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updates #7

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@arfazhxss arfazhxss commented Oct 16, 2024

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dependabot bot and others added 30 commits August 19, 2024 14:43
Bumps [org.junit.jupiter:junit-jupiter](https://github.com/junit-team/junit5) from 5.10.3 to 5.11.0.
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](junit-team/junit5@r5.10.3...r5.11.0)

---
updated-dependencies:
- dependency-name: org.junit.jupiter:junit-jupiter
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
)

Bumps org.glassfish.jersey.core:jersey-server from 3.1.7 to 3.1.8.

---
updated-dependencies:
- dependency-name: org.glassfish.jersey.core:jersey-server
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 2.32.0 to 2.43.0.
- [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases)
- [Changelog](https://github.com/dlsc-software-consulting-gmbh/GemsFX/blob/master/jreleaser.yml)
- [Commits](dlsc-software-consulting-gmbh/GemsFX@v2.32.0...v2.43.0)

---
updated-dependencies:
- dependency-name: com.dlsc.gemsfx:gemsfx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps org.apache.commons:commons-lang3 from 3.15.0 to 3.16.0.

---
updated-dependencies:
- dependency-name: org.apache.commons:commons-lang3
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [src/main/resources/csl-locales](https://github.com/citation-style-language/locales) from `242640a` to `195bef8`.
- [Release notes](https://github.com/citation-style-language/locales/releases)
- [Commits](citation-style-language/locales@242640a...195bef8)

---
updated-dependencies:
- dependency-name: src/main/resources/csl-locales
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Fix FetcherTests

* Discard changes to src/test/java/org/jabref/logic/importer/fetcher/OpenAccessDoiTest.java
…11647)

Bumps [org.jetbrains.kotlin:kotlin-stdlib-jdk8](https://github.com/JetBrains/kotlin) from 1.9.24 to 2.0.10.
- [Release notes](https://github.com/JetBrains/kotlin/releases)
- [Changelog](https://github.com/JetBrains/kotlin/blob/master/ChangeLog.md)
- [Commits](JetBrains/kotlin@v1.9.24...v2.0.10)

---
updated-dependencies:
- dependency-name: org.jetbrains.kotlin:kotlin-stdlib-jdk8
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Add link to the moderne platform
* Update Linux Mint from 21 to 22

* Add section on multiple screens

* Fix filename in howto

* Refine VirtualBox howto

* Add comment to script

* Add hint on Video Memory

* Switch back to Mint v21

* Refine section on alternatives

* Refine howto for guest additions

* Add new FAQ

* Enable building virtual box guest additions

* Refine installation howto

* Try more modern kernel

* Refine howto
* Enable org.openrewrite.java.testing.junit5.JUnit5BestPractices

* Fix compile error

* Duplcite test files (to have them in the "right" folder)

* Add missing file

* Fix import order

* Fix GVK test

* Fix more tests

* Fix query transformer and tests

* Compilefix - and enumare rules explicitely
* New translations jabref_en.properties (French)

* New translations jabref_en.properties (Spanish)

* New translations jabref_en.properties (German)

* New translations jabref_en.properties (Greek)

* New translations jabref_en.properties (Italian)

* New translations jabref_en.properties (Japanese)

* New translations jabref_en.properties (Korean)

* New translations jabref_en.properties (Dutch)

* New translations jabref_en.properties (Polish)

* New translations jabref_en.properties (Russian)

* New translations jabref_en.properties (Turkish)

* New translations jabref_en.properties (Chinese Simplified)

* New translations jabref_en.properties (Portuguese, Brazilian)
* Update PreviewView to listen for library search queries

* unnecessary updates in PreviewViewer when hovering over entries

* Update CHANGELOG.md

* Update CommentsTabTest.java

* Invert "if" condition
* Highlight search bar on wrong syntax

* Update CHANGELOG.md
* Fix the ability to save preferences if API key is missing

* Fix the ability to save preferences if API key is missing
* New translations jabref_en.properties (French)

* New translations jabref_en.properties (Polish)

* New translations jabref_en.properties (Portuguese, Brazilian)
* Attempt: Persist selection of databases

* Use ObservableSet

* ObservableList

* set fetchers

* Revise architecture

* Revise test

* Fix indent

* Fix indent 2

* Add changelog entry

* Fix indent

* Update CHANGELOG.md

* Chris' update

Co-authored-by: Christoph <[email protected]>

* Update src/main/java/org/jabref/preferences/WorkspacePreferences.java

Co-authored-by: Christoph <[email protected]>

* Update src/main/java/org/jabref/preferences/JabRefPreferences.java

Co-authored-by: Christoph <[email protected]>

* !Remove duplicated line

* Return ObservableList

* Remove unused import

* Rename foreach loop variable

* Rename foreach loop variable

* Rename fetcher->catalog

* Fix overwriting of existing study catalogs

* Merge upstream/main

* Fix merge issue

* Persist for edits on existing studies

* Save preferences only on a "new run" or "save".

