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

* upstream/main: (259 commits)
  Fix exception on preview style edit and selection (#8293)
  Fix icon picker excpetion in groups dialog (#8290)
  Add doc tests (#8242)
  fix merge conflict
  Squashed 'buildres/csl/csl-locales/' changes from 0cc3885f61..d5ee85de8e
  Squashed 'buildres/csl/csl-styles/' changes from 3a6a0a7..3bb4b5f
  Consider directory pattern when checking if a file can be moved (#8244)
  Bump byte-buddy-parent from 1.12.1 to 1.12.2 (#8285)
  Bump unirest-java from 3.13.3 to 3.13.4 (#8283)
  Bump checkstyle from 9.1 to 9.2 (#8284)
  Bump classgraph from 4.8.135 to 4.8.137 (#8282)
  Do not resize main table columns in search dialog window (#8253)
  Fix NegativeArraySizeException (#8270)
  Update deployment.yml
  TEst
  Grand unified library properties (GRULPS) (#8264)
  Fixes RFC fetcher test case (#8271)
  Update Gradle Wrapper from 7.2 to 7.3 (#8246)
  Observable Preferences H (WorkingDir, getUser, NameFormatter, Version, SpecialFields) (#8260)
  Bump checkstyle from 9.0.1 to 9.1 (#8266)
  ...

Author: Siedlerchr

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -27,7 +27,7 @@ body:
       options:
         - Windows
         - GNU / Linux
-        - mac OS
+        - macOS
         - Other (please describe below)
     validations:
       required: true
@@ -36,7 +36,7 @@ body:
     attributes:
       label: Details on version and operating system
       description: OS Version, distribution, desktop environment, older JabRef version etc.
-      placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / Mac OS 10.14
+      placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / macOS 10.14
     validations:
       required: false
 
