Merge remote-tracking branch 'upstream/master' into allowReordering

* upstream/master:
  Fix image path
  Check for secrets being present at GitHub workflows (#5973)
  Add "JabRef and Software Engineering"
  Make Java code acceptable for GitBook - and fix link to JUnit antipatterns
  Let "Contributing" be displayed
  Merge the reviewing steops of "Code Quality" to "Development Strategy"
  Try to include CONTRIBUTING.md in devdocs.jabref.org
  Minor improvments in CONTRIBUTING.md
  Update Codecov yaml with proper indentation (#6156)
  Complete refactor of LibraryProperties to mvvm (#6107)
  Try comment:false
  Remove duplicated line
  Fix: Only if `.sav` file has changes a recovery dialog is shown (#6116)
  Fix formatting for GitBook
  Add hint to scroll down

Author: Siedlerchr

.github/workflows/check-outdated-dependencies.yml

@@ -1,6 +1,6 @@
 name: Check dependencies
 
-on: 
+on:
   schedule:
     - cron:  '0 0 * * TUE' # Run every Tuesday (after dependabot, which runs Monday)
 
@@ -9,21 +9,18 @@ jobs:
     name: Check dependencies
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout source
-      uses: actions/checkout@v1
-      with:
-        depth: 1
-        submodules: false
-    - name: Set up JDK
-      uses: actions/setup-java@v1
-      with:
-        java-version: 14
-    - name: Look for outdated dependencies
-      run: ./gradlew -q checkOutdatedDependencies
-    - name: Report issues
-      if: failure()
-      uses: JasonEtco/create-an-issue@master
-      env: 
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-        filename: .github/outdatedDependencies.md
+      - name: Checkout source
+        uses: actions/checkout@v2
+      - name: Set up JDK
+        uses: actions/setup-java@v1
+        with:
+          java-version: 14
+      - name: Look for outdated dependencies
+        run: ./gradlew -q checkOutdatedDependencies
+      - name: Report issues
+        if: failure()
+        uses: JasonEtco/create-an-issue@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: .github/outdatedDependencies.md

.github/workflows/cleanup_pr.yml

@@ -9,15 +9,28 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Extract branch name
-      id: extract_branch
-      run: |
-        echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
-    - name: Delete folder on builds.jabref.org
-      uses: appleboy/ssh-action@v0.0.6
-      with:
-        script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }}
-        host: build-upload.jabref.org
-        port: 9922
-        username: jrrsync
-        key: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Extract branch name
+        id: extract_branch
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        run: |
+          echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
+      - name: Delete folder on builds.jabref.org
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        uses: appleboy/ssh-action@v0.0.6
+        with:
+          script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }}
+          host: build-upload.jabref.org
+          port: 9922
+          username: jrrsync
+          key: ${{ secrets.buildJabRefPrivateKey }}

.github/workflows/deployment.yml

@@ -93,6 +93,17 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build]
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Fetch all history for all tags and branches
@@ -121,6 +132,7 @@ jobs:
           path: build/distribution/
       - name: Deploy to builds.jabref.org
         id: deploy
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: Pendect/action-rsyncer@v1.1.0
         env:
           DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}

.github/workflows/snap.yml

@@ -11,6 +11,17 @@ jobs:
     name: Create snapcraft image
 
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "SNAPCRAFT_LOGIN_FILE" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
       - name: Checkout source
         uses: actions/checkout@v2
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
@@ -19,6 +30,7 @@ jobs:
         uses: jhenstridge/snapcraft-build-action@v1
         id: snapcraft
       - name: Build snap (2) Upload snap
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: jhenstridge/snapcraft-publish-action@v1
         with:
           store_login: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}

.github/workflows/tests-fetchers.yml

@@ -30,10 +30,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v1
-        with:
-          depth: 1
-          submodules: false
+        uses: actions/checkout@v2
       - name: Set up JDK
         uses: actions/setup-java@v1
         with:

