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Merge branch 'main' into remove-sav-file
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@koppor
koppor committed Mar 18, 2023
2 parents 1339588 + b8497e9 commit 8c2c704
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Showing 35 changed files with 2,355 additions and 937 deletions.
3 changes: 3 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -11,9 +11,12 @@ The title of the PR must not reference an issue, because GitHub does not support
- [x] done; [ ] not done / not applicable
-->

```[tasklist]
### Compulsory 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.
```
4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -23,8 +23,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
### Changed

- 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568)
- 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)
- We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625)
- We streamlined the paths for logs and backups: The parent path fragement is always `logs` or `backups`.
- Backups of libraries are not stored per JabRef version, but collected together.
- We modified the `Add Group` dialog to use the most recently selected group hierarchical context [#9141](https://github.com/JabRef/jabref/issues/9141)
- 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.


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12 changes: 1 addition & 11 deletions build.gradle
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Expand Up @@ -259,7 +259,6 @@ processResources {

task generateSource(dependsOn: ["generateBstGrammarSource",
"generateSearchGrammarSource",
"generateMedlineSource",
"generateBibtexmlSource",
"generateEndnoteSource",
"generateModsSource",
Expand Down Expand Up @@ -290,15 +289,6 @@ tasks.register("generateSearchGrammarSource", JavaExec) {
args = ["-o","src-gen/main/java/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
}

task generateMedlineSource(type: XjcTask) {
group = 'JabRef'
description = "Generates java files for the medline importer."

schemaFile = "src/main/resources/xjc/medline/medline.xsd"
outputDirectory = "src-gen/main/java"
javaPackage = "org.jabref.logic.importer.fileformat.medline"
}

task generateBibtexmlSource(type: XjcTask) {
group = 'JabRef'
description = "Generates java files for the bibtexml importer."
Expand Down Expand Up @@ -424,7 +414,7 @@ test {
}

moduleOptions {
// TODO: Remove this as soon as archunit is modularized
// TODO: Remove this as soon as ArchUnit is modularized
runOnClasspath = true
}

