diff --git a/.editorconfig b/.editorconfig index 1c2922925f4..95915a432b7 100644 --- a/.editorconfig +++ b/.editorconfig @@ -5,3 +5,6 @@ charset = utf-8 indent_style = space insert_final_newline = true trim_trailing_whitespace = true + +[*.md] +trim_trailing_whitespace = false diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 03dff7e01a6..3f15c4f0c6f 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -20,7 +20,7 @@ JabRef version on -- [ ] I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists +- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists diff --git a/.github/outdatedDependencies.md b/.github/outdatedDependencies.md index 62b87165631..e4e9947d92a 100644 --- a/.github/outdatedDependencies.md +++ b/.github/outdatedDependencies.md @@ -1,5 +1,5 @@ --- title: Outdated dependencies -labels: t: dependencies +labels: type: dependencies --- [There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22) diff --git a/.gitignore b/.gitignore index ba242f57346..48fb0aa7dad 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,9 @@ src/main/gen/ src/main/generated/ +# the journal list cache +*.mv + # private data /buildres/jabref-cert-2016.p12 diff --git a/.mailmap b/.mailmap index ccfae69b00e..cb4da018a86 100644 --- a/.mailmap +++ b/.mailmap @@ -193,3 +193,10 @@ Christoph Treude Goutam Lavudiya Shikun Xiong <53288073+ShikunXiong@users.noreply.github.com> Fabiani Giovanni +Dimitra Karadima <44123133+dimitra-karadima@users.noreply.github.com> +Dimitra Karadima <44123133+dimitra-karadima@users.noreply.github.com> +Cai Zhichun <54977532+braincident@users.noreply.github.com> +Gennadiy Stakhovskiy +Mootez Saad <34676841+MootezSaaD@users.noreply.github.com> +Mootez Saad <34676841+MootezSaaD@users.noreply.github.com> +Chen Yuheng diff --git a/AUTHORS b/AUTHORS index dfde5b567dd..40b6b524e3f 100644 --- a/AUTHORS +++ b/AUTHORS @@ -41,6 +41,7 @@ Ayachi Nene Bartosz J. Kaczkowski Bartłomiej Dach Behrouz Javanmardi +Benedikt Tutzer Benjamin Köhler Berk Gureken Bernd Kalbfuss @@ -51,15 +52,18 @@ Bherwani Ayush Bitor Tonixa Biriato Balença Brian Quistorff Brian Van Essen +Cai Zhichun captain123 Carl Christian Snethlage carlg0ransson Carlos Morales Carlos Silla Carlos Silva +Catarina Gomes Cerrianne Santos Chamod Shehanka Chelsey Ong +Chen Yuheng Chris Brown Christian Bartsch Christian Kopf @@ -88,6 +92,7 @@ Dennis Tschechlov DevSiroukane Dilan Coss dima +Dimitra Karadima Domenico Cufalo Dominik Schrempf Dominik Traczyk @@ -126,15 +131,20 @@ frasca80 Fred Stevens Frédéric Darboux Galileo Sartor +Gennadiy Stakhovskiy Geoffrey Taerim Kim Gert Renckens Goutam Lavudiya Gregor Herrmann +Grzegorz Popiel guenesaydin Guillaume Gardey Hakan Duran Hannes Restel Harinda Samarasekara +HifeFish +hrandrianasolo +Hussain Arif Igor Chernyavsky Igor Steinmacher Illes Solt @@ -146,6 +156,7 @@ Jan Schäfer Janosch Kutscherauer Jason Pickering Javier Muñoz Ferrara +jcampbell11245 Jeff Kerr Jeff Miller Jeffrey Kuhn @@ -158,6 +169,7 @@ John David John Relph John Zedlewski Jonas Lähnemann +Jonas Moosmann Jonathan Powell Jong-Ho Shinn Jorge Tornero @@ -173,6 +185,7 @@ Jörg Wegner Jörg Zieren Jørgen Kvalsvik Jürgen Lange +k3KAW8Pnf7mkmdSMPHz27 Kai Mindermann Kai Takac Kaique Komata @@ -213,6 +226,7 @@ Martin Stolle Martina Catizone Mathias Walter Matthias Geiger +Matthias Mayr Matthias Mueller Mattia Bunel Mattias Ulbrich @@ -232,6 +246,7 @@ Michel Krämer Mihu Mike Smoot mohamean +Mootez Saad Morgan Lovato Moritz Ringler Morten Alver @@ -312,6 +327,7 @@ Stanley Foerster Stefan Feyer Stefan Gerzmann Stefan Kolb +Stefan Kufer Stefan Robert Stefan Scheffel Stefano Gariazzo @@ -360,6 +376,7 @@ Yara Grassi Gouffon Yash Kothari Yichen Sun Yifan Peng +Yunsheng Luo Yurick Honda zacmks Zeabin diff --git a/CHANGELOG.md b/CHANGELOG.md index f5f4e34895c..250a94eb626 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve - We added support for basic markdown in custom formatted previews [#6194](https://github.com/JabRef/jabref/issues/6194) - We now show the number of items found and selected to import in the online search dialog. [#6248](https://github.com/JabRef/jabref/pull/6248) - We created a new install screen for macOS. [#5759](https://github.com/JabRef/jabref/issues/5759) +- We added a new integrity check for duplicate DOIs. [koppor#339](https://github.com/koppor/jabref/issues/339) - We