From 0161a812e652f41ff4b616637a215b5bc0f29867 Mon Sep 17 00:00:00 2001 From: Oliver Kopp Date: Thu, 2 Nov 2023 15:49:11 +0100 Subject: [PATCH 1/4] Update mlc_config.json --- mlc_config.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/mlc_config.json b/mlc_config.json index e4ae50df899..ae514be4261 100644 --- a/mlc_config.json +++ b/mlc_config.json @@ -39,6 +39,9 @@ { "pattern": "^http://localhost" }, + { + "pattern": "^http://127.0.0.1" + }, { "pattern": "^https://demo.teamscale.com" } From dbdd0b5311d3b256d1dfae366c412bd7d7741311 Mon Sep 17 00:00:00 2001 From: Oliver Kopp Date: Thu, 2 Nov 2023 22:46:49 +0100 Subject: [PATCH 2/4] Update link checker and fix links --- .github/workflows/check-links.yaml | 22 --------- .github/workflows/check-links.yml | 31 ++++++++++++ .gitignore | 2 + .lycheeignore | 14 ++++++ CHANGELOG.md | 14 +++--- PRIVACY.md | 4 +- buildres/LICENSE_with_Privacy.md | 6 +-- docs/code-howtos/IntelliJ.md | 2 +- docs/code-howtos/index.md | 2 +- docs/code-howtos/javafx.md | 2 +- .../openoffice/code-reorganization.md | 27 +++++----- docs/code-howtos/remote-storage.md | 2 +- docs/code-howtos/tools.md | 6 +-- docs/contributing.md | 2 +- .../0009-use-plain-junit5-for-testing.md | 2 +- .../development-strategy.md | 4 +- docs/teaching.md | 11 ++--- external-libraries.md | 2 +- lychee.toml | 1 + mlc_config.json | 49 ------------------- .../importer/fetcher/MedlineFetcher.java | 2 +- 21 files changed, 92 insertions(+), 115 deletions(-) delete mode 100644 .github/workflows/check-links.yaml create mode 100644 .github/workflows/check-links.yml create mode 100644 .lycheeignore create mode 100644 lychee.toml delete mode 100644 mlc_config.json diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml deleted file mode 100644 index d570d9cb07e..00000000000 --- a/.github/workflows/check-links.yaml +++ /dev/null @@ -1,22 +0,0 @@ -name: Check external href links in the documentation - -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: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - with: - show-progress: 'false' - - uses: gaurav-nelson/github-action-markdown-link-check@v1 - with: - use-quiet-mode: 'yes' - use-verbose-mode: 'no' - config-file: 'mlc_config.json' - folder-path: 'docs/' - file-path: './README.md' diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml new file mode 100644 index 00000000000..99a2295c40c --- /dev/null +++ b/.github/workflows/check-links.yml @@ -0,0 +1,31 @@ +name: Check external href links in the documentation + +on: + push: + paths: + - '.github/workflows/check-links.yml' + - '**/*.md' + 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: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + show-progress: 'false' + - name: Restore lychee cache + uses: actions/cache@v3 + with: + path: .lycheecache + key: cache-lychee-${{ github.sha }} + restore-keys: cache-lychee- + - name: Link Checker + id: lychee + uses: lycheeverse/lychee-action@v1.8.0 + with: + fail: true + args: --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md' diff --git a/.gitignore b/.gitignore index 72603d9dc08..28c62cbe9f0 100644 --- a/.gitignore +++ b/.gitignore @@ -3,6 +3,8 @@ src/main/gen/ src/main/generated/ src-gen/ +.lycheecache + # generated by https://plugins.jetbrains.com/plugin/15991-plantuml-diagram-generator *.puml diff --git a/.lycheeignore b/.lycheeignore new file mode 100644 index 00000000000..8d3f2072f17 --- /dev/null +++ b/.lycheeignore @@ -0,0 +1,14 @@ +https://arxiv.org/ +https://contribute.jabref.org/ +https://donations.jabref.org/ +https://pubs.acs.org/ +https://web.archive.org/ +https://www.researchgate.net/privacy-policy +https://www.sciencedirect.com/ + +https://github.com/koppor/jabref/issue +https://github.com/koppor/jabref/pull +https://github.com/JabRef/jabref/issue +https://github.com/JabRef/jabref/pull + +0005-example.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 6060ff558b8..be194a82e5e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -90,7 +90,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv - 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) - We enabled updating an existing entry with data from InspireHEP. [#9351](https://github.com/JabRef/jabref/issues/9351) - We added a fetcher for the Bibliotheksverbund Bayern (experimental). [#9641](https://github.com/JabRef/jabref/pull/9641) -- We added support for more biblatex date formats for parsing dates. [#2753](https://github.com/JabRef/issues/2753) +- We added support for more biblatex date formats for parsing dates. [#2753](https://github.com/JabRef/jabref/issues/2753) - 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) @@ -684,7 +684,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv - We fixed an issue with toggle of special fields does