Merge remote-tracking branch 'upstream/main' into fix-for-issue-8189

* upstream/main: (27 commits)
  Bump slf4j-api from 2.0.2 to 2.0.3 (JabRef#9207)
  Bump slf4j-api from 2.0.2 to 2.0.3 in /buildSrc (JabRef#9211)
  Add mappings on ModsImporter.java (JabRef#9193)
  Improve installation of java 18 in devcontainer (JabRef#9197)
  Fix missing title for "customize entry types" (JabRef#9198) (JabRef#9201)
  Squashed 'buildres/csl/csl-locales/' changes from b2afeb4d87..cb98d36691
  Squashed 'buildres/csl/csl-styles/' changes from 201e022..7bde3e4
  "Capitalize" capitalizes words after hyphens (JabRef#9186)
  Observable Preferences O (Language and FileHistory) (JabRef#9173)
  Fix jakarta annotation missing (JabRef#9183)
  Bump junit-platform-launcher from 1.9.0 to 1.9.1 (JabRef#9177)
  Bump WyriHaximus/github-action-wait-for-status from 1.6 to 1.7.1 (JabRef#9178)
  Bump junit-jupiter from 5.9.0 to 5.9.1 (JabRef#9180)
  Bump checkstyle from 10.3.3 to 10.3.4 (JabRef#9179)
  Bump slf4j-api from 2.0.1 to 2.0.2 (JabRef#9181)
  Bump slf4j-api from 2.0.1 to 2.0.2 in /buildSrc (JabRef#9182)
  Remove Java Flight Recorder (JabRef#9174)
  Fixes fetcher tests (JabRef#9175)
  Update afterburner to jakarta (JabRef#9168)
  Improve startup-behavior of pdf indexer (JabRef#9166)
  ...

.devcontainer/devcontainer.json

@@ -0,0 +1,38 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/java
+{
+    "name": "Java",
+    "image": "mcr.microsoft.com/vscode/devcontainers/base:bullseye",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": { 
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "vscjava.vscode-java-pack"
+            ]
+        }
+    },
+
+    "onCreateCommand": "gradle assemble",
+
+    // Need to connect as root otherwise we run into issues with gradle.
+    // default option is "vscode". More info: https://aka.ms/vscode-remote/containers/non-root.
+    "remoteUser": "root",
+    "features": {
+        // Adds a lightweight desktop that can be accessed using a VNC viewer or the web
+        "desktop-lite": "latest",
+
+        // Install java
+        "java": {
+            "version": "18",
+            "installGradle": true,
+            "jdkDistro": "sem"
+        }
+    }
+}

.github/workflows/automerge.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.6"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.7.1"
         with:
           ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13

.github/workflows/deployment.yml

@@ -130,7 +130,7 @@ jobs:
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
           get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
       - name: Upload to GitHub workflow artifacts store
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v3
         with:
           name: JabRef-${{ matrix.displayName }}
           path: build/distribution

.github/workflows/gource.yml

@@ -49,7 +49,7 @@ jobs:
         run: |
           mv gource/gource.mp4 gource-videos/jabref-complete.mp4
       - name: 'Upload gource video'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: Gource
           path: ./gource-videos/

CHANGELOG.md

@@ -21,6 +21,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Changed
 
+- Genres are now mapped correctly to entry types when importing MODS files. [#9185](https://github.com/JabRef/jabref/issues/9185)
 - We improved the Citavi Importer to also import so called Knowledge-items into the field `comment` of the corresponding entry [#9025](https://github.com/JabRef/jabref/issues/9025)
 - We removed wrapping of string constants when writing to a `.bib` file.
 - We call backup files `.bak` and temporary writing files now `.sav`.
@@ -33,10 +34,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - The global default directory for storing PDFs is now the subdirectory "JabRef" in the user's home.
 - We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 - We simplified the actions to fast-resolve duplicates to 'Keep Left', 'Keep Right', 'Keep Both' and 'Keep Merged'. [#9056](https://github.com/JabRef/jabref/issues/9056)
-
+- We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
 
 ### Fixed
 
+- We fixed the display of the "Customize Entry Types" dialogue title [#9198](https://github.com/JabRef/jabref/issues/9198)
 - We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
 - We fixed an issue where the possibility to generate a subdatabase from an aux file was writing empty files when called from the commandline [#9115](https://github.com/JabRef/jabref/issues/9115), [forum#3516](https://discourse.jabref.org/t/export-subdatabase-from-aux-file-on-macos-command-line/3516)
 - We fixed the display of issue, number, eid and pages fields in the entry preview. [#8607](https://github.com/JabRef/jabref/pull/8607), [#8372](https://github.com/JabRef/jabref/issues/8372), [Koppor#514](https://github.com/koppor/jabref/issues/514), [forum#2390](https://discourse.jabref.org/t/unable-to-edit-my-bibtex-file-that-i-used-before-vers-5-1/2390), [forum#3462](https://discourse.jabref.org/t/jabref-5-6-need-help-with-export-from-jabref-to-microsoft-word-entry-preview-of-apa-7-not-rendering-correctly/3462)
@@ -52,6 +54,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where JabRef would not exit when a connection to a LibreOffice document was established previously and the document is still open. [#9075](https://github.com/JabRef/jabref/issues/9075)
 - We fixed an issue about selecting the save order in the preferences. [#9175](https://github.com/JabRef/jabref/issues/9147)
 - We fixed an issue where the CSS styles are missing in some dialogs. [#9150](https://github.com/JabRef/jabref/pull/9150)
+- We fixed an issue where pdfs were re-indexed on each startup. [#9166](https://github.com/JabRef/jabref/pull/9166)
+- We fixed an issue where Capitalize didn't capitalize words after hyphen characters. [#9157](https://github.com/JabRef/jabref/issues/9157)
 