.github/workflows/tests-oracle.yml

@@ -26,30 +26,42 @@ jobs:
     name: Oracle tests
     runs-on: ubuntu-latest
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "CCRYPT" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          SNAPCRAFT_LOGIN_FILE: ${{ secrets.CCRYPT }}
       - name: Checkout source
-        uses: actions/checkout@v1
-        with:
-          depth: 1
-          submodules: false
+        uses: actions/checkout@v2
       - name: Set up JDK
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: actions/setup-java@v1
         with:
           java-version: 14
-      - uses: actions/cache@v1
-        name: Restore gradle chache
+      - name: Restore gradle chache
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        uses: actions/cache@v1
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
           restore-keys: |
             ${{ runner.OS }}-gradle-${{ env.cache-name }}-
             ${{ runner.OS }}-gradle-
             ${{ runner.OS }}-
-      - uses: actions/cache@v1
-        name: Restore gradle wrapper
+      - name: Restore gradle wrapper
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
+        uses: actions/cache@v1
         with:
           path: ~/.gradle/wrapper
           key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
       - name: Start Oracle XE
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: |
           mkdir ~/oracle-xe || true
           cd ~/oracle-xe
@@ -71,6 +83,7 @@ jobs:
         env:
           CCRYPT: ${{ secrets.CCRYPT }}
       - name: Run database test
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: ./gradlew databaseTest --rerun-tasks
         env:
           DBMS: "oracle"

.github/workflows/tests.yml

@@ -170,6 +170,17 @@ jobs:
         # needed because the postgres container does not provide a healthcheck
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "CODECOV_TOKEN" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
       - name: Checkout source
         uses: actions/checkout@v2
       - name: Set up JDK
@@ -191,6 +202,7 @@ jobs:
           path: ~/.gradle/wrapper
           key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
       - name: Update test coverage metrics
+        if: ${{ steps.checksecrets.outputs.secretspresent }}
         run: xvfb-run --auto-servernum ./gradlew jacocoTestReport && bash <(curl -s https://codecov.io/bash);
         env:
           CI: "false" # we pretend to run locally - even if tests fail on the CI, they count towards test coverage

.gitignore

@@ -5,6 +5,10 @@ src/main/generated/
 # private data
 /buildres/jabref-cert-2016.p12
 
+# GitBook assets
+docs/book.pdf
+docs/_book/
+
 # ignore the generated markdown file if the user forgets to delete it
 status.md
 

CHANGELOG.md

@@ -16,6 +16,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We improved the arXiv fetcher. Now it should find entries even more reliably and does no longer include the version (e.g `v1`) in the `eprint` field. [forum#1941](https://discourse.jabref.org/t/remove-version-in-arxiv-import/1941)
 - We moved the group search bar and the button "New group" from bottom to top position to make it more prominent. [#6112](https://github.com/JabRef/jabref/pull/6112)
+- When JabRef finds a `.sav` file without changes, there is no dialog asking for acceptance of changes anymore.
 - We changed the buttons for import/export/show all/reset of preferences to smaller icon buttons in the preferences dialog. [#6130](https://github.com/JabRef/jabref/pull/6130)
 - We moved the functionality "Manage field names & content" from the "Library" menu to the "Edit" menu, because it affects the selected entries and not the whole library
 
@@ -41,7 +42,6 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - Filenames of external files can no longer contain curly braces. [#5926](https://github.com/JabRef/jabref/pull/5926)
 - We made the filters more easily accessible in the integrity check dialog. [#5955](https://github.com/JabRef/jabref/pull/5955)
 - We reimplemented and improved the dialog "Customize entry types". [#4719](https://github.com/JabRef/jabref/issues/4719)
-- We reimplemented and improved the dialog "Customize entry types" [#4719](https://github.com/JabRef/jabref/issues/4719)
 - We added an [American Physical Society](https://journals.aps.org/) fetcher. [#818](https://github.com/JabRef/jabref/issues/818)
 
 ### Fixed

CONTRIBUTING.md

@@ -21,14 +21,14 @@ We should also be online at [gitter](https://gitter.im/JabRef/jabref).
 