not work for sorted entries [#7016](https://github.com/JabRef/jabref/issues/7016) - We fixed an issue with the default path of external application. [#7641](https://github.com/JabRef/jabref/issues/7641) - We fixed an issue where urls must be embedded in a style tag when importing EndNote style Xml files. Now it can parse url with or without a style tag. [#6199](https://github.com/JabRef/jabref/issues/6199) -- We fixed an issue where the article title with colon fails to download the arXiv link (pdf file). [#7660](https://github.com/JabRef/issues/7660) +- We fixed an issue where the article title with colon fails to download the arXiv link (pdf file). [#7660](https://github.com/JabRef/jabref/issues/7660) - We fixed an issue where the keybinding for delete entry did not work on the main table [7580](https://github.com/JabRef/jabref/pull/7580) - We fixed an issue where the RFC fetcher is not compatible with the draft [7305](https://github.com/JabRef/jabref/issues/7305) - We fixed an issue where duplicate files (both file names and contents are the same) is downloaded and add to linked files [#6197](https://github.com/JabRef/jabref/issues/6197) @@ -786,7 +786,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv ### Added - We added a new fetcher to enable users to search mEDRA DOIs [#6602](https://github.com/JabRef/jabref/issues/6602) -- We added a new fetcher to enable users to search "[Collection of Computer Science Bibliographies](https://liinwww.ira.uka.de/bibliography/index.html)". [#6638](https://github.com/JabRef/jabref/issues/6638) +- We added a new fetcher to enable users to search "[Collection of Computer Science Bibliographies](https://en.wikipedia.org/wiki/Collection_of_Computer_Science_Bibliographies)". [#6638](https://github.com/JabRef/jabref/issues/6638) - We added default values for delimiters in Add Subgroup window [#6624](https://github.com/JabRef/jabref/issues/6624) - We improved responsiveness of general fields specification dialog window. [#6604](https://github.com/JabRef/jabref/issues/6604) - We added support for importing ris file and load DOI [#6530](https://github.com/JabRef/jabref/issues/6530) @@ -879,7 +879,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv - We fixed an issue about duplicated group color indicators [#6175](https://github.com/JabRef/jabref/issues/6175) - We fixed an issue where entries with the entry type Misc from an imported aux file would not be saved correctly to the bib file on disk [#6405](https://github.com/JabRef/jabref/issues/6405) - We fixed an issue where percent sign ('%') was not formatted properly by the HTML formatter [#6753](https://github.com/JabRef/jabref/issues/6753) -- We fixed an issue with the [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/import-using-online-bibliographic-database/ads) fetcher where `\textbackslash` appeared at the end of the abstract. +- We fixed an issue with the [SAO/NASA Astrophysics Data System](https://docs.jabref.org/collect/add-entry-using-an-id#sao-nasa-a-ds) fetcher where `\textbackslash` appeared at the end of the abstract. - We fixed an issue with the Science Direct fetcher where PDFs could not be downloaded. Fixes [#5860](https://github.com/JabRef/jabref/issues/5860) - We fixed an issue with the Library of Congress importer. - We fixed the [link to the external libraries listing](https://github.com/JabRef/jabref/blob/master/external-libraries.md) in the about dialog @@ -889,7 +889,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv - We removed the option of the "enforce legal key". [#6295](https://github.com/JabRef/jabref/issues/6295) - We removed the obsolete `External programs / Open PDF` section in the preferences, as the default application to open PDFs is now set in the `Manage external file types` dialog. [#6130](https://github.com/JabRef/jabref/pull/6130) -- We removed the option to configure whether a `.bib.bak` file should be generated upon save. It is now always enabled. Documentation at . [#6092](https://github.com/JabRef/jabref/issues/6092) +- We removed the option to configure whether a `.bib.bak` file should be generated upon save. It is now always enabled. Documentation at . [#6092](https://github.com/JabRef/jabref/issues/6092) - We removed the built-in list of IEEE journal abbreviations using BibTeX strings. If you still want to use them, you have to download them separately from . ## [5.0] – 2020-03-06 @@ -1019,7 +1019,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv ### Removed - We removed some obsolete notifications. [#5555](https://github.com/JabRef/jabref/issues/5555) -- We removed an internal step in the [ISBN-to-BibTeX fetcher](https://docs.jabref.org/import-using-publication-identifiers/isbntobibtex): The [ISBN to BibTeX