Merge remote-tracking branch 'upstream/master' into fix_6453

* upstream/master: (243 commits)
  fix checkstyle
  mEDRA DOI fetcher implementation. (#6641)
  Bump bcprov-jdk15on from 1.65.01 to 1.66 (#6676)
  Bump appleboy/ssh-action from v0.0.6 to v0.1.2 (#6674)
  Add localisation strings and renamed formatter
  Bump gittools/actions from v0.9.2 to v0.9.3 (#6675)
  Skip non-working sourcespy site
  Let dependabot update github actions
  Add three formatters to fix new lines in abstract and digits in editors
  Update src/test/java/org/jabref/logic/importer/fetcher/CollectionOfComputerScienceBibliographiesParserTest.java
  Fix to imports
  Make fetcher test more specific by checking each field explicitly
  Use builder instead of "setField" statements
  (docs) fix styling
  Update jpackage notes
  Fix automerge workflow
  fix markdown
  Bump org.beryx.jlink from 2.20.0 to 2.21.0
  Bump unirest-java from 3.8.00 to 3.8.06
  Fix to dependency on Global
  ...

.github/dependabot.yml

@@ -0,0 +1,25 @@
+version: 2
+updates:
+- package-ecosystem: gradle
+  directory: "/"
+  schedule:
+    interval: weekly
+  open-pull-requests-limit: 10
+  labels:
+  - "type: dependencies"
+  ignore:
+  - dependency-name: com.microsoft.azure:applicationinsights-core
+    versions:
+    - ">= 2.5.a, <= 2.6.1" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
+  - dependency-name: com.microsoft.azure:applicationinsights-logging-log4j2
+    versions:
+    - ">= 2.5.a, <= 2.6.1" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
+  - dependency-name: de.jensd:fontawesomefx-materialdesignfont
+    versions:
+    - "> 1.7.22-4" # Strange versioning format
+- package-ecosystem: "github-actions"
+  directory: "/"
+  schedule:
+    interval: weekly
+  labels:
+  - "type: dependencies"

.github/workflows/automerge.yml

@@ -0,0 +1,24 @@
+name: Automerge Pull Requests
+on: [pull_request]
+
+jobs:
+  automerge:
+    name: Automerge Dependabot
+    runs-on: ubuntu-latest
+    if: github.actor == 'dependabot[bot]'
+    steps:
+      - name: 'Wait for status checks'
+        id: waitforstatuschecks
+        uses: "WyriHaximus/github-action-wait-for-status@0.1.0"
+        with:
+          ignoreActions: automerge
+          checkInterval: 13
+        env:
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+      - name: Merge pull requests
+        uses: pascalgn/automerge-action@v0.8.4
+        if: steps.waitforstatuschecks.outputs.status == 'success'
+        env:
+          MERGE_METHOD: "squash"
+          MERGE_LABELS: ""
+          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/cleanup_pr.yml

@@ -27,7 +27,7 @@ jobs:
           echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
       - name: Delete folder on builds.jabref.org
         if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/ssh-action@v0.0.6
+        uses: appleboy/ssh-action@v0.1.2
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

.github/workflows/deployment.yml

@@ -17,6 +17,8 @@ on:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
+  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
+  IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
 
 jobs:
   build:
@@ -44,12 +46,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.2
+        uses: gittools/actions/gitversion/setup@v0.9.3
         with:
           versionSpec: '5.2.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.2
+        uses: gittools/actions/gitversion/execute@v0.9.3
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:
@@ -101,12 +103,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.2
+        uses: gittools/actions/gitversion/setup@v0.9.3
         with:
           versionSpec: '5.2.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.2
+        uses: gittools/actions/gitversion/execute@v0.9.3
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.github/workflows/tests-fetchers.yml

@@ -23,6 +23,8 @@ on:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
+  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
+  IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
 
 jobs:
   fetchertests:

.github/workflows/tests.yml

@@ -9,6 +9,8 @@ on:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
+  AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
+  IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
 
 jobs:
   checkstyle:
@@ -37,6 +39,20 @@ jobs:
           key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
       - name: Run checkstyle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
+      - name: Run markdown-lint
+        uses: avto-dev/markdown-lint@v1
+        with:
+          args: CHANGELOG.md CONTRIBUTING.md README.md docs/
+          config: '.markdownlint.yml'
+      - name: Prepare markdown-link-check
+        run: mkdir docs/ROOT && cp CHANGELOG.md README.md docs/ROOT
+      - name: Run markdown-link-check
+        uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          use-quiet-mode: 'yes'
+          use-verbose-mode: 'no'
+          config-file: 'mlc_config.json'
+          folder-path: 'docs/'
   tests:
     name: Unit tests
     runs-on: ubuntu-latest

.mailmap

@@ -200,3 +200,5 @@ Gennadiy Stakhovskiy <GennadiyStakhovskiy@gmail.com>
 Mootez Saad <34676841+MootezSaaD@users.noreply.github.com>
 Mootez Saad <34676841+MootezSaaD@users.noreply.github.com> <mootez.saad@medtech.tn>
 Chen Yuheng <pass@chenyuheng.cn>
+Dominik Voigt <43381984+DominikVoigt@users.noreply.github.com>
+Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com> <cc.snethlage@gmail.com>

.markdownlint.yml

@@ -0,0 +1,18 @@
+default: true
+
+# Using h2 has side effects in GitBook's toc. Thus, we sometimes switch from h1 to h3
+MD001: false
+
+MD012:
+  # 2 are required, because GitBook adss two blank lines at the end of a file
+  maximum: 2
+
+MD013: false
+
+# The FAQs state questions - we allow them
+MD026:
+  punctuation: ".,;:!"
+
+MD033:
+  # we have <a> tags with ids
+  allowed_elements: ['a']

AUTHORS

@@ -29,6 +29,7 @@ Andreas Buhr
 Andreas Rudert
 Andrew Collins
 Andrew Levit
+André Schlichting
 Andrés Sánchez
 Anh Nghia Tran
 Anita Armbruster
@@ -40,6 +41,7 @@ August Janse
 Ayachi Nene
 Bartosz J. Kaczkowski
 Bartłomiej Dach
+Baruch Oltman
 Behrouz Javanmardi
 Benedikt Tutzer
 Benjamin Köhler
@@ -96,6 +98,7 @@ Dimitra Karadima
 Domenico Cufalo
 Dominik Schrempf
 Dominik Traczyk
+Dominik Voigt
 Dominik Waßenhoven
 Douglas Nassif Roma Junior
 Eduard Braun
@@ -260,6 +263,7 @@ Nick S. Weatherley
 Nico Schlömer
 Nicolas Pavillon
 Nikita Borovikov
+Niklas Schmitt
 nikmilpv
 NikodemKch
 Niv Ierushalmi

CHANGELOG.md

@@ -10,6 +10,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ## [Unreleased]
 
 ### Added
+
+- We added a new fetcher to enable users to search mEDRA DOIs [#6602](https://github.com/JabRef/jabref/issues/6602)
+- We added a new fetcher to enable users to search "[Collection of Computer Science Bibliographies](https://liinwww.ira.uka.de/bibliography/index.html)". [#6638](https://github.com/JabRef/jabref/issues/6638)
+- We added default values for delimiters in Add Subgroup window [#6624](https://github.com/JabRef/jabref/issues/6624)
+- We improved responsiveness of general fields specification dialog window. [#6643](https://github.com/JabRef/jabref/issues/6604)
+- We added support for importing ris file and load DOI [#6530](https://github.com/JabRef/jabref/issues/6530)
 - We added the Library properties to a context menu on the library tabs [#6485](https://github.com/JabRef/jabref/issues/6485)
 - We added a new field in the preferences in 'BibTeX key generator' for unwanted characters that can be user-specified. [#6295](https://github.com/JabRef/jabref/issues/6295)
 - We added support for searching ShortScience for an entry through the user's browser. [#6018](https://github.com/JabRef/jabref/pull/6018)
@@ -24,6 +30,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed the bug when strike the delete key in the text field. [#6421](https://github.com/JabRef/jabref/issues/6421)
 - We added a BibTex key modifier for truncating strings. [#3915](https://github.com/JabRef/jabref/issues/3915)
 - We added support for jumping to target entry when typing letter/digit after sorting a column in maintable [#6146](https://github.com/JabRef/jabref/issues/6146)
+- We added a new fetcher to enable users to search all available E-Libraries simultaneously. [koppor#369](https://github.com/koppor/jabref/issues/369)
+- We added the field "entrytype" to the export sort criteria [#6531](https://github.com/JabRef/jabref/pull/6531)
+- We added the possibility to change the display order of the fields in the entry editor. The order can now be configured using drag and drop in the "Customize entry types" dialog [#6152](https://github.com/JabRef/jabref/pull/6152)
 
