diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index cb65efe6a7c..ef4a1dd6b23 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -12,7 +12,7 @@ body: attributes: label: JabRef version options: - - "5.6 (latest release)" + - "5.7 (latest release)" - "3.8.2" - Latest development branch build (please note build date below) - Other (please describe below) diff --git a/.github/workflows/cleanup_pr.yml b/.github/workflows/cleanup_pr.yml index 63090aba74a..20747030207 100644 --- a/.github/workflows/cleanup_pr.yml +++ b/.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: ${{ steps.checksecrets.outputs.secretspresent }} - uses: appleboy/ssh-action@v0.1.4 + uses: appleboy/ssh-action@v0.1.5 with: script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true host: build-upload.jabref.org diff --git a/CHANGELOG.md b/CHANGELOG.md index 30f70513fe9..2a0f551366f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,12 +11,30 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve ### Added +### Changed + +### Fixed + +### Removed + + + + + + + + +## [5.7] - 2022-08-05 + +### Added + - We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539) - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340) - We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373) - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version` - We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322) - We added a feature to drag selected entries and drop them to other opened inactive library tabs [koppor521](https://github.com/koppor/jabref/issues/521). +- We added support for the [biblatex-apa](https://github.com/plk/biblatex-apa) legal entry types `Legislation`, `Legadminmaterial`, `Jurisdiction`, `Constitution` and `Legal` [#8931](https://github.com/JabRef/jabref/issues/8931) ### Changed @@ -42,6 +60,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve ### Fixed +- We fixed an issue where the user could not rate an entry in the main table when an entry was not yet ranked. [#5842](https://github.com/JabRef/jabref/issues/5842) - We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653) - We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930) - We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849) @@ -59,20 +78,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve - We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939) - We fixed a bug where files that were deleted in the source bibtex file were kept in the index. [#8962](https://github.com/JabRef/jabref/pull/8962) - We fixed "Error while sending to JabRef" when the browser extension interacts with JabRef. [JabRef-Browser-Extension#479](https://github.com/JabRef/JabRef-Browser-Extension/issues/479) +- We fixed a bug where updating group view mode (intersection or union) requires re-selecting groups to take effect. [#6998](https://github.com/JabRef/jabref/issues/6998) +- We fixed a bug that prevented external group metadata changes from being merged. [#8873](https://github.com/JabRef/jabref/issues/8873) +- We fixed the shared database opening dialog to remember autosave folder and tick. [#7516](https://github.com/JabRef/jabref/issues/7516) ### Removed - We removed the social media buttons for our Twitter and Facebook pages. [#8774](https://github.com/JabRef/jabref/issues/8774) - - - - - - - - - ## [5.6] - 2022-04-25 ### Added @@ -843,7 +856,8 @@ The changelog of JabRef 4.x is available at the [v4.3.1 