implemented an option to download fulltext files while importing. [#6381](https://github.com/JabRef/jabref/pull/6381) +- We added a progress-indicator showing the average progress of background tasks to the toolbar. Clicking it reveals a pop-over with a list of running background tasks. [6443](https://github.com/JabRef/jabref/pull/6443) +- 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) ### Changed @@ -41,6 +46,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve - We fixed an issue where opening a library from the recent libraries menu was not possible. [#5939](https://github.com/JabRef/jabref/issues/5939) - We fixed an issue with inconsistent capitalization of file extensions when downloading files. [#6115](https://github.com/JabRef/jabref/issues/6115) - We fixed the display of language and encoding in the preferences dialog. [#6130](https://github.com/JabRef/jabref/pull/6130) +- We fixed the issue that groups panel does not keep size when resizing window. [#6180](https://github.com/JabRef/jabref/issues/6180) - We fixed an error that sometimes occurred when using the context menu. [#6085](https://github.com/JabRef/jabref/issues/6085) - We fixed an issue where search full-text documents downloaded files with same name, overwriting existing files. [#6174](https://github.com/JabRef/jabref/pull/6174) - We fixed an issue when importing into current library an erroneous message "import cancelled" is displayed even though import is successful. [#6266](https://github.com/JabRef/jabref/issues/6266) @@ -50,9 +56,17 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve - We fixed the display of icon both in the main table and linked file editor. [#6169](https://github.com/JabRef/jabref/issues/6169) - We fixed the paste entry command in the menu and toolbar, that did not do anything. [#6293](https://github.com/JabRef/jabref/issues/6293) - We fixed an issue where the windows installer did not create an entry in the start menu [bug report in the forum](https://discourse.jabref.org/t/error-while-fetching-from-doi/2018/3) +- We fixed an issue where only the field `abstract` and `comment` were declared as multiline fields. Other fields can now be configured in the preferences using "Do not wrap the following fields when saving" [4373](https://github.com/JabRef/jabref/issues/4373) - We fixed an issue where JabRef switched to discrete graphics under macOS [#5935](https://github.com/JabRef/jabref/issues/5935) - We fixed an issue where the Preferences entry preview will be unexpected modified leads to Value too long exception [#6198](https://github.com/JabRef/jabref/issues/6198) - We fixed an issue where custom jstyles for Open/LibreOffice would only be valid if a layout line for the entry type `default` was at the end of the layout section [#6303](https://github.com/JabRef/jabref/issues/6303) +- We fixed an issue where long directory names created from patterns could create an exception. [#3915](https://github.com/JabRef/jabref/issues/3915) +- We fixed an issue where sort on numeric cases was broken. [#6349](https://github.com/JabRef/jabref/issues/6349) +- We fixed an issue where year and month fields were not cleared when converting to biblatex [#6224](https://github.com/JabRef/jabref/issues/6224) +- 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 LaTeX citations for specific commands (\autocites) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476) ### Removed diff --git a/README.md b/README.md index 7f7567724aa..da480916196 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,5 @@ # JabRef Bibliography Management -[![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment) -[![Build Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests) -[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master) -[![Paypal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef) -[![Crowdin](https://d322cqt584bo4o.cloudfront.net/jabref/localized.svg)](https://crowdin.com/project/jabref) - 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. @@ -62,6 +56,7 @@ The [latest stable release is available at FossHub](https://www.fosshub.com/JabR ## 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) 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 our forum](http://discourse.jabref.org/c/features)! @@ -72,14 +67,19 @@ An explanation of donation possibilities and