 ### Changed
 
@@ -37,9 +46,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We improved the error message for invalid jstyles. [#6303](https://github.com/JabRef/jabref/issues/6303)
 - We changed the section name of 'Advanced' to 'Network' in the preferences and removed some obsolete options.[#6489](https://github.com/JabRef/jabref/pull/6489)
 - We improved the context menu of the column "Linked identifiers" of the main table, by truncating their texts, if they are too long. [#6499](https://github.com/JabRef/jabref/issues/6499)
+- We merged the main table tabs in the preferences dialog. [#6518](https://github.com/JabRef/jabref/pull/6518)
+- We changed the command line option 'generateBibtexKeys' to the more generic term 'generateCitationKeys' while the short option remains 'g'.[#6545](https://github.com/JabRef/jabref/pull/6545)
+- We improved the "Possible duplicate entries" window to remember its size and position throughout a session. [#6582](https://github.com/JabRef/jabref/issues/6582)
 
 ### Fixed
 
+- We fixed an issue where entry preview tab has no name in drop down list. [#6591](https://github.com/JabRef/jabref/issues/6591)
+- We fixed to only search file links in the BIB file location directory when preferences has corresponding checkbox checked. [#5891](https://github.com/JabRef/jabref/issues/5891)
 - We fixed wrong button order (Apply and Cancel) in ManageProtectedTermsDialog.
 - We fixed an issue with incompatible characters at BibTeX key [#6257](https://github.com/JabRef/jabref/issues/6257)
 - We fixed an issue where dash (`-`) was reported as illegal BibTeX key [#6295](https://github.com/JabRef/jabref/issues/6295)
@@ -70,8 +84,17 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where an "Not on FX thread" exception occured when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
 - We fixed an issue where the library sort order was lost. [#6091](https://github.com/JabRef/jabref/issues/6091)
 - We fixed an issue where brackets in regular expressions were not working. [6469](https://github.com/JabRef/jabref/pull/6469)
+- We fixed an issue where multiple background task popups stacked over each other.. [#6472](https://github.com/JabRef/jabref/issues/6472)
 - We fixed an issue where LaTeX citations for specific commands (\autocites) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
 - We fixed an issue where drag and drop was not working on empty database. [#6487](https://github.com/JabRef/jabref/issues/6487)
+- We fixed an issue where the name fields were not updated after the preferences changed. [#6515](https://github.com/JabRef/jabref/issues/6515)
+- We fixed an issue where "null" appeared in generated BibTeX keys. [#6459](https://github.com/JabRef/jabref/issues/6459)
+- We fixed an issue where the authors' names were incorrectly displayed in the authors' column when they were bracketed. [#6465](https://github.com/JabRef/jabref/issues/6465) [#6459](https://github.com/JabRef/jabref/issues/6459)
+- We fixed an issue where importing certain unlinked files would result in an exception [#5815](https://github.com/JabRef/jabref/issues/5815)
+- We fixed an issue where downloaded files would be moved to a directory named after the citationkey when no file directory pattern is specified [#6589](https://github.com/JabRef/jabref/issues/6589)
+- We fixed an issue with the creation of a group of cited entries which incorrectly showed the message that the library had been modified externally whenever saving the library. [#6420](https://github.com/JabRef/jabref/issues/6420)
+- We fixed an issue with the creation of a group of cited entries. Now the file path to an aux file gets validated. [#6585](https://github.com/JabRef/jabref/issues/6585)
+- We fixed an issue on Linux systems where the application would crash upon inotify failure. Now, the user is prompted with a warning, and given the choice to continue the session. [#6073](https://github.com/JabRef/jabref/issues/6073)
 
