Store journal abbreviation lists in specified directory

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,27 +1,21 @@
-<!-- YOU HAVE TO MODIFY THE TEXT BELOW TO FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT. -->
+<!-- YOU HAVE TO MODIFY THIS TEXT TO FIT YOUR PR. OTHERWISE, YOUR PR WILL BE CLOSED WITHOUT FURTHER COMMENT. -->
 
-<!-- LINK THE ISSUE WITH THE "Closes" KEYWORD -->
-<!-- Example: Closes (link) OR Closes #12345 -->
+Describe the changes you have made here: what, why, ...
 
-Closes _____
-Describe the changes you have made here: what, where, why, ...
-If your work is not yet complete, please open a draft pull request. In that case, outline your intended next steps. Do you need feedback? Will you continue in parallel? ...
+<!-- LINK THE ISSUE WITH THE "Closes" KEYWORD -->
+<!-- Example: Closes (link) OR Closes #xyz -->
 
 ### Mandatory checks
 
 <!--
-Go throgh the checklist below. It is mandatory, even for a draft pull request.
-
-Keep ALL the items. Mark them as follows: 
-[x] done 
-[ ] not done 
-[/] not applicable
+- Go through the list below. Please don't remove any items.
+- [x] done; [ ] not done / not applicable
 -->
 
 - [x] I own the copyright of the code submitted and I license it under the [MIT license](https://github.com/JabRef/jabref/blob/main/LICENSE)
 - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if change is visible to the user)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
-- [ ] Screenshots added in PR description (if change is visible to the user)
+- [ ] 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.

.github/ghprcomment.yml

@@ -58,6 +58,15 @@
   message: |
     While the PR was in progress, a new version of JabRef has been released.
     You have to merge `upstream/main` and move your entry in `CHANGELOG.md` up to the section `## [Unreleased]`.
+- jobName: 'Unit tests'
+  message: >
+    JUnit tests are failing.
+    In the area "Some checks were not successful", locate "Tests / Unit tests (pull_request)" and click on "Details".
+    This brings you to the test output.
+
+
+    You can then run these tests in IntelliJ to reproduce the failing tests locally.
+    We offer a quick test running howto in the section [Final build system checks](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.html#final-build-system-checks) in our setup guide.
 - jobName: no-force-push
   message: >
     Do not force-push!
@@ -96,18 +105,11 @@
     - ✅ `Fixes https://github.com/JabRef/jabref/issues/xyz` links pull-request to issue. Merging the PR will close the issue.
     - ✅ `Fixes https://github.com/Koppor/jabref/issues/xyz` links pull-request to issue. Merging the PR will close the issue.
     - ❌ `Fixes [#xyz](https://github.com/JabRef/jabref/issues/xyz)` links pull-request to issue. Merging the PR will **NOT** close the issue.
-- jobName: 'Submodules not modified'
-  message: >
-    Your pull request modified git submodules.
-
-
-    Please follow our [FAQ on submodules](https://devdocs.jabref.org/code-howtos/faq.html#submodules) to fix.
-- jobName: 'Unit tests'
+- jobName: 'Conflicts with target branch'
   message: >
-    JUnit tests are failing.
-    In the area "Some checks were not successful", locate "Tests / Unit tests (pull_request)" and click on "Details".
-    This brings you to the test output.
+    Your pull request conflicts with the target branch.
 
 
-    You can then run these tests in IntelliJ to reproduce the failing tests locally.
-    We offer a quick test running howto in the section [Final build system checks](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.html#final-build-system-checks) in our setup guide.
+    Please merge `upstream/main` with your code.
+    Preferrably, do this using `git` in your machine:
+    Conflicts in `CHANGELOG.md` will be handled by a union of changes.

.github/workflows/on-issue-comment.yml

@@ -16,7 +16,7 @@ jobs:
         uses: takanome-dev/assign-issue-action@edge
         with:
           github_token: '${{ secrets.GITHUB_TOKEN }}'
-          days_until_unassign: 14
+          days_until_unassign: 45
           maintainers: 'koppor,Siedlerchr,ThiloteE,calixtus,HoussemNasri,subhramit,LinusDietz'
           assigned_comment: |
             👋 Hey @{{ handle }}, thank you for your interest in this issue! 🎉
@@ -29,7 +29,7 @@ jobs:
 
             Happy coding! 🚀
 
-            ⏳ Please note, you will be automatically unassigned if there is not a (draft) pull request within **{{ total_days }} days** (by **{{ unassigned_date }}**).
+            ⏳ Please note, you will be automatically unassigned if the issue isn't closed within **{{ total_days }} days** (by **{{ unassigned_date }}**). A maintainer can also add the "**{{ pin_label }}**" label to prevent automatic unassignment.
           assignment_suggestion_comment: >
             👋 Hey @{{ handle }}, looks like you’re eager to work on this issue—great! 🎉
             It also looks like you skipped reading our [CONTRIBUTING.md](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md), which explains exactly how to participate. No worries, it happens to the best of us.