Converter](https://manas.tungare.name/software/isbn-to-bibtex) by [@manastungare](https://github.com/manastungare) is not used anymore, because it is offline: "people using this tool have not been generating enough sales for Amazon." +- We removed an internal step in the [ISBN-to-BibTeX fetcher](https://docs.jabref.org/collect/add-entry-using-an-id#isbn): The [ISBN to BibTeX Converter](https://manas.tungare.name/software/isbn-to-bibtex) by [@manastungare](https://github.com/manastungare) is not used anymore, because it is offline: "people using this tool have not been generating enough sales for Amazon." - We removed the option to control the default drag and drop behaviour. You can use the modifier keys (like CtrL or Alt) instead. ## [5.0-alpha] – 2019-08-25 @@ -1052,7 +1052,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv - Change default icon for groups to a circle because a colored version of the old icon was hard to distinguish from its black counterpart. - In the main table, the context menu appears now when you press the "context menu" button on the keyboard. [feature request in the forum](https://discourse.jabref.org/t/how-to-enable-keyboard-context-key-windows) - We added icons to the group side panel to quickly switch between `union` and `intersection` group view mode. [#3269](https://github.com/JabRef/jabref/issues/3269). -- We use `https` for [fetching from most online bibliographic database](https://docs.jabref.org/import-using-online-bibliographic-database). +- We use `https` for [fetching from most online bibliographic database](https://docs.jabref.org/collect/import-using-online-bibliographic-database). - We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀alt + up/down. - Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file. - Window state is saved on close and restored on start. diff --git a/PRIVACY.md b/PRIVACY.md index d7a1ca68b48..91df8163523 100644 --- a/PRIVACY.md +++ b/PRIVACY.md @@ -46,7 +46,7 @@ These third-party services are the following: | [arXiv.org](https://arxiv.org/) | | | [Bibliotheksverbund Bayern](https://www.bib-bvb.de/) | | | [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/) | | -| [Collection of Computer Science Bibliographies](http://liinwww.ira.uka.de/) | **currently unavailable**, offline | +| [Collection of Computer Science Bibliographies](https://en.wikipedia.org/wiki/Collection_of_Computer_Science_Bibliographies) | **currently unavailable**, offline | | [CrossRef](https://www.crossref.org/) | | | [dblp](https://dblp.uni-trier.de/) | | | [Directory of Open Access Books](https://www.doabooks.org/) | | @@ -62,7 +62,7 @@ These third-party services are the following: | [Library of Congress](https://lccn.loc.gov/) | | | [National Library of Medicine](https://www.ncbi.nlm.nih.gov/) | | | [MathSciNet](http://www.ams.org/mathscinet) | | -| [mEDRA](https://medra.org/) | | +| [mEDRA](https://www.medra.org/) | | | [Mr. DLib](https://mr-dlib.org/) [1] | | | [Openlibrary](https://openlibrary.org) | | | [ResearchGate](https://www.researchgate.net/) | | diff --git a/buildres/LICENSE_with_Privacy.md b/buildres/LICENSE_with_Privacy.md index 41264b1efcc..291dd3e5f34 100644 --- a/buildres/LICENSE_with_Privacy.md +++ b/buildres/LICENSE_with_Privacy.md @@ -1,6 +1,6 @@ MIT License -Copyright © 2003-2021 [JabRef Authors](https://github.com/JabRef/jabref/blob/master/AUTHORS) +Copyright © 2003-2021 JabRef Authors Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -89,7 +89,7 @@ Service;Privacy Policy [arXiv.org](https://arxiv.org/); [Bibliotheksverbund Bayern](https://www.bib-bvb.de/); [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/); -[Collection of Computer Science Bibliographies](http://liinwww.ira.uka.de/);**currently unavailable**, offline +[Collection of Computer Science Bibliographies](https://en.wikipedia.org/wiki/Collection_of_Computer_Science_Bibliographies);**currently unavailable**, offline [CrossRef](https://www.crossref.org/); [dblp](https://dblp.uni-trier.de/); [Directory of Open Access Books](https://www.doabooks.org/); @@ -105,7 +105,7 @@ Service;Privacy Policy [Library of Congress](https://lccn.loc.gov/); [National Library of Medicine](https://www.ncbi.nlm.nih.gov/); [MathSciNet](http://www.ams.org/mathscinet); -[mEDRA](https://medra.org/); +[mEDRA](https://www.medra.org/); [Mr. DLib](https://mr-dlib.org/) [1]; [Openlibrary](https://openlibrary.org); [ResearchGate](https://www.researchgate.net/); diff --git a/docs/code-howtos/IntelliJ.md b/docs/code-howtos/IntelliJ.md index 5cac3dac319..be1e13d611c 100644 --- a/docs/code-howtos/IntelliJ.md +++ b/docs/code-howtos/IntelliJ.md @@ -17,7 +17,7 @@ Did you know that [IntelliJ allows for reformatting selected code](https://www.j ## Show variable values in