 The main goal of the formal requirements is to provide credit to you and to be able to understand the patch.
 
-### Add your change to CHANGELOG.md
+### Add your change to `CHANGELOG.md`
 
 You should edit the [CHANGELOG.md](CHANGELOG.md) located in the root directory of the JabRef source.
 Add a line with your changes in the appropriate section.
 
 If you did internal refactorings or improvements not visible to the user (e.g., UI, .bib file), then you don't need to put an entry there.
 
-#### Key format
+#### Format of keyboard shortcuts
 
 Example: `<kbd>Ctrl</kbd> + <kbd>Enter</kbd>`
 
@@ -95,7 +95,7 @@ accepting <downside / undesired consequences>,
 because <additional rationale>.
 ```
 
-### When adding a new Localization.lang entry
+### When adding a new `Localization.lang` entry
 
 Add new `Localization.lang("KEY")` to a Java file.
 The tests will fail. In the test output a snippet is generated, which must be added to the English translation file.
@@ -119,9 +119,9 @@ You can also directly run the specific test in your IDE.
 The test "LocalizationConsistencyTest" is placed under `src/test/java/net.sf.jabref.logic.l10n/LocalizationConsistencyTest.java`
 Find more information in the [JabRef Wiki](https://github.com/JabRef/jabref/wiki/Code-Howtos#using-localization-correctly).
 
-### Create a pull request
+## Create a pull request
 
-Create a pull request on GitHub.
+Create a pull request on GitHub following GitHub's guide "[Creating a pull request from a fork](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request-from-a-fork)".
 For text inspirations, consider [How to write the perfect pull request](https://github.com/blog/1943-how-to-write-the-perfect-pull-request).
 
 If you want to indicate that a pull request is not yet complete **before** creating the pull request, you may consider creating a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).

codecov.yml

@@ -3,9 +3,7 @@ coverage:
   - src/gen/.*
   status:
     patch: false
-  project:
-    default:
-      threshold: 0.005
-comment:
-  branches:
-    - "do-not-add-comment-to-any-branch-please"
+    project:
+      default:
+        threshold: 0.01
+comment: false

docs/README.md

@@ -2,9 +2,10 @@
 
 This page presents all development informatation around JabRef. For users documentation see [https://docs.jabref.org](https://docs.jabref.org).
 
-## Excersises
+## Teaching Excersises
 
-Uni Basel offers a German \(🇩🇪\) Software Engineering course which uses JabRef as one example. Look at [Exercise 5](https://github.com/unibas-marcelluethi/software-engineering/blob/master/docs/week5/exercises/practical-exercises.md) for an exercise where some important points of JabRef are touched.
+We are very happy that JabRef is part of [Software Engineering](https://en.wikipedia.org/wiki/Software_engineering) trainings.
+Please head to [Teaching](teaching.md) for more information on using JabRef as teaching object and on previous courses where JabRef was used.
 
 ## How tos
 
@@ -17,7 +18,7 @@ The package `org.jabref.cli` is responsible for handling the command line option
 
 During development, one can configure IntelliJ to pass command line paramters:
 
-![IntelliJ-run-configuration](.gitbook/assets/intellij-run-configuration-command-line%20%282%29.png)
+![IntelliJ-run-configuration](images/intellij-run-configuration-command-line.png)
 
 Passing command line arguments using gradle is currently not possible as all arguments \(such as `-Dfile.encoding=windows-1252`\) are passed to the application.
 

docs/SUMMARY.md

@@ -1,6 +1,7 @@
 # Table of contents
 
 * [Overview on Developing](README.md)
+  * [Contributing](contributing.md)
 * [Architectural Decisions](adr/README.md)
 * Getting into the code
   * [Set up a local workspace](guidelines-for-setting-up-a-local-workspace.md)
@@ -13,6 +14,7 @@
   * [Recommendations for UI design](ui-recommendations.md)
   * [Custom SVG icons](custom-svg-icons.md)
   * [Creating a binary and debug it](jpackage.md)
+* [JabRef and Software Engineering](teaching.md)
 * Readings on Coding
   * [Readings on JavaFX](javafx.md)
   * [Useful development tooling](tools.md)

docs/code-howtos.md

@@ -227,13 +227,11 @@ Imagine you want to test the method `format(String value)` in the class `BracesF
   testFormat() {
    assertEqual("test", format("test"));
    assertEqual("{test", format("{test"));
-   assertEqual("test", format("{{test"));
    assertEqual("test", format("test}}"));
-   assertEqual("test", format("{{test}}"));
   }
   ```
 
