11881)
 - When renaming a file, the old extension is now used if there is none provided in the new name. [#11903](https://github.com/JabRef/jabref/issues/11903)
 - When importing a file using "Find Unlinked Files", when one or more file directories are available, the file path will be relativized where possible [koppor#549](https://github.com/koppor/jabref/issues/549)
+- We changed the name of the library-based file directory from 'General File Directory' to 'Library-specific File Directory' per issue [#571](https://github.com/koppor/jabref/issues/571)
+- The CitationKey column is now a default shown column for the entry table. [#10510](https://github.com/JabRef/jabref/issues/10510)
 
 ### Fixed
 
@@ -99,12 +101,13 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where recently opened files were not displayed in the main menu properly. [#9042](https://github.com/JabRef/jabref/issues/9042)
 - We fixed an issue where the DOI lookup would show an error when a DOI was found for an entry. [#11850](https://github.com/JabRef/jabref/issues/11850)
 - We fixed an issue where <kbd>Tab</kbd> cannot be used to jump to next field in some single-line fields. [#11785](https://github.com/JabRef/jabref/issues/11785)
+- We fixed an issue where we display warning message for moving attached open files. [#10121](https://github.com/JabRef/jabref/issues/10121)
 - We fixed an issue where it was not possible to select selecting content of other user's comments.[#11106](https://github.com/JabRef/jabref/issues/11106)
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)
+- We fixed an issue where trying to open a library from a failed mounted directory on Mac would cause an error. [#10548](https://github.com/JabRef/jabref/issues/10548)
 
 ### Removed
 
-- We removed support for case-sensitive and exact search. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We removed the description of search strings. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We removed support for importing using the SilverPlatterImporter (`Record INSPEC`). [#11576](https://github.com/JabRef/jabref/pull/11576)
 - We removed support for automatically generating file links using the CLI (`--automaticallySetFileLinks`).

CHANGELOG.md

@@ -29,9 +29,9 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '6.23.4'
+    id 'org.openrewrite.rewrite' version '6.25.1'
 
-    id "org.itsallcode.openfasttrace" version "3.0.0"
+    id "org.itsallcode.openfasttrace" version "3.0.1"
 }
 
 // Enable following for debugging
@@ -238,7 +238,7 @@ dependencies {
     }
     implementation 'org.fxmisc.flowless:flowless:0.7.3'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.3'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.58.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.60.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude module: 'commons-lang3'
         exclude group: 'org.apache.commons.validator'
@@ -304,7 +304,7 @@ dependencies {
     // Implementation of the API
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.9'
     // injection framework
-    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.8'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.9'
     implementation 'org.glassfish.hk2:hk2-api:3.1.1'
     // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
     // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
@@ -370,11 +370,14 @@ dependencies {
     // Even if "compileOnly" is used, IntelliJ always adds to module-info.java. To avoid issues during committing, we use "implementation" instead of "compileOnly"
     implementation 'io.github.adr:e-adr:2.0.0-SNAPSHOT'
 
+    implementation 'io.zonky.test:embedded-postgres:2.0.7'
+    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.0.0')
+
     testImplementation 'io.github.classgraph:classgraph:4.8.177'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
 
-    testImplementation 'org.mockito:mockito-core:5.14.1'
+    testImplementation 'org.mockito:mockito-core:5.14.2'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
@@ -793,9 +796,13 @@ jlink {
         requires 'org.apache.commons.lang3'
         requires 'org.apache.commons.logging'
         requires 'org.apache.commons.text'
+        requires 'org.apache.commons.codec'
+        requires 'org.apache.commons.io'
+        requires 'org.apache.commons.compress'
         requires 'org.freedesktop.dbus'
         requires 'org.jsoup'
         requires 'org.slf4j'
+        requires 'org.tukaani.xz';
         uses 'ai.djl.engine.EngineProvider'
         uses 'ai.djl.repository.RepositoryFactory'
         uses 'ai.djl.repository.zoo.ZooProvider'
@@ -807,6 +814,7 @@ jlink {
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
+        uses 'org.postgresql.shaded.com.ongres.stringprep.Profile'
 
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
         provides 'java.sql.Driver' with 'org.postgresql.Driver'