IntelliJ -1. Go to a test case (example: [`org.jabref.model.entry.BibEntryTest#settingTypeToNullThrowsException`](https://github.com/JabRef/jabref/blob/refine-intellij-howto/src/test/java/org/jabref/model/entry/BibEntryTest.java#L52-L52) +1. Go to a test case (example: [`org.jabref.model.entry.BibEntryTest#settingTypeToNullThrowsException`](https://github.com/JabRef/jabref/blob/main/src/test/java/org/jabref/model/entry/BibEntryTest.java#L52-L52) 2. Set the breakpoint to the first line 3. Execute the test 4. Go to the settings of the debugger and activate "Show Variable Values in Editor" and "Show Method Return Values" diff --git a/docs/code-howtos/index.md b/docs/code-howtos/index.md index fff2c645b44..eb11987445d 100644 --- a/docs/code-howtos/index.md +++ b/docs/code-howtos/index.md @@ -5,7 +5,7 @@ has_children: true # Code Howtos This page provides some development support in the form of howtos. -See also [High Level Documentation](../getting-into-thecode/high-level-documentation.md). +See also [High Level Documentation](../getting-into-the-code/high-level-documentation.md). ## Generic code how tos diff --git a/docs/code-howtos/javafx.md b/docs/code-howtos/javafx.md index c045b12fc12..2dfb8514351 100644 --- a/docs/code-howtos/javafx.md +++ b/docs/code-howtos/javafx.md @@ -62,7 +62,7 @@ The goal of the MVVM architecture is to separate the state/behavior from the app The only class which access model and logic classes is the ViewModel. Controller and View have only access the ViewModel and never the backend. The ViewModel does not know the Controller or View. -More details about the MVVM pattern can be found in [an article by Microsoft](https://msdn.microsoft.com/en-us/magazine/dd419663.aspx) and in [an article focusing on the implementation with JavaFX](http://blog.buildpath.de/javafx-decouple-the-view-and-its-behavior-to-create-a-testable-ui/). +More details about the MVVM pattern can be found in [an article by Microsoft](https://msdn.microsoft.com/en-us/magazine/dd419663.aspx) and in [an article focusing on the implementation with JavaFX](https://web.archive.org/web/20140825151304/http://blog.buildpath.de/javafx-decouple-the-view-and-its-behavior-to-create-a-testable-ui/). ## An example diff --git a/docs/code-howtos/openoffice/code-reorganization.md b/docs/code-howtos/openoffice/code-reorganization.md index c9c37fe47d8..d7bd01a1244 100644 --- a/docs/code-howtos/openoffice/code-reorganization.md +++ b/docs/code-howtos/openoffice/code-reorganization.md @@ -29,15 +29,15 @@ Why * `OOListUtil`: some utilities working on List * `uno` : helpers for various tasks via UNO.\ These are conceptually independent of JabRef code and logic. - * `ootext` : to separate decisions on the format of references and citation marks from the actual insertion into the document, the earlier method [OOUtil.insertOOFormattedTextAtCurrentLocation](https://github.com/JabRef/jabref/blob/475b2989ffa8ec61c3327c62ed8f694149f83220/src/main/java/org/jabref/logic/openoffice/OOUtil.java#L112) was extended to handle new tags that describe actions earlier done in code. - * This became [OOTextIntoOO.write](https://github.com/antalk2/jabref/blob/122d5133fa6c7b44245c5ba5600d398775718664/src/main/java/org/jabref/model/openoffice/ootext/OOTextIntoOO.java#L149) + * `ootext` : to separate decisions on the format of references and citation marks from the actual insertion into the document, the earlier method `OOUtil.insertOOFormattedTextAtCurrentLocation` was extended to handle new tags that describe actions earlier done in code. + * This became `OOTextIntoOO.write` * `(change)` Now all output to the document goes through this, not only those from Layout. This allows the citation markers and `jstyle:Title` to use these tags. * This allows some backward-compatible extensions to jstyle.\ - `(change)` [Added](https://github.com/antalk2/jabref/blob/122d5133fa6c7b44245c5ba5600d398775718664/src/main/java/org/jabref/logic/openoffice/style/OOBibStyle.java#L92) some extra keywords, in `{prefix}_MARKUP_BEFORE`, `{prefix}_MARKUP_AFTER` pairs to allow bracketing some parts of citation marks with text and/or open/close tag pairs. - * [OOFormat](https://github.com/antalk2/jabref/blob/improve-reversibility-rebased-03/src/main/java/org/jabref/model/openoffice/ootext/OOFormat.java) contains helpers to create the appropriate tags - * [OOText](https://github.com/antalk2/jabref/blob/improve-reversibility-rebased-03/src/main/java/org/jabref/model/openoffice/ootext/OOText.java) formalizes the distinction from `String`. I did not change `String` to `OOText` in old code, (in particular in OOStyle). + `(change)` Added some extra keywords, in `{prefix}_MARKUP_BEFORE`, `{prefix}_MARKUP_AFTER` pairs to allow bracketing some parts of citation