Merge remote-tracking branch 'upstream/main' into controlsfx-tags

* upstream/main: (68 commits) Fix issue 9863 - Change Tab selection order (#9907) New Crowdin updates (#9994) Enable editing typo with double clicking on field name in custom entry type (#9977) Remove "Field name:" from localization - we already have "Field name" (#9991) Changed database to catalog in org.jabref.gui.slr and org.jabref.logic.crawler (#9989) Use environment variables for hostname detection (#9910) Add cleanup activity for URL field (#9970) Fix freezing when fetching IBSN and no results are found (#9987) Make Group(Node)TreeViewModel more OO (#9978) Fix container for group item count still visible if display count is off (#9980) Fix paste of BibTeX data (#9985) Bring back SimplifyBoolean* and UnnecessaryParantheses (and refine guide) (#9981) Add new menu entry to remove braces from selection, aka unprotect it. (#9968) User specific comment (#9727) Bump org.openrewrite.recipe:rewrite-recipe-bom from 1.19.3 to 2.0.0 (#9975) Fix typos Remove non-needed link Fix typos Enable RemoveJavaDocAuthorTag (#9973) Bump com.fasterxml.jackson.datatype:jackson-datatype-jsr310 (#9974) ...
JabRef · Jun 10, 2023 · 3512118 · 3512118
2 parents 77d2c0f + 94f964c
commit 3512118
Show file tree

Hide file tree

Showing 160 changed files with 6,497 additions and 2,786 deletions.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -11,12 +11,10 @@ The title of the PR must not reference an issue, because GitHub does not support
 - [x] done; [ ] not done / not applicable
 -->
 
-```[tasklist]
-### Compulsory checks
+### Mandatory checks
 - [ ] 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 developer's documentation](https://devdocs.jabref.org/): Is the information available and up to date? If not, I outlined it in this pull request.
 - [ ] [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.
-```
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.7.1"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.8.0"
         with:
           ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Added
 
 - We added a field showing the BibTeX/biblatex source for added and deleted entries in the "External Changes Resolver" dialog. [#9509](https://github.com/JabRef/jabref/issues/9509)
+- We added user-specific comment field so that multiple users can make separate comments. [#543](https://github.com/koppor/jabref/issues/543)
 - We added a search history list in the search field's right click menu. [#7906](https://github.com/JabRef/jabref/issues/7906)
 - We added a full text fetcher for IACR eprints. [#9651](https://github.com/JabRef/jabref/pull/9651)
 - We added "Attach file from URL" to right-click context menu to download and store a file with the reference library. [#9646](https://github.com/JabRef/jabref/issues/9646)
@@ -21,10 +22,19 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added support for multiple languages for exporting to and importing references from MS Office. [#9699](https://github.com/JabRef/jabref/issues/9699)
 - We enabled scrolling in the groups list when dragging a group on another group. [#2869](https://github.com/JabRef/jabref/pull/2869)
 - We added the option to automatically download online files when a new entry is created from an existing ID (e.g., DOI). The option can be disabled in the preferences under "Import and Export". [#9756](https://github.com/JabRef/jabref/issues/9756)
-- We added a new Integrity check for unscaped ampersands. [koppor#585](https://github.com/koppor/jabref/issues/585)
+- We added a new Integrity check for unescaped ampersands. [koppor#585](https://github.com/koppor/jabref/issues/585)
 - We added support for parsing `$\backslash$` in file paths (as exported by Mendeley). [forum#3470](https://discourse.jabref.org/t/mendeley-bib-import-with-linked-files/3470)
 - We added the possibility to automatically fetch entries when an ISBN is pasted on the main table. [#9864](https://github.com/JabRef/jabref/issues/9864)
 - We added the option to disable the automatic linking of files in the entry editor [#5105](https://github.com/JabRef/jabref/issues/5105)
+- We added the link icon for ISBNs in linked identifiers column. [#9819](https://github.com/JabRef/jabref/issues/9819)
+- We added key binding to focus on groups <kbd>alt</kbd> + <kbd>s</kbd> [#9863](https://github.com/JabRef/jabref/issues/9863)
+- We added the option to unprotect a text selection, which strips all pairs of curly braces away. [#9950](https://github.com/JabRef/jabref/issues/9950)
+- We added drag and drop events for field 'Groups' in entry editor panel. [#569](https://github.com/koppor/jabref/issues/569)
+- We added support for parsing MathML in the Medline importer. [#4273](https://github.com/JabRef/jabref/issues/4273)
+- We added the ability to search for a DOI directly from 'Web Search'. [#9674](https://github.com/JabRef/jabref/issues/9674)
+- We added a cleanup activity that identifies a URL in the `note` field and moves it to the `url` field. [koppor#216](https://github.com/koppor/jabref/issues/216)
+- We enabled the user to change the name of a field in a custom entry type by double-clicking on it. [#9840](https://github.com/JabRef/jabref/issues/9840)
+
 