---------

Co-authored-by: Christoph <[email protected]>
Co-authored-by: Oliver Kopp <[email protected]>
- Fix some markdown and spaces
Add Debian VM (and improve other Vagrant files)
* Attempt: Persist selection of databases

* Use ObservableSet

* ObservableList

* set fetchers

* Revise architecture

* Revise test

* Fix indent

* Fix indent 2

* Add changelog entry

* Fix indent

* Update CHANGELOG.md

* Chris' update

Co-authored-by: Christoph <[email protected]>

* Update src/main/java/org/jabref/preferences/WorkspacePreferences.java

Co-authored-by: Christoph <[email protected]>

* Update src/main/java/org/jabref/preferences/JabRefPreferences.java

Co-authored-by: Christoph <[email protected]>

* !Remove duplicated line

* Return ObservableList

* Remove unused import

* Rename foreach loop variable

* Rename foreach loop variable

* Rename fetcher->catalog

* Fix overwriting of existing study catalogs

* Merge upstream/main

* Fix merge issue

* Persist for edits on existing studies

* Save preferences only on a "new run" or "save".

* Maintain abstraction

---------

Co-authored-by: Christoph <[email protected]>
Co-authored-by: Oliver Kopp <[email protected]>
* Refine ProgressCounter

* Revert PROGRESS_MESSAGES
* Improve AI preferences UI and add temperature help

* Fix checkstyle
dependabot bot and others added 29 commits October 14, 2024 14:35
Bumps [io.github.classgraph:classgraph](https://github.com/classgraph/classgraph) from 4.8.176 to 4.8.177.
- [Release notes](https://github.com/classgraph/classgraph/releases)
- [Commits](classgraph/classgraph@classgraph-4.8.176...classgraph-4.8.177)

---
updated-dependencies:
- dependency-name: io.github.classgraph:classgraph
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [thollander/actions-comment-pull-request](https://github.com/thollander/actions-comment-pull-request) from 2 to 3.
- [Release notes](https://github.com/thollander/actions-comment-pull-request/releases)
- [Commits](thollander/actions-comment-pull-request@v2...v3)

---
updated-dependencies:
- dependency-name: thollander/actions-comment-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [lycheeverse/lychee-action](https://github.com/lycheeverse/lychee-action) from 1.10.0 to 2.0.2.
- [Release notes](https://github.com/lycheeverse/lychee-action/releases)
- [Commits](lycheeverse/lychee-action@v1.10.0...v2.0.2)

---
updated-dependencies:
- dependency-name: lycheeverse/lychee-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…11963)

Bumps org.glassfish.jersey.containers:jersey-container-grizzly2-http from 3.1.8 to 3.1.9.

---
updated-dependencies:
- dependency-name: org.glassfish.jersey.containers:jersey-container-grizzly2-http
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Oliver Kopp <[email protected]>
* Added double click to jump to entry in CitationRelationsTab

* CHANGELOG.md

---------

Co-authored-by: Oliver Kopp <[email protected]>
* Bump luceneVersion from 9.12.0 to 10.0.0

Bumps `luceneVersion` from 9.12.0 to 10.0.0.

Updates `org.apache.lucene:lucene-core` from 9.12.0 to 10.0.0

Updates `org.apache.lucene:lucene-queryparser` from 9.12.0 to 10.0.0

Updates `org.apache.lucene:lucene-queries` from 9.12.0 to 10.0.0

Updates `org.apache.lucene:lucene-analysis-common` from 9.12.0 to 10.0.0

Updates `org.apache.lucene:lucene-highlighter` from 9.12.0 to 10.0.0

---
updated-dependencies:
- dependency-name: org.apache.lucene:lucene-core
  dependency-type: direct:production
  update-type: version-update:semver-major
- dependency-name: org.apache.lucene:lucene-queryparser
  dependency-type: direct:production
  update-type: version-update:semver-major
- dependency-name: org.apache.lucene:lucene-queries
  dependency-type: direct:production
  update-type: version-update:semver-major
- dependency-name: org.apache.lucene:lucene-analysis-common
  dependency-type: direct:production
  update-type: version-update:semver-major
- dependency-name: org.apache.lucene:lucene-highlighter
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* fix lucene

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Siedlerchr <[email protected]>
* Add assign-me-action

* Fix linting issues.