marks with text and/or open/close tag pairs. + * `OOFormat` contains helpers to create the appropriate tags + * `OOText` formalizes the distinction from `String`. I did not change `String` to `OOText` in old code, (in particular in OOStyle). * `rangesort` : ordering objects that have an `XTextRange`, optionally with an extra integer to break ties. - * `RangeSort.partitionAndSortRanges` : since `XTextRangeCompare` can only compare `XTextRange` values in the same `XText`, we partition them accordingly and only sort within each partiion. + * `RangeSort.partitionAndSortRanges` : since `XTextRangeCompare` can only compare `XTextRange` values in the same `XText`, we partition them accordingly and only sort within each partition. * `RangeSortable` (interface), `RangeSortEntry` (implements) :\ When we replace `XTextRange` of citation marks in footnotes with the range of the footnote mark, multiple citation marks may be mapped to the same location. To preserve the order between these, `RangeSortable` allows this order to be indicated by returning appropriate indices from `getIndexInPosition` * `RangeSortVisual` : sort in top-to-bottom left-to-right order.\ @@ -61,12 +61,12 @@ At the core, * a list of citations (`citationsInStorageOrder`) * an identifier `CitationGroupId cgid` * this allows to refer to the group - * also used to associate the group to its citation markers location (outside the style part, in [Backend](https://github.com/antalk2/jabref/blob/fed0952cbdaf7a76bcb09b3db5ac48f34f5ca388/src/main/java/org/jabref/logic/openoffice/backend/Backend52.java#L46)) + * also used to associate the group to its citation markers location (outside the style part, in `Backend52`) * `OODataModel dataModel` is here, in order to handle old (Jabref5.2) structure where pageInfo belonged to CitationGroup not Citation * `referenceMarkNameForLinking` is optional: can be used to crosslink to the citation marker from the bibliography. * `CitationGroups` represents the collection of citation groups.\ Processing starts with creating a `CitationGroups` instance from the data stored in the document. -* `CitedKey` represents a cited source, with ordered backreferences (using `CitationPath`) to the correponding citations. +* `CitedKey` represents a cited source, with ordered back references (using `CitationPath`) to the corresponding citations. * `CitedKeys` is just an order-preserving collection of `CitedKeys` that also supports lookup by `citationKey`. While producing citation markers, we also create a corresponding `CitedKeys` instance, and store it in `CitationGroups.bibliography`. This is already sorted, its entries have `uniqueLetter` or `number` assigned, but not converted to markup yet. Common processing steps: @@ -79,10 +79,11 @@ Common processing steps: We can create a `CitedKeys` instance (`bibliography`) according to this order. * For citations numbered in order of first appearance we number the sources and distribute the numbers to the corresponding citations. * For citations numbered in order of bibliography, we sort the bibliography, number, distribute. -* For author-year citations we have to decide on the letters `uniqueLetter` used to distinguish sources. This needs order of first appearance of the sources and recognizing clashing citation markers. This is done in logic, in [`OOProcessAuthorYearMarkers.createUniqueLetters()`](https://github.com/antalk2/jabref/blob/122d5133fa6c7b44245c5ba5600d398775718664/src/main/java/org/jabref/logic/openoffice/style/OOProcessAuthorYearMarkers.java#L49) -* We also mark first appearance of each source ([`setIsFirstAppearanceOfSourceInCitations`](https://github.com/antalk2/jabref/blob/fed0952cbdaf7a76bcb09b3db5ac48f34f5ca388/src/main/java/org/jabref/logic/openoffice/style/OOProcessAuthorYearMarkers.java#L146)) +* For author-year citations we have to decide on the letters `uniqueLetter` used to distinguish sources. This needs order of first appearance of the sources and recognizing clashing citation markers. This is done in logic, in `OOProcessAuthorYearMarkers.createUniqueLetters()` +* We also mark first appearance of each source (`setIsFirstAppearanceOfSourceInCitations`) + +The entry point for this processing is: `OOProcess.produceCitationMarkers`. -The entry point for this processing is: [`OOProcess.produceCitationMarkers`](https://github.com/antalk2/jabref/blob/fed0952cbdaf7a76bcb09b3db5ac48f34f5ca388/src/main/java/org/jabref/logic/openoffice/style/OOProcess.java#L69).