 ### Changed
 
@@ -35,10 +45,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625)
 - JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
 - Backups of libraries are not stored per JabRef version, but collected together.
-- We streamlined the paths for logs and backups: The parent path fragement is always `logs` or `backups`.
+- We streamlined the paths for logs and backups: The parent path fragment is always `logs` or `backups`.
 - `log.txt` now contains an entry if a BibTeX entry could not be parsed.
 - `log.txt` now contains debug messages. Debugging needs to be enabled explicitly. [#9678](https://github.com/JabRef/jabref/pull/9678)
 - `log.txt` does not contain entries for non-found files during PDF indexing. [#9678](https://github.com/JabRef/jabref/pull/9678)
+- The hostname is now determined using environment variables (`COMPUTERNAME`/`HOSTNAME`) first. [#9910](https://github.com/JabRef/jabref/pull/9910)
 - We improved the Medline importer to correctly import ISO dates for `revised`. [#9536](https://github.com/JabRef/jabref/issues/9536)
 - To avoid cluttering of the directory, We always delete the `.sav` file upon successful write. [#9675](https://github.com/JabRef/jabref/pull/9675)
 - We improved the unlinking/deletion of multiple linked files of an entry using the <kbd>Delete</kbd> key. [#9473](https://github.com/JabRef/jabref/issues/9473)
@@ -54,6 +65,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We moved the option to run JabRef in memory stick mode into the preferences dialog toolbar. [#9866](https://github.com/JabRef/jabref/pull/9866)
 - In case the library contains empty entries, they are not written to disk. [#8645](https://github.com/JabRef/jabref/issues/8645)
 - The formatter `remove_unicode_ligatures` is now called `replace_unicode_ligatures`. [#9890](https://github.com/JabRef/jabref/pull/9890)
+- We improved the error message when no terminal was found [#9607](https://github.com/JabRef/jabref/issues/9607)
+- In the context of the "systematic literature functionality", we changed the name "database" to "catalog" to use a separate term for online catalogs in comparison to SQL databases. [#9951](https://github.com/JabRef/jabref/pull/9951)
 