tag](https://github.com/ The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md). The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG). -[Unreleased]: https://github.com/JabRef/jabref/compare/v5.6...HEAD +[Unreleased]: https://github.com/JabRef/jabref/compare/v5.7...HEAD +[5.7]: https://github.com/JabRef/jabref/compare/v5.6...v5.7 [5.6]: https://github.com/JabRef/jabref/compare/v5.5...v5.6 [5.5]: https://github.com/JabRef/jabref/compare/v5.4...v5.5 [5.4]: https://github.com/JabRef/jabref/compare/v5.3...v5.4 diff --git a/build.gradle b/build.gradle index cf66cc71f28..1b72c735a24 100644 --- a/build.gradle +++ b/build.gradle @@ -85,7 +85,6 @@ repositories { } configurations { - antlr3 antlr4 // TODO: Remove the following workaround for split error messages such as // error: module java.xml.bind reads package javax.annotation from both jsr305 and java.annotation @@ -116,11 +115,11 @@ dependencies { implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1' implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1' - implementation 'org.apache.lucene:lucene-core:9.2.0' - implementation 'org.apache.lucene:lucene-queryparser:9.2.0' - implementation 'org.apache.lucene:lucene-queries:9.2.0' - implementation 'org.apache.lucene:lucene-analysis-common:9.2.0' - implementation 'org.apache.lucene:lucene-highlighter:9.2.0' + implementation 'org.apache.lucene:lucene-core:9.3.0' + implementation 'org.apache.lucene:lucene-queryparser:9.3.0' + implementation 'org.apache.lucene:lucene-queries:9.3.0' + implementation 'org.apache.lucene:lucene-analysis-common:9.3.0' + implementation 'org.apache.lucene:lucene-highlighter:9.3.0' implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0' implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.12.0' @@ -133,15 +132,12 @@ dependencies { implementation 'commons-cli:commons-cli:1.5.0' - implementation 'org.libreoffice:libreoffice:7.3.4' - implementation 'org.libreoffice:unoloader:7.3.4' + implementation 'org.libreoffice:libreoffice:7.3.5' + implementation 'org.libreoffice:unoloader:7.3.5' - implementation 'io.github.java-diff-utils:java-diff-utils:4.11' + implementation 'io.github.java-diff-utils:java-diff-utils:4.12' implementation 'info.debatty:java-string-similarity:2.0.0' - antlr3 'org.antlr:antlr:3.5.3' - implementation 'org.antlr:antlr-runtime:3.5.3' - antlr4 'org.antlr:antlr4:4.9.3' implementation 'org.antlr:antlr4-runtime:4.9.3' @@ -208,8 +204,8 @@ dependencies { implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1' testImplementation 'io.github.classgraph:classgraph:4.8.149' - testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2' - testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2' + testImplementation 'org.junit.jupiter:junit-jupiter:5.9.0' + testImplementation 'org.junit.platform:junit-platform-launcher:1.9.0' testImplementation 'org.mockito:mockito-core:4.6.1' testImplementation 'org.xmlunit:xmlunit-core:2.9.0' @@ -220,7 +216,7 @@ dependencies { testImplementation "org.testfx:testfx-junit5:4.0.16-alpha" testImplementation "org.hamcrest:hamcrest-library:2.2" - checkstyle 'com.puppycrawl.tools:checkstyle:10.3.1' + checkstyle 'com.puppycrawl.tools:checkstyle:10.3.2' // xjc needs the runtime as well for the ant task, otherwise it fails xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2' xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2' @@ -273,14 +269,14 @@ task generateSource(dependsOn: ["generateBstGrammarSource", } tasks.register("generateBstGrammarSource", JavaExec) { - main = "org.antlr.Tool" - classpath = configurations.antlr3 + main = "org.antlr.v4.Tool" + classpath = configurations.antlr4 group = "JabRef" - description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr3.' + description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr4.' - inputs.dir('src/main/antlr3/org/jabref/bst/') + inputs.dir('src/main/antlr4/org/jabref/bst/') outputs.dir("src-gen/main/java/org/jabref/logic/bst/") - args = ["-o", "src-gen/main/java/org/jabref/logic/bst/" , "$projectDir/src/main/antlr3/org/jabref/bst/Bst.g" ] + args = ["-o", "src-gen/main/java/org/jabref/logic/bst/", "-visitor", "-no-listener", "-package", "org.jabref.logic.bst", "$projectDir/src/main/antlr4/org/jabref/bst/Bst.g4"] } tasks.register("generateSearchGrammarSource", JavaExec) { diff --git a/buildres/csl/csl-styles/apa-5th-edition.csl b/buildres/csl/csl-styles/apa-5th-edition.csl index a2784ca4b5b..87cc83196a3 100644 --- a/buildres/csl/csl-styles/apa-5th-edition.csl +++ b/buildres/csl/csl-styles/apa-5th-edition.csl @@ -183,7 +183,7 @@ - + @@ -196,23 +196,37 @@ - + - + - + + + + + + + + + + + + diff --git a/buildres/csl/csl-styles/apa-6th-edition-no-ampersand.csl b/buildres/csl/csl-styles/apa-6th-edition-no-ampersand.csl index b0f618ec31f..ff55b46b98d 100644 --- a/buildres/csl/csl-styles/apa-6th-edition-no-ampersand.csl +++ b/buildres/csl/csl-styles/apa-6th-edition-no-ampersand.csl @@ -897,32 +897,52 @@ - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + @@ -1401,7 +1421,7 @@ - diff --git a/buildres/csl/csl-styles/apa-6th-edition.csl b/buildres/csl/csl-styles/apa-6th-edition.csl index 775857accbe..851a3096ab0 100644 --- a/buildres/csl/csl-styles/apa-6th-edition.csl +++ b/buildres/csl/csl-styles/apa-6th-edition.csl @@ -896,32 +896,52 @@ - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + @@ -1400,7 +1420,7 @@ - diff --git a/buildres/csl/csl-styles/apa-annotated-bibliography.csl b/buildres/csl/csl-styles/apa-annotated-bibliography.csl index 014ae44f162..0636d93db58 100644 --- a/buildres/csl/csl-styles/apa-annotated-bibliography.csl +++ b/buildres/csl/csl-styles/apa-annotated-bibliography.csl @@ -320,8 +320,8 @@ @@ -389,7 +389,7 @@ - @@ -470,7 +470,7 @@ - @@ -529,7 +529,7 @@ - @@ -1294,7 +1294,7 @@ - @@ -1559,7 +1559,7 @@ - + @@ -1567,6 +1567,20 @@ + + + + + + + + + + + @@ -1574,7 +1588,7 @@ - diff --git a/buildres/csl/csl-styles/apa-cv.csl b/buildres/csl/csl-styles/apa-cv.csl index 5a766c3dc61..228ad3ee882 100644 --- a/buildres/csl/csl-styles/apa-cv.csl +++ b/buildres/csl/csl-styles/apa-cv.csl @@ -320,8 +320,8 @@ @@ -415,7 +415,7 @@ - @@ -1085,7 +1085,7 @@ - @@ -1301,12 +1301,12 @@ + both publisher-place and event-place. Remove this 'choose' when that is changed. --> - + @@ -1314,6 +1314,20 @@ + + + + + + + + + + + @@ -1321,7 +1335,7 @@ - diff --git a/buildres/csl/csl-styles/apa-fr-provost.csl b/buildres/csl/csl-styles/apa-fr-provost.csl index 4b068cf752d..9e7928dca71 100644 --- a/buildres/csl/csl-styles/apa-fr-provost.csl +++ b/buildres/csl/csl-styles/apa-fr-provost.csl @@ -245,7 +245,7 @@ - + @@ -298,17 +298,17 @@ - + - + - + @@ -317,6 +317,20 @@ + + + + + + + + + + + diff --git a/buildres/csl/csl-styles/apa-no-ampersand.csl b/buildres/csl/csl-styles/apa-no-ampersand.csl index 446103abb69..5759e34ec4a 100644 --- a/buildres/csl/csl-styles/apa-no-ampersand.csl +++ b/buildres/csl/csl-styles/apa-no-ampersand.csl @@ -320,8 +320,8 @@ @@ -389,7 +389,7 @@ - @@ -470,7 +470,7 @@ - @@ -529,7 +529,7 @@ - @@ -1294,7 +1294,7 @@ - @@ -1554,12 +1554,12 @@ + both publisher-place and event-place. Remove this 'choose' when that is changed. --> - + @@ -1567,6 +1567,20 @@ + + + + + + + + + + + @@ -1574,7 +1588,7 @@ - diff --git a/buildres/csl/csl-styles/apa-no-doi-no-issue.csl b/buildres/csl/csl-styles/apa-no-doi-no-issue.csl index 08306362d76..c72c8bdf126 100644 --- a/buildres/csl/csl-styles/apa-no-doi-no-issue.csl +++ b/buildres/csl/csl-styles/apa-no-doi-no-issue.csl @@ -903,32 +903,52 @@ - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + @@ -1414,7 +1434,7 @@ - diff --git a/buildres/csl/csl-styles/apa-no-initials.csl b/buildres/csl/csl-styles/apa-no-initials.csl index b8bcab11e79..4695cd9b6fb 100644 --- a/buildres/csl/csl-styles/apa-no-initials.csl +++ b/buildres/csl/csl-styles/apa-no-initials.csl @@ -320,8 +320,8 @@ @@ -389,7 +389,7 @@ - @@ -470,7 +470,7 @@ - @@ -529,7 +529,7 @@ - @@ -1294,7 +1294,7 @@ - @@ -1559,7 +1559,7 @@ - + @@ -1567,6 +1567,20 @@ + + + + + + + + + + + @@ -1574,7 +1588,7 @@ - diff --git a/buildres/csl/csl-styles/apa-numeric-superscript-brackets.csl b/buildres/csl/csl-styles/apa-numeric-superscript-brackets.csl index c6d3de36f82..ba3dadf6d20 100644 --- a/buildres/csl/csl-styles/apa-numeric-superscript-brackets.csl +++ b/buildres/csl/csl-styles/apa-numeric-superscript-brackets.csl @@ -123,8 +123,8 @@ @@ -192,7 +192,7 @@ - @@ -273,7 +273,7 @@ - @@ -332,7 +332,7 @@ - @@ -1097,7 +1097,7 @@ - @@ -1362,7 +1362,7 @@ - + @@ -1370,6 +1370,20 @@ + + + + + + + + + + + @@ -1377,7 +1391,7 @@ - diff --git a/buildres/csl/csl-styles/apa-numeric-superscript.csl b/buildres/csl/csl-styles/apa-numeric-superscript.csl index 0a6af38540b..1ed0ae88b7c 100644 --- a/buildres/csl/csl-styles/apa-numeric-superscript.csl +++ b/buildres/csl/csl-styles/apa-numeric-superscript.csl @@ -123,8 +123,8 @@ @@ -192,7 +192,7 @@ - @@ -273,7 +273,7 @@ - @@ -332,7 +332,7 @@ - @@ -1097,7 +1097,7 @@ - @@ -1362,7 +1362,7 @@ - + @@ -1370,6 +1370,20 @@ + + + + + + + + + + + @@ -1377,7 +1391,7 @@ - diff --git a/buildres/csl/csl-styles/apa-old-doi-prefix.csl b/buildres/csl/csl-styles/apa-old-doi-prefix.csl index 02ecfc75fac..cdfaa73a451 100644 --- a/buildres/csl/csl-styles/apa-old-doi-prefix.csl +++ b/buildres/csl/csl-styles/apa-old-doi-prefix.csl @@ -897,32 +897,52 @@ - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + @@ -1401,7 +1421,7 @@ - diff --git a/buildres/csl/csl-styles/apa-single-spaced.csl b/buildres/csl/csl-styles/apa-single-spaced.csl index c2157cb296a..ff224f6a405 100644 --- a/buildres/csl/csl-styles/apa-single-spaced.csl +++ b/buildres/csl/csl-styles/apa-single-spaced.csl @@ -320,8 +320,8 @@ @@ -389,7 +389,7 @@ - @@ -470,7 +470,7 @@ - @@ -529,7 +529,7 @@ - @@ -1294,7 +1294,7 @@ - @@ -1554,12 +1554,12 @@ + both publisher-place and event-place. Remove this 'choose' when that is changed. --> - + @@ -1567,6 +1567,20 @@ + + + + + + + + + + + @@ -1574,7 +1588,7 @@ - diff --git a/buildres/csl/csl-styles/apa-tr.csl b/buildres/csl/csl-styles/apa-tr.csl index 557066dafd8..d17be770985 100644 --- a/buildres/csl/csl-styles/apa-tr.csl +++ b/buildres/csl/csl-styles/apa-tr.csl @@ -223,7 +223,7 @@ - + @@ -241,15 +241,15 @@ - + - + - + @@ -257,6 +257,20 @@ + + + + + + + + + + + diff --git a/buildres/csl/csl-styles/apa-with-abstract.csl b/buildres/csl/csl-styles/apa-with-abstract.csl