\ It fills * each `CitationGroup.citationMarker` @@ -94,7 +95,7 @@ It fills * `StyleLoader` : not changed (knows about default styles) Used by GUI * `OOPreFormatter` : LaTeX code to unicode and OOText tags. (not changed) * `OOBibStyle` : is mostly concerned by loading/parsing jstyle files and presenting its pieces to the rest. Originally it also contains code to format numeric and author-year citation markers. - * Details of their new implementations are in [`OOBibStyleGetNumCitationMarker`](https://github.com/antalk2/jabref/blob/improve-reversibility-rebased-03/src/main/java/org/jabref/logic/openoffice/style/OOBibStyleGetNumCitationMarker.java) and [`OOBibStyleGetCitationMarker`](https://github.com/antalk2/jabref/blob/improve-reversibility-rebased-03/src/main/java/org/jabref/logic/openoffice/style/OOBibStyleGetCitationMarker.java) + * Details of their new implementations are in `OOBibStyleGetNumCitationMarker` and `OOBibStyleGetCitationMarker` * The new implementations * support pageInfo for each citation * support unresolved citations @@ -106,7 +107,7 @@ It fills * `CitationMarkerNumericBibEntry` * `CitationMarkerNormEntry`\ describe their expected input entries. -* [`OOProcess.produceCitationMarkers`](https://github.com/antalk2/jabref/blob/fed0952cbdaf7a76bcb09b3db5ac48f34f5ca388/src/main/java/org/jabref/logic/openoffice/style/OOProcess.java#L69) is the main entry point for style application. Calls to specific implementations in `OOProcessCitationKeyMarkers`, `OOProcessNumericMarkers` and `OOProcessAuthorYearMarkers` according to jstyle flags. +* `OOProcess.produceCitationMarkers` is the main entry point for style application. Calls to specific implementations in `OOProcessCitationKeyMarkers`, `OOProcessNumericMarkers` and `OOProcessAuthorYearMarkers` according to jstyle flags. ## logic/backend diff --git a/docs/code-howtos/remote-storage.md b/docs/code-howtos/remote-storage.md index 0f845913aa5..01a402afc79 100644 --- a/docs/code-howtos/remote-storage.md +++ b/docs/code-howtos/remote-storage.md @@ -12,4 +12,4 @@ JabRef supports kinds of remote storage: The first one is the more modern approach allowing offline-work. The second approach makes use of the SQL features of databases and require direct online connections. -More details in [JabDrive](remote-storeage-jabdrive.md) and [SQL Storage](remote-storage-sql.md) respectively. +More details in [JabDrive](remote-storage-jabdrive.md) and [SQL Storage](remote-storage-sql.md) respectively. diff --git a/docs/code-howtos/tools.md b/docs/code-howtos/tools.md index c4e9853a21f..f2b344da05a 100644 --- a/docs/code-howtos/tools.md +++ b/docs/code-howtos/tools.md @@ -16,9 +16,9 @@ This page lists some software we consider useful. Here, we collect some helpful git hints -* [https://github.com/blog/2019-how-to-undo-almost-anything-with-git](https://github.com/blog/2019-how-to-undo-almost-anything-with-git) -* [https://github.com/RichardLitt/docs/blob/master/amending-a-commit-guide.md](https://github.com/RichardLitt/docs/blob/master/amending-a-commit-guide.md) -* awesome hints and tools regarding git: [https://github.com/dictcp/awesome-git](https://github.com/dictcp/awesome-git) +* +* [So you need to change your commit](https://github.com/RichardLitt/knowledge/blob/master/github/amending-a-commit-guide.md#so-you-need-to-change-your-commit) +* awesome hints and tools regarding git: ### Rebase everything as one commit on main diff --git a/docs/contributing.md b/docs/contributing.md index bd187bf1f3f..06451efcbc9 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -78,7 +78,7 @@ Actual :[Opens\ JabRef's\ Twitter\ page (src\main\java\org\jabref\gui\JabRefFr Add the above snippet to the English translation file located at `src/main/resources/l10n/JabRef_en.properties`. [Crowdin](https://crowdin.com/project/jabref) will automatically pick up the new string and add it to the other translations. -You can also directly run the specific test in your IDE. The test "LocalizationConsistencyTest" is placed under `src/test/java/org.jabref.logic.l10n/LocalizationConsistencyTest.java`. Find more information in the [JabRef developer docs](https://devdocs.jabref.org/getting-into-the-code/code-howtos#using-localization-correctly). +You can also directly run the specific test in your IDE. The test "LocalizationConsistencyTest" is placed under `src/test/java/org.jabref.logic.l10n/LocalizationConsistencyTest.java`. Find more information in the [JabRef developer docs](code-howtos/localization.md). #### When adding a library diff --git a/docs/decisions/0009-use-plain-junit5-for-testing.md b/docs/decisions/0009-use-plain-junit5-for-testing.md index 3d88c5989e3..5ca034a33cd 100644 --- a/docs/decisions/0009-use-plain-junit5-for-testing.md +++ b/docs/decisions/0009-use-plain-junit5-for-testing.md @@ -34,7 +34,7 @@ Chosen option: "Plain JUnit5", because comes out best \(see below\). ### Plain JUnit5 Homepage: -JabRef testing guidelines: +JabRef testing guidelines: <../testing.md> Example: diff --git a/docs/getting-into-the-code/development-strategy.md