Merge branch 'master' into customizeEntrydlg

* master: (297 commits)
  Replace link to Workspace set-up with new one (#5896)
  Fixes making paths of linked files relative (web urls will not be touched anymore) (#5879)
  Switch to our IntelliJ config (#5881)
  Bump unirest-java from 3.4.00 to 3.4.01 (#5874)
  Bump junit-vintage-engine from 5.5.2 to 5.6.0 (#5875)
  Bump checkstyle from 8.28 to 8.29 (#5876)
  Bump junit-jupiter from 5.5.2 to 5.6.0 (#5877)
  Bump junit-platform-launcher from 1.5.2 to 1.6.0 (#5878)
  Change \ to /
  Bump byte-buddy-parent from 1.10.6 to 1.10.7 (#5873)
  Fix opening pdf with okular in linux (#5253) (#5855)
  Fixed Test
  Refactored constructors, PreferencesService and some minor improvements.
  Remove ampersand escape when writing to bib file (#5869)
  Fix #5862. It was indeed the throttler (at least it is working now for me) (#5868)
  duplicate query parameter removed (#5865)
  New Crowdin translations (#5864)
  Minor refactoring, and changed comment
  Bump antlr4 from 4.7.2 to 4.8-1 (#5852)
  Reintroducing master table index column (#5844)
  ...

Author: Siedlerchr

.gitbook.yaml

@@ -0,0 +1 @@
+root: ./docs/

.github/workflows/cleanup_pr.yml

@@ -5,20 +5,19 @@ on:
     types: [closed]
 
 jobs:
-  build:
-
+  cleanup:
     runs-on: ubuntu-latest
-    
+
     steps:
     - name: Extract branch name
       id: extract_branch
       run: |
-        echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        echo "##[set-output name=branch;]$(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: builds.jabref.org
+        host: build-upload.jabref.org
         port: 9922
         username: jrrsync
         key: ${{ secrets.buildJabRefPrivateKey }}

.github/workflows/deployment.yml

@@ -1,6 +1,18 @@
 name: Deployment
 
-on: [push]
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+      - 'src/test/**'
+      - 'README.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - 'src/test/**'
+      - 'README.md'
 
 jobs:
   build:
@@ -11,17 +23,17 @@ jobs:
         include:
          - os: ubuntu-latest
            displayName: linux
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_linux-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/30/GPL/openjdk-14-ea+30_linux-x64_bin.tar.gz
            jdk14Path: /jdk-14
            archivePortable: tar -c -C build/distribution JabRef | pigz --rsyncable > build/distribution/JabRef-portable_linux.tar.gz && rm -R build/distribution/JabRef
          - os: windows-latest
            displayName: windows
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_windows-x64_bin.zip
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/30/GPL/openjdk-14-ea+30_windows-x64_bin.zip
            jdk14Path: /jdk-14
            archivePortable: 7z a -r build/distribution/JabRef-portable_windows.zip ./build/distribution/JabRef && rm -R build/distribution/JabRef
          - os: macOS-latest
            displayName: macOS
-           jpackageDownload: https://download.java.net/java/early_access/jdk14/27/GPL/openjdk-14-ea+27_osx-x64_bin.tar.gz
+           jpackageDownload: https://download.java.net/java/early_access/jdk14/30/GPL/openjdk-14-ea+30_osx-x64_bin.tar.gz
            jdk14Path: /jdk-14.jdk/Contents/Home
            archivePortable: brew install pigz && tar -c -C build/distribution JabRef.app | pigz --rsyncable > build/distribution/JabRef-portable_macos.tar.gz && rm -R build/distribution/JabRef.app
 