usage of donations is available at ## Contributing +[![dev-docs](https://img.shields.io/badge/dev-docs-blue)](https://devdocs.jabref.org/) [![Help Contribute to Open Source](https://www.codetriage.com/jabref/jabref/badges/users.svg)](https://www.codetriage.com/jabref/jabref) [![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![OpenHub](https://www.openhub.net/p/jabref/widgets/project_thin_badge.gif)](https://www.openhub.net/p/jabref) +[![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment) +[![Test Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests) +[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master) -> Not a programmer? [Learn how to help.](https://contribute.jabref.org) - -Want to be part of a free and open-source project that tens of thousands of scientists use every day? Check out the ways you can contribute, below: +Want to be part of a free and open-source project that tens of thousands of scientists use every day? +Check out the ways you can contribute, below: +- Not a programmer? Help translating JabRef at [Crowdin](https://crowdin.com/project/jabref) or learn how to help at [contribute.jabref.org](https://contribute.jabref.org) +- Quick overview on the architecture needed? Look at our [high-level documentation](https://devdocs.jabref.org/getting-into-the-code/high-level-documentation) - For details on how to contribute, have a look at our [guidelines for contributing](CONTRIBUTING.md). - You are welcome to contribute new features. To get your code included into JabRef, just [fork](https://help.github.com/en/articles/fork-a-repo) the JabRef repository, make your changes, and create a [pull request](https://help.github.com/en/articles/about-pull-requests). - To work on existing JabRef issues, check out our [issue tracker](https://github.com/JabRef/jabref/issues). New to open source contributing? Look for issues with the ["good first issue"](https://github.com/JabRef/jabref/labels/good%20first%20issue) label to get started. @@ -98,8 +98,8 @@ 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 +[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 diff --git a/build.gradle b/build.gradle index 2d6959fd4c7..8f2df80ed2d 100644 --- a/build.gradle +++ b/build.gradle @@ -16,7 +16,7 @@ plugins { id 'com.github.ben-manes.versions' version '0.28.0' id 'org.javamodularity.moduleplugin' version '1.5.0' id 'org.openjfx.javafxplugin' version '0.0.8' - id 'org.beryx.jlink' version '2.18.0' + id 'org.beryx.jlink' version '2.19.0' // nicer test outputs during running and completion id 'com.adarshr.test-logger' version '2.0.0' @@ -81,6 +81,7 @@ sourceSets { } repositories { + mavenLocal() jcenter() maven { url 'https://oss.sonatype.org/content/groups/public' } maven { url 'https://repository.apache.org/snapshots' } @@ -158,7 +159,7 @@ dependencies { implementation 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-11' implementation 'de.saxsys:mvvmfx-validation:1.9.0-SNAPSHOT' implementation 'de.saxsys:mvvmfx:1.8.0' - implementation 'org.fxmisc.easybind:easybind:1.0.3' + implementation 'com.tobiasdiez:easybind:2.0.0-SNAPSHOT' implementation 'org.fxmisc.flowless:flowless:0.6.1' implementation 'org.fxmisc.richtext:richtextfx:0.10.5' implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1' @@ -191,9 +192,9 @@ dependencies { exclude module: "log4j-core" } - implementation 'com.vladsch.flexmark:flexmark:0.61.24' - implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.24' - implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.24' + implementation 'com.vladsch.flexmark:flexmark:0.61.26' + implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.61.26' + implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.61.26' testImplementation 'io.github.classgraph:classgraph:4.8.78' testImplementation 'org.junit.jupiter:junit-jupiter:5.6.2' @@ -543,7 +544,7 @@ task deleteInstallerTemp(type: Delete) { jpackage.dependsOn deleteInstallerTemp jlink { - options = ['--strip-debug','--compress', '2', '--no-header-files', '--no-man-pages'] + options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages'] launcher { name = 'JabRef' } diff --git a/config/IntelliJ Code Style.xml b/config/IntelliJ Code Style.xml index 489f44c1a5c..6a03e104d9d 100644 --- a/config/IntelliJ Code Style.xml +++ b/config/IntelliJ Code Style.xml @@ -1,37 +1,38 @@ - - - -