 ### Fixed
 
@@ -67,7 +80,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the Merge Entries Toolbar configuration was not saved after hitting 'Merge Entries' button. [#9091](https://github.com/JabRef/jabref/issues/9091)
 - We fixed an issue where the password is saved locally if user wants to use proxy with authentication. [#8055](https://github.com/JabRef/jabref/issues/8055)
 - JabRef is now more relaxed when parsing field content: In case a field content ended with `\`, the combination `\}` was treated as plain `}`. [#9668](https://github.com/JabRef/jabref/issues/9668)
-- We resolved an issue that cut off the number of group entries when it exceedet four digits. [#8797](https://github.com/JabRef/jabref/issues/8797)
+- We resolved an issue that cut off the number of group entries when it exceeded four digits. [#8797](https://github.com/JabRef/jabref/issues/8797)
 - We fixed the issue where the size of the global search window was not retained after closing. [#9362](https://github.com/JabRef/jabref/issues/9362)
 - We fixed an issue where the Global Search UI preview is still white in dark theme. [#9362](https://github.com/JabRef/jabref/issues/9362)
 - We fixed the double paste issue when <kbd>Cmd</kbd> + <kbd>v</kbd> is pressed on 'New entry from plaintext' dialog. [#9367](https://github.com/JabRef/jabref/issues/9367)
@@ -76,14 +89,26 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where searching for unlinked files would include the current library's .bib file. [#9735](https://github.com/JabRef/jabref/issues/9735)
 - We fixed an issue where it was no longer possible to connect to a shared mysql database due to an exception. [#9761](https://github.com/JabRef/jabref/issues/9761)
 - We fixed an issue where an exception was thrown for the user after <kbd>Ctrl</kbd>+<kbd>Z</kbd> command. [#9737](https://github.com/JabRef/jabref/issues/9737)
-- We fixed the citation key generation for (`[authors]`, `[authshort]`, `[authorsAlpha]`, `authIniN`, `authEtAl`, `auth.etal`)[https://docs.jabref.org/setup/citationkeypatterns#special-field-markers] to handle `and others` properly. [koppor#626](https://github.com/koppor/jabref/issues/626)
+- We fixed the citation key generation for [`[authors]`, `[authshort]`, `[authorsAlpha]`, `[authIniN]`, `[authEtAl]`, `[auth.etal]`](https://docs.jabref.org/setup/citationkeypatterns#special-field-markers) to handle `and others` properly. [koppor#626](https://github.com/koppor/jabref/issues/626)
 - We fixed the Save/save as file type shows BIBTEX_DB instead of "Bibtex library". [#9372](https://github.com/JabRef/jabref/issues/9372)
 - We fixed the default main file directory for non-English Linux users. [#8010](https://github.com/JabRef/jabref/issues/8010)
+- We fixed an issue when overwriting the owner was disabled. [#9896](https://github.com/JabRef/jabref/pull/9896)
 - We fixed an issue regarding recording redundant prefixes in search history. [#9685](https://github.com/JabRef/jabref/issues/9685)
 - We fixed an issue where passing a URL containing a DOI led to a "No entry found" notification. [#9821](https://github.com/JabRef/jabref/issues/9821)
 - We fixed some minor visual inconsistencies and issues in the preferences dialog. [#9866](https://github.com/JabRef/jabref/pull/9866)
 - The order of save actions is now retained. [#9890](https://github.com/JabRef/jabref/pull/9890)
+- We fixed an issue where the order of save actions was not retained in the bib file. [#9890](https://github.com/JabRef/jabref/pull/9890)
+- We fixed an issue in the preferences 'External file types' tab ignoring a custom application path in the edit dialog. [#9895](https://github.com/JabRef/jabref/issues/9895)
 - We fixed an issue in the preferences where custom columns could be added to the entry table with no qualifier. [#9913](https://github.com/JabRef/jabref/issues/9913)
+- We fixed an issue where the encoding header in a bib file was not respected when the file contained a BOM (Byte Order Mark). [#9926](https://github.com/JabRef/jabref/issues/9926)
+- We fixed an issue where cli help output for import and export format was inconsistent. [koppor#429](https://github.com/koppor/jabref/issues/429)
+- We fixed an issue where no preview could be generated for some entry types and led to an exception. [#9947](https://github.com/JabRef/jabref/issues/9947)
+- We fixed an issue where the Linux terminal working directory argument was malformed and therefore ignored upon opening a terminal [#9953](https://github.com/JabRef/jabref/issues/9953)
+- We fixen an issue under Linux where under some systems the file instead of the folder was opened. [#9607](https://github.com/JabRef/jabref/issues/9607)
+- We fixed an issue where an Automatic Keyword Group could not be deleted in the UI. [#9778](https://github.com/JabRef/jabref/issues/9778)
+- We fixed an issue where the citation key pattern `[edtrN_M]` returned the wrong editor. [#9946](https://github.com/JabRef/jabref/pull/9946)
+- We fixed an issue where empty grey containers would remain in the groups panel, if displaying of group item count is turned off. [#9972](https://github.com/JabRef/jabref/issues/9972)
+- We fixed an issue where fetching an ISBN could lead to application freezing when the fetcher did not return any results. [#9979](https://github.com/JabRef/jabref/issues/9979)
 
