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

* upstream/main: (149 commits)
  Add Tutorials for javafx
  lint
  Add changelot
  Open folder on mac and highlight file
  Add Tests to DoiCleanup (#8124)
  Improve Drag and Drop in Custom Entry types dialog (#8121)
  Show preview also for available styles (#8110)
  udpate to javafx 17.0.0.1
  Don't throw exception when validating invalid paths (#8112)
  Bump jackson-dataformat-yaml from 2.12.5 to 2.13.0
  Bump jackson-datatype-jsr310 from 2.12.5 to 2.13.0
  Bump byte-buddy-parent from 1.11.15 to 1.11.18
  Bump classgraph from 4.8.116 to 4.8.121
  Bump checkstyle from 9.0 to 9.0.1
  remove iso charset, website returns utf8 for icar comp sci only returns one result
  fix springer fetcher Fix computer science fetcher
  Squashed 'buildres/csl/csl-locales/' changes from 7a507fc008..495f888637
  Squashed 'buildres/csl/csl-styles/' changes from 5facb37..3b00357
  Update CHANGELOG.md
  snap: Use lzo compression & switch to core20 base
  ...

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,8 +11,8 @@ The title of the PR must not reference an issue, because GitHub does not support
 - [x] done; [ ] not done / not applicable
 -->
 
-- [] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
-- [] Tests created for changes (if applicable)
-- [] Manually tested changed features in running JabRef (always required)
-- [] Screenshots added in PR description (for UI changes)
-- [] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, submitted a pull request to the documentation repository.
+- [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
+- [ ] Tests created for changes (if applicable)
+- [ ] Manually tested changed features in running JabRef (always required)
+- [ ] Screenshots added in PR description (for UI changes)
+- [ ] [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.

.github/workflows/automerge.yml

@@ -21,7 +21,7 @@ jobs:
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/[email protected].2
+        uses: pascalgn/[email protected].3
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

.github/workflows/check-outdated-dependencies.yml

@@ -16,6 +16,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
+          cache: 'gradle'
       - name: Look for outdated dependencies
         run: ./gradlew -q checkOutdatedDependencies
       - name: Report issues

.github/workflows/deployment.yml

@@ -23,7 +23,8 @@ env:
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
   OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
-  GRADLE_OPTS: -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
+  GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
+  JAVA_OPTS: -Xmx4g
 
 jobs:
   build:
@@ -64,15 +65,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - name: Restore gradle cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7x-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle7x-
+          cache: 'gradle'
       - name: Setup OSX key chain on OSX
         if: matrix.os == 'macos-latest'
         uses: apple-actions/import-codesign-certs@v1
@@ -105,7 +98,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/') 
+        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/')
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')

.github/workflows/refresh-journal-lists.yml

@@ -20,11 +20,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+          cache: 'gradle'
       - name: Update journal lists
         run: |
           set +o pipefail

.github/workflows/tests-fetchers.yml

@@ -38,15 +38,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - uses: actions/cache@v2
-        name: Restore gradle cache
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle-
+          cache: 'gradle'
       - name: Run fetcher tests
         run: ./gradlew fetcherTest
         env:

.github/workflows/tests.yml

@@ -11,6 +11,8 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  GRADLE_OPTS: -Xmx4g
+  JAVA_OPTS: -Xmx4g
 
 jobs:
   checkstyle:
@@ -28,15 +30,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - name: Restore gradle cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle7-
+          cache: 'gradle'
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
@@ -60,15 +54,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - uses: actions/cache@v2
-        name: Restore gradle cache
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle7-
+          cache: 'gradle'
       - name: Run tests
         run: xvfb-run --auto-servernum ./gradlew check -x checkstyleJmh -x checkstyleMain -x checkstyleTest
         env:
@@ -100,15 +86,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - name: Restore gradle cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle7-
+          cache: 'gradle'
       - name: Run tests on PostgreSQL
         run: ./gradlew databaseTest --rerun-tasks
         env:
@@ -142,15 +120,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - uses: actions/cache@v2
-        name: Restore gradle cache
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle7-
+          cache: 'gradle'
       - name: Run GUI tests
         run: xvfb-run --auto-servernum ./gradlew guiTest
         env:
@@ -188,15 +158,7 @@ jobs:
         with:
           java-version: 16
           distribution: 'adopt'
-      - name: Restore gradle cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            ~/.gradle/caches
-            ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle7-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
-          restore-keys: |
-            ${{ runner.os }}-gradle7-
+          cache: 'gradle'
       - name: Update test coverage metrics
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);