b/docs/getting-into-the-code/development-strategy.md index 8fddcd79b47..b58387ba1c8 100644 --- a/docs/getting-into-the-code/development-strategy.md +++ b/docs/getting-into-the-code/development-strategy.md @@ -12,7 +12,7 @@ To ensure high code-quality, * We follow the principles of [Effective Java](https://www.oreilly.com/library/view/effective-java-3rd/9780134686097/). * We use [Design Patterns](https://java-design-patterns.com/patterns/) when applicable. * We document our design decisions using the lightweight architectural decision records [MADR](https://adr.github.io/madr/). -* We review each external pull request by at least two [JabRef Core Developers](https://github.com/JabRef/jabref/blob/main/MAINTAINERS/README.md). +* We review each external pull request by at least two [JabRef Core Developers](https://github.com/JabRef/jabref/blob/main/MAINTAINERS). Read on about our automated quality checks at [Code Quality](../code-howtos/code-quality.md). @@ -35,7 +35,7 @@ Other branches are used for discussing improvements with the help of [pull reque ## How JabRef acquires contributors -* We participate in [Hacktoberfest](https://hacktoberfest.digitalocean.com). See [https://www.jabref.org/hacktoberfest/](https://www.jabref.org/hacktoberfest/) for details. +* We participate in [Hacktoberfest](https://www.hacktoberfest.com). * We participate in [Google Summer of Code](https://developers.google.com/open-source/gsoc/). ## Historical notes diff --git a/docs/teaching.md b/docs/teaching.md index dedc12bde3f..6c617826f50 100644 --- a/docs/teaching.md +++ b/docs/teaching.md @@ -21,7 +21,6 @@ By using JabRef as training object in exercises and labs, students can level-up implementation effort, testing effort, and "issue understanding effort". The latter category is important, because some issues are "quick wins" and others need thorough thinking. - In general, all issues of JabRef are free to take. Be aware that the difficulty of bugs and feature vary. For the brave, the [Bug Board](https://github.com/orgs/JabRef/projects/7) or the [Feature Board](https://github.com/JabRef/jabref/projects/6) provide other issue sources. @@ -34,7 +33,7 @@ By using JabRef as training object in exercises and labs, students can level-up 6. Students address review feedback 7. Students submit pull request 8. Code reviews by JabRef maintainers -9. Students address feedback and learn more about good coding practices by incoporating feedback +9. Students address feedback and learn more about good coding practices by incorporating feedback 10. Students update their pull request 11. Pull request is merged @@ -50,19 +49,19 @@ There is no special process for student contributions. We want to discuss it nev The process for accepting contributions is as below. The syntax is [BPMN](https://en.wikipedia.org/wiki/Business\_Process\_Model\_and\_Notation) modeled using [bpmn.io](https://bpmn.io). -[![process]()](https://github.com/JabRef/jabref/tree/ed275b62fe7dac57a086e43802e36deb93c63e31/docs/images/contribution-process-reviews.svg) +[![process](images/contribution-process-reviews.svg)](https://raw.githubusercontent.com/JabRef/jabref/main/docs/images/contribution-process-reviews.svg) In short, the contribution is **reviewed by two JabRef developers**. Typically, they have constructive feedback on their contribution. This means, that the contributors get comments on their contribution enabling them to level-up their coding skill. Incorporating improvements takes time, too. The benefit is two-fold: a) contributors improve their coding skills and b) JabRef's code quality improves. All in all, we ask to respect the aims of the JabRef team and to reserve time to incorporate the reviewer's comments. GitHub describes that in their page [Understanding the GitHub flow](https://guides.github.com/introduction/flow/): -[![GitHub flow]()](https://github.com/JabRef/jabref/tree/ed275b62fe7dac57a086e43802e36deb93c63e31/docs/images/github-flow.png) +[![GitHub flow](images/github-flow.png)](https://raw.githubusercontent.com/JabRef/jabref/main/docs/images/github-flow.png) ## Process for Java newcomers Newcomers contributing in the context of a university teaching experience are invited to follow the process described above. In case the capacity of the instructing university allows, we propose a three-step approach. First, the contributors prepare their contribution as usual. Then, they submit the pull request _to a separate repository_. There, the instructor reviews the pull request and provides feedback. This happens in a loop until the instructor shows the green light. Then, the pull request can be submitted to the main JabRef repository. This will help to reduce the load on the JabRef team and improve