.github/workflows/on-pr-closed.yml

@@ -56,10 +56,6 @@ jobs:
         run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📍 Assigned"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Remove pinned label
-        run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "📌 Pinned"
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Remove FirstTimeCodeContribution label
         run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --remove-label "FirstTimeCodeContribution"
         env:

.github/workflows/on-pr-opened.yml

@@ -92,7 +92,6 @@ jobs:
         run: gh issue edit ${{ steps.get_issue_number.outputs.ticketNumber }} --add-label "📌 Pinned"
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
   conflicts_with_target:
     name: Conflicts with target branch
     runs-on: ubuntu-latest

.github/workflows/tests.yml

@@ -390,32 +390,6 @@ jobs:
             exit 1
           fi
 
-  unmodified_submodules:
-    name: Submodules not modified
-    if: github.actor != 'dependabot[bot]' && github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: true
-          show-progress: 'false'
-      - name: Check for submodule modifications
-        id: check_submodule
-        run: |
-          git fetch origin ${{ github.base_ref }}
-
-          # enable diffing of submodules
-          sed -i "s/ all/ untracked/" .gitmodules
-
-          if ! git diff --submodule=log origin/${{ github.base_ref }} HEAD | grep -vzq "Submodule src"; then
-            echo "Debug:"
-            echo git diff --submodule=log origin/${{ github.base_ref }} HEAD
-            git diff --submodule=log origin/${{ github.base_ref }} HEAD
-            echo "❌ Submodule modifications detected"
-            exit 1
-          fi
-          echo "✅ No submodule modifications"
-
   other_than_main:
     if: github.event_name == 'pull_request'
     name: Source branch is other than "main"

CHANGELOG.md

@@ -22,7 +22,6 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added an integrity check if a URL appears in a title. [#12354](https://github.com/JabRef/jabref/issues/12354)
 - We added a feature for enabling drag-and-drop of files into groups  [#12540](https://github.com/JabRef/jabref/issues/12540)
 - We added support for reordering keywords via drag and drop, automatic alphabetical ordering, and improved pasting and editing functionalities in the keyword editor. [#10984](https://github.com/JabRef/jabref/issues/10984)
-- We added a new functionality where author names having multiple spaces in-between will be considered as separate user block as it does for " and ". [#12701](https://github.com/JabRef/jabref/issues/12701)
 
 ### Changed
 

README.md

@@ -74,20 +74,20 @@ An explanation of donation possibilities and usage of donations is available at
 [![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=main)
 
-Want to be part of a free and open-source project that tens of thousands of researchers use every day?
+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:
 
-- Please have a look at our [guidelines for contributing](CONTRIBUTING.md).
-- Make sure to follow our [step-by-step guide on how to set-up your workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
-- For a quick overview of the architecture, check out our [high-level documentation](https://devdocs.jabref.org/getting-into-the-code/high-level-documentation).
-- You are welcome to fix bugs, contribute new features or add documentation. To get your contribution included into JabRef, just [fork](https://help.github.com/en/articles/fork-a-repo) the JabRef repository, make your changes, and submit a [pull request](https://help.github.com/en/articles/about-pull-requests).
+- 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.
-- Not a programmer? Help translating JabRef at [Crowdin](https://crowdin.com/project/jabref) or improve the user documentation. Learn how to help at [contribute.jabref.org](https://contribute.jabref.org).
-- To report an issue, request a feature or suggest enhancements, please open an issue at our [issues page](https://github.com/JabRef/jabref/issues).
+
+Please follow our [step-by-step guide on how to set-up your workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).
 
 We use [GitHub Actions](https://github.com/JabRef/jabref/actions) for executing the tests after each commit.
-For developing, it is sufficient to only run the associated test locally (see example [here](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.html)) for the classes you changed.
-GitHub will report any other failure. To find solutions to the most common errors that lead to such failures, check our [FAQ page](https://devdocs.jabref.org/code-howtos/faq).
+For developing, it is sufficient to locally only run the associated test for the classes you changed.
+GitHub will report any other failure.
 