index ddff715c9d6..25d185866bf 100644 --- a/buildres/csl/csl-styles/apa-with-abstract.csl +++ b/buildres/csl/csl-styles/apa-with-abstract.csl @@ -320,8 +320,8 @@ @@ -389,7 +389,7 @@ - @@ -470,7 +470,7 @@ - @@ -529,7 +529,7 @@ - @@ -1294,7 +1294,7 @@ - @@ -1559,7 +1559,7 @@ - + @@ -1567,6 +1567,20 @@ + + + + + + + + + + + @@ -1574,7 +1588,7 @@ - diff --git a/buildres/csl/csl-styles/apa.csl b/buildres/csl/csl-styles/apa.csl index 09f4635a505..0fd6bd71a5e 100644 --- a/buildres/csl/csl-styles/apa.csl +++ b/buildres/csl/csl-styles/apa.csl @@ -320,8 +320,8 @@ @@ -389,7 +389,7 @@ - @@ -470,7 +470,7 @@ - @@ -530,7 +530,7 @@ - @@ -1295,7 +1295,7 @@ - @@ -1560,7 +1560,7 @@ - + @@ -1568,6 +1568,20 @@ + + + + + + + + + + + @@ -1575,7 +1589,7 @@ - diff --git a/buildres/csl/csl-styles/association-for-computational-linguistics.csl b/buildres/csl/csl-styles/association-for-computational-linguistics.csl index 63ea2e0f2a4..ec95b2a95b5 100644 --- a/buildres/csl/csl-styles/association-for-computational-linguistics.csl +++ b/buildres/csl/csl-styles/association-for-computational-linguistics.csl @@ -67,11 +67,6 @@ - - - - - @@ -199,7 +194,6 @@ - @@ -212,7 +206,6 @@ - @@ -236,7 +229,6 @@ - @@ -244,7 +236,6 @@ - @@ -262,18 +253,10 @@ - - - - - - - - - + @@ -282,7 +265,6 @@ - @@ -293,13 +275,11 @@ - - diff --git a/buildres/csl/csl-styles/beilstein-journal-of-organic-chemistry.csl b/buildres/csl/csl-styles/beilstein-journal-of-organic-chemistry.csl index 8487b04c1ee..2ab0fe83caf 100644 --- a/buildres/csl/csl-styles/beilstein-journal-of-organic-chemistry.csl +++ b/buildres/csl/csl-styles/beilstein-journal-of-organic-chemistry.csl @@ -3,7 +3,7 @@ Beilstein Journal of Organic Chemistry - Beilstein + BJOC http://www.zotero.org/styles/beilstein-journal-of-organic-chemistry @@ -154,7 +154,6 @@ - diff --git a/buildres/csl/csl-styles/dependent/liver-transplantation.csl b/buildres/csl/csl-styles/dependent/liver-transplantation.csl new file mode 100644 index 00000000000..fd358188785 --- /dev/null +++ b/buildres/csl/csl-styles/dependent/liver-transplantation.csl @@ -0,0 +1,16 @@ + + diff --git a/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl b/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl index f017c7c9f94..0941c0564b0 100644 --- a/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl +++ b/buildres/csl/csl-styles/food-and-agriculture-organization-of-the-united-nations.csl @@ -31,7 +31,7 @@ This style is created to meet the citation and bibliographical requirements of FAOSTYLE, and has been tested with Zotero and Mendeley. Last update: February 2022. - 2022-02-02T16:03:38+00:00 + 2022-08-02T08:28:31+00:00 This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License @@ -180,6 +180,20 @@ + + + + + + + + + + + @@ -298,7 +312,7 @@ - + @@ -310,7 +324,7 @@ - + diff --git a/buildres/csl/csl-styles/vancouver-author-date.csl b/buildres/csl/csl-styles/vancouver-author-date.csl index 13b1bc2d023..4bd51dd6b9d 100644 --- a/buildres/csl/csl-styles/vancouver-author-date.csl +++ b/buildres/csl/csl-styles/vancouver-author-date.csl @@ -7,6 +7,7 @@ + Charles Parnot charles.parnot@gmail.com @@ -15,7 +16,7 @@ Vancouver style as outlined by International Committee of Medical Journal Editors Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Sample References - 2012-11-09T12:00:00+00:00 + 2022-07-18T16:49:43+00:00 This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License @@ -47,6 +48,16 @@