@@ -101,13 +113,21 @@ jobs:
       - name: Package application image
         run: ${{ matrix.archivePortable }}
         shell: bash
-      - name: Build and publish snap
+      - name: Build snap (1) Setup snapcraft
+        uses: jhenstridge/snapcraft-build-action@v1
+        id: snapcraft
+        if: matrix.displayName == 'linux'
+      - name: Build snap (2) Run build
+        run: |
+          mv ${{ steps.snapcraft.outputs.snap }} build/distribution/
+        if: matrix.displayName == 'linux'
+      - name: Build snap (3) Upload snap
         if: matrix.displayName == 'linux' && github.ref == 'refs/heads/master'
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
         run: |
             mkdir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg
-            docker run -v $(pwd):$(pwd) -t lyzardking/snapcraft-bionic sh -c "apt update -qq && cd $(pwd) && snapcraft && mv jabref*.snap build/distribution/ && snapcraft push build/distribution/jabref*.snap --release edge || true"
+            snapcraft push build/distribution/jabref*.snap --release edge || true
         shell: bash
       - name: Rename files
         run: |
@@ -169,4 +189,4 @@ jobs:
           options: ''
           ssh_options: '-p 9922'
           src: 'build/distribution/'
-          dest: jrrsync@builds.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
+          dest: jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/

.github/workflows/refresh-csl-subtrees.yml

@@ -1,6 +1,10 @@
 name: Refresh Citation Style Language Files
 
 on:
+  push:
+    paths:
+      - '.github/workflows/refresh-csl-subtrees.yml'
+      - 'src/main/resources/csl-locales/**'
   schedule:
     # run on 1st and 15th of each month
     - cron: '1 2 1,15 * *'
@@ -11,28 +15,32 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2-beta
+        uses: actions/checkout@v2
         with:
           ref: master
+          fetch-depth: 0
       - name: Add csl-styles remote
         run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
       - name: Update csl-styles
-        run: | 
+        run: |
           git checkout master
+          git config --local core.editor /usr/bin/cat
+          git config user.name "github actions"
+          git config user.email "jabrefmail+webfeedback@gmail.com"
           git subtree pull --prefix src/main/resources/csl-styles csl-styles master --squash
       - name: Add csl-locales remote
         run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
       - name: Update csl-locales
         run: |
-          git checkout master
           git subtree pull --prefix src/main/resources/csl-locales csl-locales master --squash
       - uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: master
       - name: Report issues
         if: failure()
         uses: JasonEtco/create-an-issue@master
-        env: 
+        env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           filename: .github/failure-csl-update.md

.github/workflows/tests-fetchers.yml

@@ -0,0 +1,55 @@
+name: Fetcher Tests
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'src/main/java/org/jabref/logic/importer/fetcher/**'
+      - 'src/test/java/org/jabref/logic/importer/fetcher/**'
+      - '.github/workflows/tests-fetchers.yml'
+      - 'build.gradle'
+  pull_request:
+    paths:
+      - 'src/main/java/org/jabref/logic/**'
+      - 'src/test/java/org/jabref/logic/**'
+      - 'src/main/java/org/jabref/model/**'
+      - 'src/test/java/org/jabref/model/**'
+      - '.github/workflows/tests-fetchers.yml'
+      - 'build.gradle'
+  schedule:
+    # run on each Wednesday
+    - cron: '2 3 * * 3'
+
+jobs:
+  fetchertests:
+    name: Fetcher tests
+    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: 13
+      - uses: actions/cache@v1
+        name: Restore gradle chache
+        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
+        with:
+          path: ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
+      - name: Run fetcher tests
+        run: ./gradlew fetcherTest
+        env:
+          CI: "true"

.github/workflows/tests-oracle.yml

@@ -2,6 +2,7 @@ name: Oracle Tests
 
 on:
   push:
+    # we need to trigger on all branches, because sometimes need copy of branches, because secrets are only available on "internal" pull requests
     paths:
       - 'src/test/java/org/jabref/model/database/**'
       - 'src/test/java/org/jabref/logic/shared/**'

.github/workflows/tests.yml

@@ -1,6 +1,11 @@
 name: Tests
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    # always run on pull requests
 
 jobs:
   checkstyle:
@@ -128,37 +133,6 @@ jobs:
         env:
           CI: "true"
           DBMS: "mysql"
-  fetchertests:
-    name: Fetcher tests
-    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: 13
-      - uses: actions/cache@v1
-        name: Restore gradle chache
-        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
-        with:
-          path: ~/.gradle/wrapper
-          key: ${{ runner.os }}-gradle-${{ hashFiles('gradle/wrapper/gradle-wrapper.properties') }}
-      - name: Run fetcher tests
-        run: ./gradlew fetcherTest
-        env:
-          CI: "true"
   guitests:
     name: GUI tests
     runs-on: ubuntu-latest