 ### Removed
 

build.gradle

@@ -132,8 +132,8 @@ dependencies {
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.4.0'
-    implementation 'org.libreoffice:unoloader:7.4.0'
+    implementation 'org.libreoffice:libreoffice:7.4.1'
+    implementation 'org.libreoffice:unoloader:7.4.1'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
     implementation 'info.debatty:java-string-similarity:2.0.0'
@@ -160,24 +160,25 @@ dependencies {
         exclude module: "jsr305"
     }
 
-    implementation group: 'jakarta.annotation', name: 'jakarta.annotation-api', version: '1.3.5'
+    implementation 'jakarta.annotation:jakarta.annotation-api:2.1.1'
+    implementation 'jakarta.inject:jakarta.inject-api:2.0.1'
 
-    // JavaFX stuff
+
+    implementation 'com.github.JabRef:afterburner.fx:testmoduleinfo-SNAPSHOT'
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
     implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
     implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2.1-SNAPSHOT'
     implementation 'org.fxmisc.flowless:flowless:0.6.10'
     implementation 'org.fxmisc.richtext:richtextfx:0.10.9'
-    implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.1.1'
 
     implementation 'org.jsoup:jsoup:1.15.3'
     implementation 'com.konghq:unirest-java:3.13.11'
 
-    implementation 'org.slf4j:slf4j-api:2.0.0'
+    implementation 'org.slf4j:slf4j-api:2.0.3'
     implementation "org.tinylog:tinylog-api:2.5.0"
     implementation "org.tinylog:slf4j-tinylog:2.5.0"
     implementation "org.tinylog:tinylog-impl:2.5.0"
@@ -204,8 +205,8 @@ dependencies {
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.149'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.0'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.9.0'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.1'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.9.1'
 
     testImplementation 'org.mockito:mockito-core:4.8.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
@@ -216,7 +217,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.3'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.4'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
@@ -560,7 +561,6 @@ jlink {
         requires 'java.transaction.xa'
         requires 'java.rmi'
         requires 'java.xml'
-        requires 'jdk.jfr'
         requires 'jdk.jsobject'
         requires 'jdk.unsupported'
         requires 'jdk.unsupported.desktop'
@@ -569,8 +569,6 @@ jlink {
         requires 'com.google.gson'
         requires 'org.slf4j'
         requires 'jakarta.xml.bind'
-        uses 'com.airhacks.afterburner.views.ResourceLocator'
-        uses 'com.airhacks.afterburner.injection.PresenterFactory'
         uses 'org.mariadb.jdbc.credential.CredentialPlugin'
         uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
         uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'

buildSrc/build.gradle

@@ -8,7 +8,7 @@ repositories {
 dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.214'
     implementation 'org.apache.commons:commons-csv:1.9.0'
-    implementation 'org.slf4j:slf4j-api:2.0.0'
+    implementation 'org.slf4j:slf4j-api:2.0.3'
 }
 
 sourceSets{

buildres/csl/csl-locales/.github/workflows/label-gun.yml

@@ -6,8 +6,13 @@ on:
   issue_comment:
     types: [created, edited, closed]
 
+permissions: {}
 jobs:
   label:
+    permissions:
+      issues: write # to add label to an issues (retorquere/label-gun)
+      pull-requests: write # to add label, comment on pull request (retorquere/label-gun)
+
     runs-on: ubuntu-latest
     steps:
       - uses: retorquere/label-gun@main

buildres/csl/csl-locales/.github/workflows/merge.yaml

@@ -12,8 +12,13 @@ on:
         description: Commit message
         required: true
 
+permissions: {}
 jobs:
   release:
+    permissions:
+      contents: write # to create a release
+      pull-requests: read # to read pull requests (dorny/paths-filter)
+
     runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

buildres/csl/csl-locales/.github/workflows/sheldon.yaml

@@ -4,8 +4,13 @@ on:
   pull_request_target:
     types: [ opened, synchronize, workflow_dispatch]
 
+permissions: {}
 jobs:
   test:
+    permissions:
+      contents: write # to push code in repo (stefanzweifel/git-auto-commit-action)
+      pull-requests: write # to comment on pull requests
+
     runs-on: ubuntu-latest
     env:
       GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"