 We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.

build.gradle

@@ -8,7 +8,7 @@ plugins {
 
     id 'com.github.andygoossens.modernizer' version '1.10.0'
 
-    id 'me.champeau.jmh' version '0.7.3'
+    id 'me.champeau.jmh' version '0.7.2'
 
     // This is https://github.com/java9-modularity/gradle-modules-plugin/pull/282
     id 'com.github.koppor.gradle-modules-plugin' version 'v1.8.15-cmd-1'
@@ -29,7 +29,7 @@ plugins {
 
     id 'idea'
 
-    id 'org.openrewrite.rewrite' version '7.2.0'
+    id 'org.openrewrite.rewrite' version '7.1.4'
 
     id "org.itsallcode.openfasttrace" version "3.0.1"
 }
@@ -277,7 +277,7 @@ dependencies {
     implementation 'org.tinylog:tinylog-impl:2.7.0'
 
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
-    implementation 'org.slf4j:jul-to-slf4j:2.0.17'
+    implementation 'org.slf4j:jul-to-slf4j:2.0.16'
     // route all requests to log4j to SLF4J
     implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.24.3'
 
@@ -382,7 +382,7 @@ dependencies {
     implementation 'io.zonky.test.postgres:embedded-postgres-binaries-linux-arm64v8'
 
     testImplementation 'io.github.classgraph:classgraph:4.8.179'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.12.1'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.12.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.11.4'
 
     testImplementation 'org.mockito:mockito-core:5.16.0'

src/main/java/org/jabref/gui/preferences/journals/AbbreviationsFileViewModel.java

@@ -18,6 +18,7 @@
 import org.jabref.logic.journals.Abbreviation;
 import org.jabref.logic.journals.AbbreviationWriter;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
+import org.jabref.logic.journals.JournalAbbreviationMvGenerator;
 
 /**
  * This class provides a model for abbreviation files. It actually doesn't save the files as objects but rather saves
@@ -58,13 +59,27 @@ public void readAbbreviations() throws IOException {
         }
     }
 
+    public void readAbbreviationsFromMv() throws IOException {
+        if (path.isPresent()) {
+            // Load abbreviations from the MV file using MV processor.
+            Collection<Abbreviation> abbreviationList = JournalAbbreviationMvGenerator.loadAbbreviationsFromMv(path.get());
+
+            // Convert each Abbreviation into an AbbreviationViewModel and add it to the internal list.
+            for (Abbreviation abbreviation : abbreviationList) {
+                abbreviations.add(new AbbreviationViewModel(abbreviation));
+            }
+        } else {
+            throw new FileNotFoundException("MV file not specified");
+        }
+    }
+
     /**
      * This method will write all abbreviations of this abbreviation file to the file on the file system.
      * It essentially will check if the current file is a builtin list and if not it will call
      * {@link AbbreviationWriter#writeOrCreate}.
      */
     public void writeOrCreate() throws IOException {
-        if (!isBuiltInList.get()) {
+        if (!isBuiltInList.get() && !isMvFile()) {
             List<Abbreviation> actualAbbreviations =
                     abbreviations.stream().filter(abb -> !abb.isPseudoAbbreviation())
                                  .map(AbbreviationViewModel::getAbbreviationObject)
@@ -107,4 +122,8 @@ public boolean equals(Object obj) {
             return false;
         }
     }
+
+    public boolean isMvFile() {
+        return path.isPresent() && path.get().toString().endsWith(".mv");
+    }
 }

src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTab.fxml

@@ -49,6 +49,11 @@
         </Button>
     </HBox>
 
+    <HBox spacing="10.0" alignment="CENTER_LEFT">
+        <Button fx:id="changeDirectoryButton" onAction="#handleChangeDirectory" text="Change Directory"/>
+        <CustomTextField fx:id="directoryPathField" editable="false" minWidth="250"/>
+    </HBox>
+
     <VBox spacing="10.0" HBox.hgrow="ALWAYS">
         <CustomTextField fx:id="searchBox" promptText="%Filter" VBox.vgrow="NEVER">
             <VBox.margin>

src/main/java/org/jabref/gui/preferences/journals/JournalAbbreviationsTab.java

@@ -60,6 +60,9 @@ public class JournalAbbreviationsTab extends AbstractPreferenceTabView<JournalAb
     @FXML private CustomTextField searchBox;
     @FXML private CheckBox useFJournal;
 
+    @FXML private Button changeDirectoryButton;
+    @FXML private CustomTextField directoryPathField;
+
     @Inject private TaskExecutor taskExecutor;
     @Inject private JournalAbbreviationRepository abbreviationRepository;
 
@@ -87,6 +90,7 @@ private void initialize() {
 
         searchBox.setPromptText(Localization.lang("Search..."));
         searchBox.setLeft(IconTheme.JabRefIcons.SEARCH.getGraphicNode());
+        directoryPathField.textProperty().bind(viewModel.directoryPathProperty());
     }
 
     private void setUpTable() {
@@ -190,6 +194,11 @@ private void editAbbreviation() {
                 journalTableNameColumn);
     }
 
+    @FXML
+    private void handleChangeDirectory() {
+        viewModel.handleChangeDirectory();
+    }
+
     private void selectNewAbbreviation() {
         int lastRow = viewModel.abbreviationsCountProperty().get() - 1;
         journalAbbreviationsTable.scrollTo(lastRow);