.gitignore

@@ -1,5 +1,6 @@
 # no generated files in version control
 src/main/gen/
+src/main/generated/
 
 # private data
 /buildres/jabref-cert-2016.p12

AUTHORS

@@ -151,6 +151,7 @@ Jong-Ho Shinn
 Jorge Tornero
 josephshin93
 Joshua Ramon Enslin
+José Jesús Sinohui Fernández
 Julian Pfeifer
 Jure Slak
 József Pallagi
@@ -182,6 +183,7 @@ Ling Wang
 Linus Dietz
 Lorenzo Genta
 Luciana de Melo e Abud
+Luis Romero
 Mairieli Wessel
 Malik Atalla
 Malte Deiseroth
@@ -196,6 +198,7 @@ Martin Stolle
 Martina Catizone
 Mathias Walter
 Matthias Geiger
+Matthias Mueller
 Mattia Bunel
 Mattias Ulbrich
 mcmoody

CHANGELOG.md

@@ -13,14 +13,23 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
+- We cleaned up the group add/edit dialog. [#5826](https://github.com/JabRef/jabref/pull/5826)
+- We reintroduced the index column. [#5844](https://github.com/JabRef/jabref/pull/5844)
+
 ### Fixed
 
-- We fixed an issue where the Medline fetcher was only working when JabRef was running from source [#5645](https://github.com/JabRef/jabref/issues/5645)
-- We fixed some visual issues in the dark theme [#5764](https://github.com/JabRef/jabref/pull/5764) [#5753](https://github.com/JabRef/jabref/issues/5753)
+- We fixed and issue where pdf files will not open under some KDE linux distributions when using okular. [#5253](https://github.com/JabRef/jabref/issues/5253)
+- We fixed an issue where the Medline fetcher was only working when JabRef was running from source. [#5645](https://github.com/JabRef/jabref/issues/5645)
+- We fixed some visual issues in the dark theme. [#5764](https://github.com/JabRef/jabref/pull/5764) [#5753](https://github.com/JabRef/jabref/issues/5753)
 - We fixed an issue where non-default previews didn't handle unicode characters. [#5779](https://github.com/JabRef/jabref/issues/5779)
-
+- We improved the performance, especially changing field values in the entry should feel smoother now.
+- We fixed an issue where the ampersand character wasn't rendering correctly on previews. [#3840](https://github.com/JabRef/jabref/issues/3840)
+- We fixed an issue where an erroneous "The library has been modified by another program" message was shown when saving. [#4877](https://github.com/JabRef/jabref/issues/4877)
+- We fixed an issue where the file extension was missing after downloading a file (we now fall-back to pdf). [#5816](https://github.com/JabRef/jabref/issues/5816)
+- We fixed an issue where cleaning up entries broke web URLs, if "Make paths of linked files relative (if possible)" was enabled, which resulted in various other issues subsequently. [#5861](https://github.com/JabRef/jabref/issues/5861)
 
 ### Removed
+- Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action.
 
 
 ## [5.0-beta] – 2019-12-15

DEVELOPERS

@@ -5,3 +5,4 @@ Matthias Geiger (since 2015)
 Tobias Diez (since 2015)
 Christoph Schwentker (since 2016)
 Linus Dietz (since 2017)
+Carl Christian Snethlage (since 2020)

README.md

@@ -87,7 +87,7 @@ We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.
 We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS) approve.
 
-If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace).
+If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://devdocs.jabref.org/guidelines-for-setting-up-a-local-workspace/).
 
 To compile JabRef from source, you need a Java Development Kit 13 and `JAVA_HOME` pointing to this JDK.
 To run it, just execute `gradlew run`.