Merge branch 'linkedFilesfixesRelative' of github.com:JabRef/jabref into linkedFilesfixesRelative

* 'linkedFilesfixesRelative' of github.com:JabRef/jabref: (52 commits)
  Enable files/files
  Don't show the info button when the authors field content is identical (#9128)
  "study.yml" is static now (#9125)
  fix l10n
  Compile fix
  Fix parsing of JabRef v5.7 study.yml files (#9124)
  Fix integrity check  for tilde accents in author names (#9097)
  Rework the Define study parameters dialog (#9123)
  Fix parsing of save actions (#9122)
  Fix exception that occurs when saving name formatters (#9121)
  Refine code for BibEntry#replaceDownloadedFile (#9118)
  Show a warning in the merge dialog when authors are the same but formatted differently (#9088)
  Fix subdatabase from aux on cli (#9117)
  Visual improvements to LinkedFilesEditor (#9114)
  SLR Remove "last-search-date" (#9116)
  Hide diffs when one of the field values is blank a.k.a no conflict (#9110)
  Squashed 'buildres/csl/csl-locales/' changes from e637746677..b2afeb4d87
  Squashed 'buildres/csl/csl-styles/' changes from c750b6e..8d69f16
  Fix title case capitalization after en-dash characters (#9102)
  Update journal abbrev list (#9109)
  ...

Author: Siedlerchr

.github/workflows/automerge.yml

@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v2.2.1
+        uses: hmarr/auto-approve-action@v2.4.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"

CHANGELOG.md

@@ -11,15 +11,39 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- In case a backup is found, the filename of the backup is shown.
+- On startup, JabRef notifies the user if there were parsing errors during opening.
+- We integrated a new three-way merge UI for merging entries in the Entries Merger Dialog, the Duplicate Resolver Dialog, the Entry Importer Dialog, and the External Changes Resolver Dialog. [#8945](https://github.com/JabRef/jabref/pull/8945)
+- We added the ability to merge groups, keywords, comments and files when merging entries. [#9022](https://github.com/JabRef/jabref/pull/9022)
+- We added a warning message next to the authors field in the merge dialog to warn users when the authors are the same but formatted differently. [#8745](https://github.com/JabRef/jabref/issues/8745)
+
 ### Changed
 
 - We improved the Citavi Importer to also import so called Knowledge-items into the field `comment` of the corresponding entry [#9025](https://github.com/JabRef/jabref/issues/9025)
 - We removed wrapping of string constants when writing to a `.bib` file.
+- We call backup files `.bak` and temporary writing files now `.sav`.
+- JabRef keeps 10 older versions of a `.bib` file in the [user data dir](https://github.com/harawata/appdirs#supported-directories) (instead of a single `.sav` (now: `.bak`) file in the directory of the `.bib` file)
 - We changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.
+- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs. [#9116](https://github.com/JabRef/jabref/pull/9116)
+- A user can now add arbitrary data into `study.yml`. JabRef just ignores this data. [#9124](https://github.com/JabRef/jabref/pull/9124)
+- We reworked the External Changes Resolver dialog. [#9021](https://github.com/JabRef/jabref/pull/9021)
+- We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 
 ### Fixed
 
+- We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
+- We fixed an issue where the possibility to generate a subdatabase from an aux file was writing empty files when called from the commandline [#9115](https://github.com/JabRef/jabref/issues/9115), [forum#3516](https://discourse.jabref.org/t/export-subdatabase-from-aux-file-on-macos-command-line/3516)
+- We fixed the display of issue, number, eid and pages fields in the entry preview. [#8607](https://github.com/JabRef/jabref/pull/8607), [#8372](https://github.com/JabRef/jabref/issues/8372), [Koppor#514](https://github.com/koppor/jabref/issues/514), [forum#2390](https://discourse.jabref.org/t/unable-to-edit-my-bibtex-file-that-i-used-before-vers-5-1/2390), [forum#3462](https://discourse.jabref.org/t/jabref-5-6-need-help-with-export-from-jabref-to-microsoft-word-entry-preview-of-apa-7-not-rendering-correctly/3462)
+- We fixed the page ranges checker to detect article numbers in the pages field (used at [Check Integrity](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity)). [#8607](https://github.com/JabRef/jabref/pull/8607)
+- The [HtmlToLaTeXFormatter](https://docs.jabref.org/finding-sorting-and-cleaning-entries/saveactions#html-to-latex) keeps single `<` characters.
 - We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
+- We fixed a bug where spaces are trimmed when highlighting differences in the Entries merge dialog. [koppor#371](https://github.com/koppor/jabref/issues/371)
+- We fixed some visual glitches with the linked files editor field in the entry editor and increased its height. [#8823](https://github.com/JabRef/jabref/issues/8823)
+- We fixed several bugs regarding the manual and the autosave of library files that sometimes lead to exceptions or data loss. [#9067](https://github.com/JabRef/jabref/pull/9067), [#8448](https://github.com/JabRef/jabref/issues/8484), [#8746](https://github.com/JabRef/jabref/issues/8746), [#6684](https://github.com/JabRef/jabref/issues/6684), [#6644](https://github.com/JabRef/jabref/issues/6644), [#6102](https://github.com/JabRef/jabref/issues/6102), [#6002](https://github.com/JabRef/jabref/issues/6000)
+- We fixed an issue where applied save actions on saving the library file would lead to the dialog "The libary has been modified by another program" popping up [#4877](https://github.com/JabRef/jabref/issues/4877)
+- We fixed issues with save actions not correctly loaded when opening the library. [#9122](https://github.com/JabRef/jabref/pull/9122)
+- We fixed an issue where title case didn't capitalize words after en-dash characters. [#9068](https://github.com/JabRef/jabref/pull/9068)
+- We fixed an issue where JabRef would not exit when a connection to a LibreOffice document was established previously and the document is still open. [#9075](https://github.com/JabRef/jabref/issues/9075)
 