-  we would have five tests containing a single `assert` statement and named accordingly \(`formatDoesNotChangeStringWithoutBraces`, `formatDoesNotRemoveSingleBrace`, `formatRemovesDoubleBracesAtBeginning`, etc.\). See [JUnit AntiPattern](http://www.exubero.com/junit/antipatterns.html#Multiple_Assertions) for background.
+  we would have five tests containing a single `assert` statement and named accordingly \(`formatDoesNotChangeStringWithoutBraces`, `formatDoesNotRemoveSingleBrace`, , etc.\). See [JUnit AntiPattern](https://exubero.com/junit/anti-patterns/#Multiple_Assertions) for background.
 
 * Do _not just test happy paths_, but also wrong/weird input.
 * It is recommend to write tests _before_ you actually implement the functionality \(test driven development\).

docs/code-quality.md

@@ -11,10 +11,4 @@ We strongly recommend to read following two books on code quality:
 * [Java by Comparison](https://github.com/JabRef/jabref/tree/c81740b3818c7f9311a6d7ff063243e672c821b4/docs/java.by-comparison.com) is a book by three JabRef developers which focuses on code improvements close to single statements. It is fast to read and one gains much information from each recommendation discussed in the book.
 * [Effective Java](https://www.oreilly.com/library/view/effective-java-3rd/9780134686097/) is the standard book for advanced Java programming. Did you know that `enum` is the [recommended way to enforce a singleton instance of a class](https://learning.oreilly.com/library/view/effective-java-3rd/9780134686097/ch2.xhtml#lev3)? Did you know that one should [refer to objects by their interfaces](https://learning.oreilly.com/library/view/effective-java-3rd/9780134686097/ch9.xhtml#lev64)?
 
-This is how we ensure code quality in JabRef:
-
-* we review each external pull request by at least two [JabRef Core Developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS).
-* we document our design decisions using the lightweight architectural decision records [MADR](https://adr.github.io/madr/).
-* we follow the principles of [Java by Comparison](https://java.by-comparison.com/).
-* we follow the principles of [Effective Java](https://www.oreilly.com/library/view/effective-java-3rd/9780134686097/).
-* we use [Design Pattners](https://java-design-patterns.com/patterns/) when applicable.
+The principles we follow to ensure high code quality in JabRef is stated at our [Development Strategy](development-strategy.md).

docs/contributing.md

@@ -0,0 +1 @@
+{% include "git+https://github.com/JabRef/jabref.git/CONTRIBUTING.md#master" %}

docs/development-strategy.md

@@ -4,11 +4,11 @@ We aim to keep up to high-quality code standards and use code quality tools wher
 
 To ensure high code-quality,
 
-* we follow the principles of [Java by Comparison](https://java.by-comparison.com/).
-* 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/master/DEVELOPERS).
+* We follow the principles of [Java by Comparison](https://java.by-comparison.com/).
+* 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/master/DEVELOPERS).
 
 Read on about our automated quality checks at [Code Quality](code-quality.md).