 ### Removed
 
@@ -109,6 +134,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We now have more "dots" in the offered journal abbreviations. [#9504](https://github.com/JabRef/jabref/pull/9504)
 - We now disable the button "Full text search" in the Searchbar by default [#9527](https://github.com/JabRef/jabref/pull/9527)
 
+
 ### Fixed
 
 - The tab "deprecated fields" is shown in biblatex-mode only. [#7757](https://github.com/JabRef/jabref/issues/7757)
@@ -121,8 +147,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - For portable versions, the `.deb` file now works on plain debian again. [#9472](https://github.com/JabRef/jabref/issues/9472)
 - We fixed an issue where the download of linked online files failed after an import of entries for certain urls. [#9518](https://github.com/JabRef/jabref/issues/9518)
 - We fixed an issue where an exception occurred when manually downloading a file from an URL in the entry editor. [#9521](https://github.com/JabRef/jabref/issues/9521)
-- We fixed an issue with open office csv file formatting where commas in the abstract field where not escaped. [#9087][https://github.com/JabRef/jabref/issues/9087]
-- We fixed an issue with deleting groups where subgroups different from the selected group were deleted. [#9281][https://github.com/JabRef/jabref/issues/9281]
+- We fixed an issue with open office csv file formatting where commas in the abstract field where not escaped. [#9087](https://github.com/JabRef/jabref/issues/9087)
+- We fixed an issue with deleting groups where subgroups different from the selected group were deleted. [#9281](https://github.com/JabRef/jabref/issues/9281)
 
 ## [5.8] - 2022-12-18
 

diff --git a/README.md b/README.md
@@ -3,7 +3,8 @@
 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](docs/images/jabref-mainscreen.png)](http://www.jabref.org/img/jabref-mainscreen.png)
+
+![main table](docs/images/jabref-mainscreen.png)
 
 ## Features
 
@@ -23,7 +24,7 @@ It supports you in every step of your research work.
 
 - Group your research into hierarchical collections and organize research items based on keywords/tags, search terms or your manual assignments
 - Advanced search and filter features
-- Complete and fix bibliographic data by comparing with curated online catalogues such as Google Scholar, Springer or MathSciNet
+- Complete and fix bibliographic data by comparing with curated online catalogs such as Google Scholar, Springer or MathSciNet
 - Customizable citation key generator
 - Customize and add new metadata fields or reference types
 - Find and merge duplicates
@@ -41,7 +42,7 @@ It supports you in every step of your research work.
 ### Share
 
 - Many built-in export options or create your export format
-- Library is saved as a simple text file and thus it is easy to share with others via Dropbox and is version-control friendly
+- Library is saved as a simple text file, and thus it is easy to share with others via Dropbox and is version-control friendly
 - Work in a team: sync the contents of your library via a SQL database
 
 ## Installation
@@ -54,7 +55,7 @@ Please see our [Installation Guide](https://docs.jabref.org/installation).
 ## Bug Reports, Suggestions, Other Feedback
 
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
-[![Paypal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef)
+[![PayPal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef)
 
 We are thankful for any bug reports or other feedback.
 If you have ideas for new features you want to be included in JabRef, tell us in [the feature section](http://discourse.jabref.org/c/features) of our forum!
@@ -94,7 +95,7 @@ When you want to develop, it is necessary to generate additional sources using `
 and then generate the Eclipse `gradlew eclipse`.
 For IntelliJ IDEA, just import the project via a Gradle Import by pointing at the `build.gradle`.
 
-`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.
+`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