 ### Removed
 
@@ -29,7 +53,6 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 
 
-
 ## [5.7] - 2022-08-05
 
 ### Added
@@ -88,6 +111,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
+- We fixed an issue where name formatter could not be saved. [#9120](https://github.com/JabRef/jabref/issues/9120)
 
 ### Removed
 

build.gradle

@@ -128,12 +128,12 @@ dependencies {
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.4.1'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.71'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.71.1'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.3.5'
-    implementation 'org.libreoffice:unoloader:7.3.5'
+    implementation 'org.libreoffice:libreoffice:7.4.0'
+    implementation 'org.libreoffice:unoloader:7.4.0'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
     implementation 'info.debatty:java-string-similarity:2.0.0'
@@ -148,7 +148,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
-    implementation 'org.postgresql:postgresql:42.4.1'
+    implementation 'org.postgresql:postgresql:42.5.0'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -174,13 +174,13 @@ dependencies {
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.1.1'
 
-    implementation 'org.jsoup:jsoup:1.15.1'
-    implementation 'com.konghq:unirest-java:3.13.10'
+    implementation 'org.jsoup:jsoup:1.15.3'
+    implementation 'com.konghq:unirest-java:3.13.11'
 
-    implementation 'org.slf4j:slf4j-api:2.0.0-beta1'
-    implementation "org.tinylog:tinylog-api:2.4.1"
-    implementation "org.tinylog:slf4j-tinylog:2.4.1"
-    implementation "org.tinylog:tinylog-impl:2.4.1"
+    implementation 'org.slf4j:slf4j-api:2.0.0'
+    implementation "org.tinylog:tinylog-api:2.5.0"
+    implementation "org.tinylog:slf4j-tinylog:2.5.0"
+    implementation "org.tinylog:tinylog-impl:2.5.0"
 
     implementation 'de.undercouch:citeproc-java:3.0.0-alpha.6'
 
@@ -207,7 +207,7 @@ dependencies {
     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.mockito:mockito-core:4.7.0'
     testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
@@ -216,7 +216,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.2'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.3'
     // 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'

buildSrc/build.gradle

@@ -8,7 +8,7 @@ repositories {
 dependencies {
     implementation 'com.h2database:h2-mvstore:2.1.214'
     implementation 'org.apache.commons:commons-csv:1.9.0'
-    implementation 'org.slf4j:slf4j-api:2.0.0-beta1'
+    implementation 'org.slf4j:slf4j-api:2.0.0'
 }
 
 sourceSets{

buildres/csl/csl-locales/.github/workflows/merge.yaml

@@ -136,14 +136,14 @@ jobs:
 
     - name: Bump version and push tag
       id: tag_version
-      uses: mathieudutour/github-tag-action@v5.6
+      uses: mathieudutour/github-tag-action@v6.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         default_bump: patch
       if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
 
     - name: Create a GitHub release
-      uses: softprops/action-gh-release@v0.1.14
+      uses: softprops/action-gh-release@v1
       env:
         github_token: ${{ secrets.GITHUB_TOKEN }}
       with:

buildres/csl/csl-styles/.github/workflows/merge.yaml

@@ -136,14 +136,14 @@ jobs:
 
     - name: Bump version and push tag
       id: tag_version
-      uses: mathieudutour/github-tag-action@v5.6
+      uses: mathieudutour/github-tag-action@v6.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         default_bump: patch
       if: github.event_name == 'push' && hashFiles('composer.json') != '' && (steps.update.outputs.updated == 'true' || steps.update.outputs.deleted == 'true')
 