* Fix grammar

* Add reaction on 📍 Assigned
* Add check for AI-generated PRs

* Refine

* Add to greeting

* Remove reference to code of conduct

* Change mandatory check

* Refine condition

Co-authored-by: Ruslan <[email protected]>
Co-authored-by: Subhramit Basu Bhowmick <[email protected]>
Co-authored-by: Carl Christian Snethlage <[email protected]>
Co-authored-by: ThiloteE <[email protected]>

* Discard changes to .github/workflows/add-greeting-to-issue.yml

* Update CONTRIBUTING.md

Co-authored-by: Ruslan <[email protected]>
Co-authored-by: Subhramit Basu Bhowmick <[email protected]>
Co-authored-by: Carl Christian Snethlage <[email protected]>
Co-authored-by: ThiloteE <[email protected]>

* Update PULL_REQUEST_TEMPLATE.md

Co-authored-by: Ruslan <[email protected]>
Co-authored-by: Subhramit Basu Bhowmick <[email protected]>
Co-authored-by: Carl Christian Snethlage <[email protected]>
Co-authored-by: ThiloteE <[email protected]>

---------

Co-authored-by: Oliver Kopp <[email protected]>
Co-authored-by: Ruslan <[email protected]>
Co-authored-by: Carl Christian Snethlage <[email protected]>
Co-authored-by: ThiloteE <[email protected]>
* Replace new instantiation of BuildInfo with calls to Injector

* Extract call to default keys out of fetchers

* Inject buildInfo

* Integrate SemanticScholarFetcher

* Integrate IEEE

* Add warning log

* Adapt devdocs

* Integrate SpringerLink

* Add comment

* Enhance doc

* Enhance doc
* added search for key binds

* use the correct localization key to deal with ellipsis

---------

Co-authored-by: Carl Christian Snethlage <[email protected]>
* Move information generator for AUX import to logic

Co-authored-by: Carl Christian Snethlage <[email protected]>

* Add "static" to de-facto static methods

* Use BibEntryTypesManager from preferences

* Inline variables

* Remove Injector from JabRefCLI

* Remove --automaticallySetFileLinks because of UI dependency

* Remove GuiPreferences from ArgumentProcessor

* CLI must not depepend on GUI

* Rename JabRefCLI to CliOptions

* Introduce JabKit (by moving much Gui launching code to there)

* Remove hiearchy

* Fix compilation error

* Fix usage of GuiPreferences in JabKit

* Fix use of GUI monitors at JabKit

* Remove unused variable

* Rename JabKit to JabRefCli (and add logging if UICommands are left in Cli)

---------

Co-authored-by: Carl Christian Snethlage <[email protected]>
* in renameToName, the logic for storing old extension and using it if there is none is implemented

* Update CHANGELOG.md

updating changelog based on suggestion.

Co-authored-by: Subhramit Basu Bhowmick <[email protected]>

* added optionals, file cannot be renamed without any extension now, added testclass for linkedFileHandler

* removed unnecesary cookiehandler, fixed the code so it doesnt violate checkstyle

* removed duplicated tests, switched to parameterized tests, unnecesary comments removed

* Improve readability and fix logic for no extensions present

* Fix test parameter order

---------

Co-authored-by: Ivo Bubeňko <[email protected]>
Co-authored-by: Subhramit Basu Bhowmick <[email protected]>
Co-authored-by: Oliver Kopp <[email protected]>
* Add links to our setup guideline.

* Add link to PRs (to ensore that not koppors fork is used)

* Fix casing
* - Added a "Compare" button for duplicate entries in the CitationRelationsTab.
- Added localization key for 'Compare with duplicate entries'.

* - Implemented functionality to open a "Possible duplicate entries" for comparing and merging duplicate entries.
- Updated changelog for compare button feature.

* Updated changelog

* - Updated localization key for compare button tooltip.
- Fixed bug that when adding an entry to the library from Citation Relations Tab by adding the entry's clone instead of itself.
- Optimised openPossibleDuplicateEntriesWindow function in CitationRelationsTab.java to show result of undo and redo.
- Implemented that After clicking "merge", the current entry will be kept selected - and not the merged entry be selected.

* Modified CitationsRelationsTabViewModel and ImportHandler to pass CitationsRelationsTabViewModelTest with clone entries.

* - Deleted old code in CitationRelationTab.java which to implement that original entry be selected after citation item merge.
- Modified MainTable#clearAndSelect to ensure original entry be selected after citation item merge.
- Added some comments.

* Optimised citation relations item merge: Added a citation merge flag in MainTable.java to let original entry get selected after merge instead of selecting new merged entry.

* Optimised MainTable#clearAndSelect: make the code look more concise.

* Fixed bug: As original local entry of citation relation item has been changed to new merged entry, need to refresh selected citation relation item to ensure that the item link to current local entry instead of the old one.

* Adapted tool tip of compare button.

* - renamed some variables to make them more understandable
- fixed wrong position codes: codes that updating citation relation item and setting state of citationMergeMode now be moved into CitationRelationsTab#openPossibleDuplicateEntriesWindow
- modified some comments and Java doc

* Move statement closer to intended use

* Modified the column headings of the merge entries dialog to make them more self-explanatory.

---------

Co-authored-by: Oliver Kopp <[email protected]>
* Add references to other tests

* Simplify code

* Add test for extracting the first word

* Relax escaping

* Add link to PR

* Add tests

Refs #11367

* Refine CHANGELOG.md

* Refine CHANGELOG.md
@arfazhxss arfazhxss closed this Oct 16, 2024
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