CHANGELOG.md

@@ -11,11 +11,18 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added import support for CFF files. [#7945](https://github.com/JabRef/jabref/issues/7945)
 - We added the option to copy the DOI of an entry directly from the context menu copy submenu. [#7826](https://github.com/JabRef/jabref/issues/7826)
 - We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)
 - We improved the deduction of bib-entries from imported fulltext pdfs. [#7947](https://github.com/JabRef/jabref/pull/7947)
 - We added unprotect_terms to the list of bracketed pattern modifiers [#7826](https://github.com/JabRef/jabref/pull/7960)
+- We added a dialog that allows to parse metadata from linked pdfs. [#7929](https://github.com/JabRef/jabref/pull/7929)
 - We added an icon picker in group edit dialog. [#6142](https://github.com/JabRef/jabref/issues/6142)
+- We added a preference to Opt-In to JabRef's online metadata extraction service (Grobid) usage. [#8002](https://github.com/JabRef/jabref/pull/8002)
+- We readded the possibility to display the search results of all databases ("Global Search"). It is shown in a separate window. [#4096](https://github.com/JabRef/jabref/issues/4096)
+- We readded the possibility to keep the search string when switching tabs. It is implemented by a toggle button. [#4096](https://github.com/JabRef/jabref/issues/4096#issuecomment-575986882)
+- We allowed the user to also preview the available citation styles in the preferences besides the selected ones [#8108](https://github.com/JabRef/jabref/issues/8108)
+- We added an option to search the available citation styles by name in the preferences [#8108](https://github.com/JabRef/jabref/issues/8108)
 
 ### Changed
 
@@ -25,14 +32,21 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We merged the barely used ImportSettingsTab and the CustomizationTab in the preferences into one single tab and moved the option to allow Integers in Edition Fields in Bibtex-Mode to the EntryEditor tab. [#7849](https://github.com/JabRef/jabref/pull/7849)
 - We moved the export order in the preferences from `File` to `Import and Export`. [#7935](https://github.com/JabRef/jabref/pull/7935)
 - We reworked the export order in the preferences and the save order in the library preferences. You can now set more than three sort criteria in your library preferences. [#7935](https://github.com/JabRef/jabref/pull/7935)
+- The metadata-to-pdf actions now also embeds the bibfile to the PDF. [#8037](https://github.com/JabRef/jabref/pull/8037)
+- The snap was updated to use the core20 base and to use lzo compression for better startup performance [#8109](https://github.com/JabRef/jabref/pull/8109)
+- We improved the Drag and Drop behavior in the "Customize Entry Types" Dialog [#6338](https://github.com/JabRef/jabref/issues/6338)
 
 ### Fixed
 
+- We fixed an issue where an exception ocurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
 - We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
 - We fixed some icons that were drawn in the wrong color when JabRef used a custom theme. [#7853](https://github.com/JabRef/jabref/issues/7853)
 - We fixed an issue where the `Aux file` on `Edit group` doesn't support relative sub-directories path to import. [#7719](https://github.com/JabRef/jabref/issues/7719).
 - We fixed an issue where it was impossible to add or modify groups. [#7912](https://github.com/JabRef/jabref/pull/793://github.com/JabRef/jabref/pull/7921)
 - We fixed an issue where exported entries from a Citavi bib containing URLs could not be imported [#7892](https://github.com/JabRef/jabref/issues/7882)
+- We fixed an issue where the icons in the search bar had the same color, toggled as well as untoggled. [#8014](https://github.com/JabRef/jabref/pull/8014)
+- We fixed an issue where typing an invalid UNC path into the "Main file directory" text field caused an error. [#8107](https://github.com/JabRef/jabref/issues/8107)
+- We fixed an issue where "Open Folder" didn't select the file on macOS in Finder [#8130](https://github.com/JabRef/jabref/issues/8130)
 
 ### Removed
 

MAINTAINERS

@@ -7,3 +7,4 @@ Linus Dietz (since 2017)
 Carl Christian Snethlage (since 2020)
 Dominik Voigt (since 2020)
 Jonatan Askertop (since 2021)
+Benedikt Tutzer (since 2021)

README.md

@@ -96,4 +96,9 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 
 `gradlew test` executes all tests. We use [Github Actions](https://github.com/JabRef/jabref/actions) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Github will report any other failure.
 
+## Sponsoring
+
+JabRef development is powered by YourKit Java Profiler [![YourKit Java Profiler](https://www.yourkit.com/images/yk_logo.png)](https://www.yourkit.com/java/profiler/)
+
+
 [JabRef]: https://www.jabref.org