     - name: Create a GitHub release
-      uses: softprops/action-gh-release@v0.1.14
+      uses: softprops/action-gh-release@v1
       env:
         github_token: ${{ secrets.GITHUB_TOKEN }}
       with:

buildres/csl/csl-styles/acta-universitatis-agriculturae-sueciae.csl

@@ -15,12 +15,16 @@
     </contributor>
     <category citation-format="author-date"/>
     <summary>Style as per the May 2019 guidelines.</summary>
-    <updated>2021-11-10T10:39:01+00:00</updated>
+    <updated>2022-07-13T09:26:37+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="en">
     <terms>
       <term name="edition" form="short">ed</term>
+      <term name="editor" form="short">
+        <single>ed.</single>
+        <multiple>eds</multiple>
+      </term>
     </terms>
   </locale>
   <locale xml:lang="sv">
@@ -34,15 +38,10 @@
     </terms>
   </locale>
   <macro name="container-contributors">
-    <choose>
-      <if type="chapter paper-conference" match="any">
-        <text term="in" text-case="capitalize-first" suffix=":"/>
-        <names variable="editor translator" delimiter=", " prefix=" ">
-          <name and="symbol" initialize-with="." name-as-sort-order="all"/>
-          <label form="short" prefix=" (" suffix=")"/>
-        </names>
-      </if>
-    </choose>
+    <names variable="editor translator" delimiter=", ">
+      <name and="symbol" initialize-with="." name-as-sort-order="all"/>
+      <label form="short" prefix=" (" suffix=")"/>
+    </names>
   </macro>
   <macro name="secondary-contributors">
     <choose>
@@ -93,8 +92,14 @@
   </macro>
   <macro name="title">
     <choose>
-      <if type="bill book graphic legal_case legislation motion_picture patent report song thesis webpage" match="any">
+      <if type="bill book graphic legal_case legislation motion_picture patent report song thesis webpage software" match="any">
         <text variable="title" font-style="italic"/>
+        <choose>
+          <if type="software" variable="version" match="any">
+            <text variable="version" prefix=" (" suffix=")"/>
+            <text variable="medium" prefix=" [" suffix="]"/>
+          </if>
+        </choose>
       </if>
       <else>
         <text variable="title"/>
@@ -244,20 +249,26 @@
           <text macro="publisher" prefix=". "/>
         </if>
         <else-if type="chapter entry-encyclopedia" match="any">
-          <text macro="issued" suffix=" "/>
-          <group suffix=".">
+          <group delimiter=". " suffix=".">
+            <text macro="issued"/>
             <text macro="title"/>
-            <text macro="type"/>
-          </group>
-          <text macro="container-contributors" prefix=" "/>
-          <text macro="secondary-contributors"/>
-          <text variable="container-title" font-style="italic" prefix=" " suffix="."/>
-          <group prefix=" (" suffix=")." delimiter="; ">
-            <text macro="collection-title"/>
-            <text variable="collection-number"/>
-          </group>
-          <text macro="edition" prefix=" "/>
-          <group delimiter=", " prefix=" ">
+            <group delimiter=": ">
+              <choose>
+                <if type="chapter paper-conference" match="any">
+                  <text term="in" text-case="capitalize-first"/>
+                </if>
+              </choose>
+              <group delimiter=" " suffix=".">
+                <text macro="container-contributors"/>
+                <text macro="secondary-contributors"/>
+                <text variable="container-title" font-style="italic" prefix=" " suffix="."/>
+              </group>
+            </group>
+            <group prefix=" (" suffix=")." delimiter="; ">
+              <text macro="collection-title"/>
+              <text variable="collection-number"/>
+            </group>
+            <text macro="edition" prefix=" "/>
             <text macro="publisher"/>
             <text variable="page"/>
           </group>
@@ -313,7 +324,7 @@
           <text macro="edition" prefix=" "/>
           <text macro="publisher" prefix=" " suffix="."/>
         </else-if>
-        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <else-if type="bill book graphic legal_case legislation motion_picture report song software" match="any">
           <choose>
             <if variable="URL">
               <text macro="issued" suffix=" "/>
@@ -325,7 +336,6 @@
               <text macro="secondary-contributors"/>
               <text variable="container-title" font-style="italic" prefix=" "/>
               <text macro="locators"/>
-              <text variable="version" prefix=" Version: " suffix="."/>
               <text macro="publisher" prefix=" " suffix="."/>
             </if>
             <else>
@@ -338,7 +348,6 @@
               <text macro="secondary-contributors"/>
               <text variable="container-title" font-style="italic" prefix=" "/>
               <text macro="locators"/>
-              <text variable="version" prefix=" Version: " suffix="."/>
               <text macro="publisher" prefix=". " suffix="."/>
               <group prefix=" (" suffix=")" delimiter="; ">
                 <text macro="collection-title"/>