@@ -70,10 +70,13 @@ body:
       value: |
         ...
         <details>
+
         <summary>Log File</summary>
+
         ```
         Paste an excerpt of your log file here
         ```
+
         </details>
     validations:
       required: false

.github/workflows/check-links.yaml

@@ -7,6 +7,7 @@ on:
   schedule:
     # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
     - cron: "0 9 1 * *"
+  workflow_dispatch:
 
 jobs:
   markdown-link-check:

.github/workflows/deployment.yml

@@ -26,6 +26,11 @@ env:
   GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
   JAVA_OPTS: -Xmx4g
 
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+
 jobs:
   build:
     strategy:
@@ -45,21 +50,17 @@ jobs:
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v2
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -155,12 +156,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].10
+        uses: gittools/actions/gitversion/[email protected].11
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.github/workflows/gource.yml

@@ -6,6 +6,7 @@ on:
       - gource
   schedule:
     - cron:  '15 3 1 1,4,7,10 *'
+  workflow_dispatch:
 
 jobs:
   action:

.github/workflows/snap.yml

@@ -9,6 +9,10 @@ on:
    # run on each day
   - cron: "33 4 * * *"
 
+concurrency:
+  group: snap-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest

.github/workflows/tests-fetchers.yml

@@ -20,12 +20,17 @@ on:
   schedule:
     # run on each Wednesday
     - cron: '2 3 * * 3'
+  workflow_dispatch:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
 
+concurrency:
+  group: fetcher-tests-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   fetchertests:
     name: Fetcher tests

.github/workflows/tests.yml

@@ -3,9 +3,11 @@ name: Tests
 on:
   push:
     branches:
-      - master
+      - main
+      - main-release
   pull_request:
     # always run on pull requests
+  workflow_dispatch:
 
 env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
@@ -14,15 +16,15 @@ env:
   GRADLE_OPTS: -Xmx4g
   JAVA_OPTS: -Xmx4g
 
+concurrency:
+  group: tests-${{ github.head_ref }}
+  cancel-in-progress: true
+
 jobs:
   checkstyle:
     name: Checkstyle
     runs-on: ubuntu-latest
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
@@ -41,7 +43,7 @@ jobs:
       - name: Run markdown-lint
         uses: avto-dev/markdown-lint@v1
         with:
-          args: CHANGELOG.md CONTRIBUTING.md README.md docs/
+          args: CHANGELOG.md CONTRIBUTING.md README.md
           config: '.markdownlint.yml'
   tests:
     name: Unit tests

.markdownlint.yml

@@ -1,24 +1,8 @@
 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
-
+# allow arbitrary line length
 MD013: false
 
-# The FAQs state questions - we allow them
-MD026:
-  punctuation: ".,;:!"
-
-# not supported by gitbook
-MD031: false
-
 MD033:
   # we have <a> tags with ids and superscript
   allowed_elements: ['a', 'kbd', 'sup']
-
-# seems to be unsupported by gitbook anymore
-MD045: false

CHANGELOG.md

@@ -11,6 +11,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added confirmation dialog when user wants to close a library where any empty entires are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
 - 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)
@@ -21,30 +22,61 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- We added an option to generate bib-entries from ID through a popover in the toolbar. [#4183](https://github.com/JabRef/jabref/issues/4183)
+- We added a menu option in the right click menu of the main table tabs to display the library properties. [#6527](https://github.com/JabRef/jabref/issues/6527)
+- When a `.bib` file ("library") was saved successfully, a notification is shown
 
 ### Changed
 
+- Local library settings may overwrite the setting "Search and store files relative to library file location" [#8179](https://github.com/JabRef/jabref/issues/8179)
+- The option "Fit table horizontally on screen" in the "Entry table" preferences is now disabled by default [#8148](https://github.com/JabRef/jabref/pull/8148)
+- We improved the preferences and descriptions in the "Linked files" preferences tab [#8148](https://github.com/JabRef/jabref/pull/8148)
 - We slightly changed the layout of the Journal tab in the preferences for ui consistency. [#7937](https://github.com/JabRef/jabref/pull/7937)
 - The JabRefHost on Windows now writes a temporary file and calls `-importToOpen` instead of passing the bibtex via `-importBibtex`. [#7374](https://github.com/JabRef/jabref/issues/7374), [JabRef Browser Ext #274](https://github.com/JabRef/JabRef-Browser-Extension/issues/274)
 - We reordered some entries in the right-click menu of the main table. [#6099](https://github.com/JabRef/jabref/issues/6099)
 - 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)
+- When determining the URL of an ArXiV eprint, the URL now points to the version [#8149](https://github.com/JabRef/jabref/pull/8149)
+- We Included all standard fields with citation key when exporting to Old OpenOffice/LibreOffice Calc Format [#8176](https://github.com/JabRef/jabref/pull/8176)
+- In case the database is encoded with `UTF8`, the `% Encoding` marker is not written anymore
+- The written `.bib` file has the same line endings [#390](https://github.com/koppor/jabref/issues/390)
+- The written `.bib` file always has a final line break
+- The written `.bib` file keeps the newline separator of the loaded `.bib` file
+- We present options to manually enter an article or return to the New Entry menu when the fetcher DOI fails to find an entry for an ID [#7870](https://github.com/JabRef/jabref/issues/7870)
+- We trim white space and non-ASCII characters from DOI [#8127](https://github.com/JabRef/jabref/issues/8127)
+- The duplicate checker now inspects other fields in case no difference in the required and optional fields are found.
+- We reworked the library properties dialog and integrated the `Library > Preamble`, `Library > Citation key pattern` and `Library > String constants dialogs` [#8264](https://github.com/JabRef/jabref/pulls/8264)
 
 ### 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 where an exception occured when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
+- We fixed an issue where the actions to move a file to a directory were incorrectly disabled. [#7908](https://github.com/JabRef/jabref/issues/7908)
+- We fixed an issue where an exception occurred 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)
+- We fixed an issue where importing PDFs resulted in an uncaught exception [#8143](https://github.com/JabRef/jabref/issues/8143)
+- We fixed "The library has been modified by another program" showing up when line breaks change [#4877](https://github.com/JabRef/jabref/issues/4877)
+- The default directory of the "LaTeX Citations" tab is now the directory of the currently opened database (and not the directory chosen at the last open file dialog or the last database save) [koppor#538](https://github.com/koppor/jabref/issues/538)
+- When writing a bib file, the `NegativeArraySizeException` should not occur [#8231](https://github.com/JabRef/jabref/issues/8231) [#8265](https://github.com/JabRef/jabref/issues/8265)
+- We fixed an issue where right-clicking on a tab and selecting close will close the focused tab even if it is not the tab we right-clicked [#8193](https://github.com/JabRef/jabref/pull/8193)
+- We fixed an issue where selecting a citation style in the preferences would sometimes produce an exception [#7860](https://github.com/JabRef/jabref/issues/7860)
+- We fixed an issue where an exception would occur when clicking on a DOI link in the preview pane [#7706](https://github.com/JabRef/jabref/issues/7706)
 
 ### Removed
 
-
+- We removed two orphaned preferences options [#8164](https://github.com/JabRef/jabref/pull/8164)
 
 
 

README.md

@@ -100,5 +100,4 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 
 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