 ### Removed
 
@@ -128,6 +151,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the blue and red text colors in the Merge entries dialog were not quite visible [#6334](https://github.com/JabRef/jabref/issues/6334)
 - We fixed an issue where underscore character was removed from the file name in the Recent Libraries list in File menu [#6383](https://github.com/JabRef/jabref/issues/6383)
 - We fixed an issue where few keyboard shortcuts regarding new entries were missing [#6403](https://github.com/JabRef/jabref/issues/6403)
+
 ### Removed
 
 - Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action. [#5869](https://github.com/JabRef/jabref/issues/5869)
@@ -303,8 +327,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. [#3119](https://github.com/JabRef/jabref/issues/3119)
 - We improved the parsing of author names whose infix is abbreviated without a dot. [#4864](https://github.com/JabRef/jabref/issues/4864)
-- We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
-- We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
+- We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. [#3373](https://github.com/JabRef/jabref/issues/3373)
+- We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. [#3146](https://github.com/JabRef/jabref/issues/3146)
 - We improved the integrity check for page numbers. [#4113](https://github.com/JabRef/jabref/issues/4113) and [feature request in the forum](http://discourse.jabref.org/t/pages-field-allow-use-of-en-dash/1199)
 - We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
 - We fixed an issue where renaming a group did not change the group name in the interface. [#3189](https://github.com/JabRef/jabref/issues/3189)
@@ -341,6 +365,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the "Attach file" dialog, in the right-click menu for an entry, started on the working directory instead of the user's main directory. [#4995](https://github.com/JabRef/jabref/issues/4995)
 - We fixed an issue where the JabRef Icon in the macOS launchpad was not displayed correctly [#5003](https://github.com/JabRef/jabref/issues/5003)
 - We fixed an issue where the "Search for unlinked local files" would throw an exception when parsing the content of a PDF-file with missing "series" information [#5128](https://github.com/JabRef/jabref/issues/5128)
+- We fixed an issue where the XMP Importer would incorrectly return an empty default entry when importing pdfs [#6577](https://github.com/JabRef/jabref/issues/6577)
+- We fixed an issue where opening the menu 'Library properties' marked the library as modified [#6451](https://github.com/JabRef/jabref/issues/6451)
 
 ### Removed
 

README.md

@@ -3,12 +3,12 @@
 JabRef is an open-source, cross-platform citation and reference management tool.
 
 Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research.
-![main table](https://www.jabref.org/img/jabref-5-0-maintable.png)
+![main table](http://www.jabref.org/img/jabref-mainscreen.png)
 
 ## Features
 
-JabRef is a cross-platform application that works on Windows, Linux and Mac OS X. It is available free of charge and is actively developed.
-JabRef supports you in every step of your research work.
+JabRef is available free of charge and is actively developed.
+It supports you in every step of your research work.
 
 ### Collect
 
@@ -33,7 +33,7 @@ JabRef supports you in every step of your research work.
 
 ### Cite
 
-- Native [BibTeX] and [Biblatex] support
+- Native BibTeX and Biblatex support
 - Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt.
 - Format references in one of the many thousand built-in citation styles or create your style
 - Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
@@ -47,11 +47,9 @@ JabRef supports you in every step of your research work.
 ## Installation
 
 Fresh development builds are available at [builds.jabref.org](https://builds.jabref.org/master/).
-The [latest stable release is available at FossHub](https://www.fosshub.com/JabRef.html).
+The [latest stable release is available at FossHub](https://downloads.jabref.org/).
 
-- Windows: JabRef offers an installer, which also adds a shortcut to JabRef to your start menu. Please also see our [Windows FAQ](https://docs.jabref.org/faq/faqwindows)
-- Linux: Please see our [Installation Guide](https://docs.jabref.org/general/installation).
-- Mac OS X: Please see our [Mac OS X FAQ](https://docs.jabref.org/faq/faqosx).
+Please see our [Installation Guide](https://docs.jabref.org/installation).
 
 ## Bug Reports, Suggestions, Other Feedback
 
@@ -98,8 +96,4 @@ 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.
 
-[BibTeX]: https://www.ctan.org/pkg/bibtex
-[Biblatex]: https://www.ctan.org/pkg/biblatex
-[install4j]: https://www.ej-technologies.com/products/install4j/overview.html
 [JabRef]: https://www.jabref.org
-[JavaFX]: https://en.wikipedia.org/wiki/JavaFX