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189 changes: 189 additions & 0 deletions buildres/csl/csl-styles/arkivoc.csl
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@@ -0,0 +1,189 @@
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
<info>
<title>Arkivoc</title>
<id>http://www.zotero.org/styles/arkivoc</id>
<link href="http://www.zotero.org/styles/arkivoc" rel="self"/>
<link href="http://www.zotero.org/styles/synthesis" rel="template"/>
<link href="https://www.arkat-usa.org/arkivoc-journal/instructions-papers/#2.2.16" rel="documentation"/>
<author>
<name>Rodolpho C. Braga</name>
<email>rodolpho.braga@icloud.com</email>
</author>
<contributor>
<name>Kuldeep Singh</name>
<email>kuldeep@orgsyn.in</email>
</contributor>
<contributor>
<name>Patrick O'Brien</name>
</contributor>
<category citation-format="numeric"/>
<category field="chemistry"/>
<issn>1551-7012</issn>
<updated>2022-07-10T01:33:03+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<macro name="editor">
<names variable="editor">
<name sort-separator=", " initialize-with=". " name-as-sort-order="all" delimiter="; " delimiter-precedes-last="always"/>
<label form="short" prefix=", " text-case="capitalize-first"/>
</names>
</macro>
<macro name="author">
<names variable="author">
<name delimiter="; " delimiter-precedes-last="always" initialize-with=". " name-as-sort-order="all"/>
<label form="short" prefix=", " text-case="capitalize-first"/>
</names>
</macro>
<macro name="publisher">
<group delimiter=": ">
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</macro>
<macro name="volume">
<group delimiter=" ">
<text term="volume" form="short" text-case="capitalize-first"/>
<text variable="volume"/>
</group>
</macro>
<macro name="series">
<text variable="collection-title"/>
</macro>
<macro name="pages">
<text variable="page-first"/>
</macro>
<macro name="book-container">
<group delimiter=" ">
<text term="in" text-case="capitalize-first"/>
<text variable="container-title" font-style="italic"/>
</group>
</macro>
<macro name="issued">
<date variable="issued" delimiter=" ">
<date-part name="year"/>
</date>
</macro>
<macro name="full-issued">
<date variable="issued" delimiter=" ">
<date-part name="month" form="long" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
</date>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
</macro>
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout delimiter="," vertical-align="sup">
<text variable="citation-number"/>
</layout>
</citation>
<bibliography second-field-align="flush" entry-spacing="0">
<layout suffix=".">
<text variable="citation-number" suffix="."/>
<text macro="author" suffix=" "/>
<choose>
<if type="article-magazine">
<group delimiter=" ">
<text variable="container-title" font-style="italic" suffix="."/>
<text macro="edition"/>
<text macro="publisher"/>
<text macro="full-issued" suffix=","/>
<text macro="pages"/>
</group>
</if>
<else-if type="thesis">
<group delimiter=", ">
<group delimiter=". ">
<text variable="title"/>
<text variable="genre"/>
</group>
<text macro="publisher"/>
<text macro="issued"/>
<text macro="volume"/>
<text macro="pages"/>
</group>
</else-if>
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter="; ">
<text variable="title" font-style="italic"/>
<text macro="editor" prefix=" "/>
<text macro="series"/>
<text macro="edition"/>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="issued" font-weight="bold"/>
</group>
<group delimiter=", ">
<text macro="volume"/>
<text macro="pages"/>
</group>
</group>
</else-if>
<else-if type="chapter paper-conference" match="any">
<group delimiter="; ">
<text macro="book-container"/>
<text macro="editor"/>
<text macro="series"/>
<group delimiter=", ">
<text macro="publisher"/>
<text macro="issued" font-weight="bold"/>
</group>
<group delimiter=", ">
<text macro="volume"/>
<text macro="pages"/>
</group>
</group>
</else-if>
<else-if type="webpage post-weblog" match="any">
<group delimiter=" ">
<text variable="title"/>
<text variable="URL"/>
<group delimiter=" " prefix="(" suffix=")">
<text term="accessed"/>
<date variable="accessed">
<date-part name="month" form="short" strip-periods="true" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
</date>
</group>
</group>
</else-if>
<else-if type="patent">
<group delimiter=", ">
<group delimiter=" ">
<text variable="authority" form="short" font-style="italic"/>
<text variable="number"/>
</group>
<text macro="issued" font-weight="bold"/>
</group>
</else-if>
<else>
<group delimiter=" ">
<text variable="container-title" form="short"/>
<group delimiter=", ">
<text macro="issued" font-weight="bold"/>
<text variable="volume" font-style="italic"/>
<text macro="pages"/>
</group>
</group>
</else>
</choose>
<text variable="DOI" prefix=". DOI:"/>
</layout>
</bibliography>
</style>
10 changes: 1 addition & 9 deletions buildres/csl/csl-styles/bibliothek-forschung-und-praxis.csl
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Expand Up @@ -146,19 +146,11 @@
<text macro="archive"/>
</else-if>
</choose>
<choose>
<if variable="issued" match="none">
<group delimiter=" ">
<text term="accessed" text-case="capitalize-first"/>
<date variable="accessed" form="text"/>
</group>
</if>
</choose>
<choose>
<if type="legal_case" match="none">
<choose>
<if variable="DOI">
<text variable="DOI" prefix="DOI:"/>
<text variable="DOI" prefix="DOI: https://doi.org/"/>
</if>
<else-if match="all" variable="URL">
<text term="available at" text-case="sentence" suffix=" "/>
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4 changes: 2 additions & 2 deletions buildres/csl/csl-styles/bio-protocol.csl
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Expand Up @@ -1125,11 +1125,11 @@
<macro name="container-periodical">
<group delimiter=". ">
<group delimiter=", ">
<text variable="container-title" font-style="italic" text-case="title"/>
<text variable="container-title" font-style="italic" form="short"/>
<choose>
<if variable="volume">
<group>
<text variable="volume" font-style="italic"/>
<text variable="volume"/>
<text variable="issue" prefix="(" suffix=")"/>
</group>
</if>
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21 changes: 13 additions & 8 deletions buildres/csl/csl-styles/guide-des-citations-references-et-abreviations-juridiques.csl
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Expand Up @@ -14,7 +14,7 @@
</author>
<category citation-format="note"/>
<category field="law"/>
<updated>2022-04-05T19:59:30+00:00</updated>
<updated>2023-03-11T23:01:32+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<locale xml:lang="fr">
Expand Down Expand Up @@ -316,18 +316,16 @@
</else-if>
</choose>
</macro>
<citation>
<citation near-note-distance="1">
<layout delimiter="&#160;; ">
<choose>
<if position="ibid-with-locator subsequent">
<if position="ibid near-note" match="all">
<group delimiter=", ">
<text term="ibid" text-case="capitalize-first" font-style="italic" suffix="."/>
<text macro="author"/>
<text term="ibid" font-style="italic" suffix="."/>
<text variable="locator" prefix="p.&#160;"/>
</group>
</if>
<else-if position="ibid">
<text term="ibid" text-case="capitalize-first" font-style="italic"/>
</else-if>
<else-if position="subsequent">
<group delimiter=", ">
<text macro="author"/>
Expand All @@ -353,7 +351,14 @@
<else-if type="article-journal" match="any">
<text term="cited" font-style="italic" suffix="."/>
<text variable="container-title" form="short" font-style="italic"/>
<date date-parts="year-month" form="text" variable="issued"/>
<choose>
<if match="any" variable="volume">
<text variable="volume"/>
</if>
<else>
<date date-parts="year-month" form="text" variable="issued"/>
</else>
</choose>
</else-if>
<else-if type="entry-encyclopedia" match="any">
<text variable="title" quotes="true"/>
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