the quality of the initial pull request. -[![process with instructor]()](https://github.com/JabRef/jabref/tree/ed275b62fe7dac57a086e43802e36deb93c63e31/docs/images/contribution-process-reviews-with-instructor.svg) +[![process with instructor](images/contribution-process-reviews-with-instructor.svg)](https://raw.githubusercontent.com/JabRef/jabref/main/docs/images/contribution-process-reviews-with-instructor.svg) ## Past courses @@ -129,7 +128,7 @@ Course "Programming and Software Development" as part of the [BSc Software Engin Course [DD2480 Software Engineering Fundamentals](https://www.kth.se/student/kurser/kurs/DD2480?l=en) -* Summary: Groups of students from three to five persons experienced the whole software engineering process within a week: From the requirements specification to the final pull request. +* Summary: Groups of students from three to five persons experienced the whole software engineering process within a week: From the requirements' specification to the final pull request. * Successfully run in 2020 ### Portuguese diff --git a/external-libraries.md b/external-libraries.md index 6e68aa9bd68..f3d05010490 100644 --- a/external-libraries.md +++ b/external-libraries.md @@ -4,7 +4,7 @@ This document lists the fonts, icons, and libraries used by JabRef. This file is manually kept in sync with build.gradle and the binary jars contained in the lib/ directory. One can list all dependencies by using Gradle task `dependencyReport`. -It generates the file [build/reports/project/dependencies.txt](build/reports/project/dependencies.txt). +It generates the file `build/reports/project/dependencies.txt`. Below, there is a howto to generate the content at "Sorted list of runtime dependencies output by gradle". ## Legend diff --git a/lychee.toml b/lychee.toml new file mode 100644 index 00000000000..ffc6ffe8716 --- /dev/null +++ b/lychee.toml @@ -0,0 +1 @@ +exclude_path = ["build/", "buildres/abbrv.jabref.org", "out/", "src/main/resources/csl-locales", "src/main/resources/csl-styles"] diff --git a/mlc_config.json b/mlc_config.json deleted file mode 100644 index ae514be4261..00000000000 --- a/mlc_config.json +++ /dev/null @@ -1,49 +0,0 @@ -{ - "ignorePatterns": [ - { - "pattern": "autohotkey.com" - }, - { - "pattern": "baeldung.com" - }, - { - "pattern": "^CONTRIBUTING\\.md" - }, - { - "pattern": "^https://codecov\\.io/" - }, - { - "pattern": "^https://dl\\.acm\\.org" - }, - { - "pattern": "^https://github\\.com" - }, - { - "pattern": "^https://.*\\.jabref\\.org" - }, - { - "pattern": "^https://sourcespy\\.com/.*" - }, - { - "pattern": "^http://purl\\.org/net/bibteXMP" - }, - { - "pattern": "tldrlegal.com" - }, - { - "pattern": "^https://web\\.archive\\.org" - }, - { - "pattern": "^https://www\\.slant\\.co/" - }, - { - "pattern": "^http://localhost" - }, - { - "pattern": "^http://127.0.0.1" - }, - { - "pattern": "^https://demo.teamscale.com" - } - ] -} diff --git a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java index f0cf950e1eb..900122f2594 100644 --- a/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java +++ b/src/main/java/org/jabref/logic/importer/fetcher/MedlineFetcher.java @@ -43,7 +43,7 @@ /** * Fetch or search from PubMed www.ncbi.nlm.nih.gov * The MedlineFetcher fetches the entries from the PubMed database. - * See docs.jabref.org for a detailed documentation of the available fields. + * See docs.jabref.org for a detailed documentation of the available fields. */ public class MedlineFetcher implements IdBasedParserFetcher, SearchBasedFetcher { private static final Logger LOGGER = LoggerFactory.getLogger(MedlineFetcher.class); From 50089f024bde40ebc392dbdbfd614685d61dc2f4 Mon Sep 17 00:00:00 2001 From: Oliver Kopp Date: Thu, 2 Nov 2023 22:52:56 +0100 Subject: [PATCH 3/4] Fix job name --- .github/workflows/check-links.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml index 99a2295c40c..0d16aa7fea6 100644 --- a/.github/workflows/check-links.yml +++ b/.github/workflows/check-links.yml @@ -11,7 +11,7 @@ on: workflow_dispatch: jobs: - markdown-link-check: + lychee: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 From 498b3312cba7ead3ef5e6c41167c09374832153e Mon Sep 17 00:00:00 2001 From: Oliver Kopp Date: Thu, 2 Nov 2023 22:54:50 +0100 Subject: [PATCH 4/4] Enable cancelling of last runs --- .github/workflows/check-links.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/check-links.yml b/.github/workflows/check-links.yml index 0d16aa7fea6..a121d295643 100644 --- a/.github/workflows/check-links.yml +++ b/.github/workflows/check-links.yml @@ -10,6 +10,10 @@ on: - cron: "0 9 1 * *" workflow_dispatch: +concurrency: + group: "${{ github.workflow }}-${{ github.head_ref }}" + cancel-in-progress: true + jobs: lychee: runs-on: ubuntu-latest