Merge remote-tracking branch 'upstream/main' into newDateFormats

* upstream/main: (61 commits) Bump jackson-datatype-jsr310 from 2.13.4 to 2.14.0 (JabRef#9357) Bump jackson-dataformat-yaml from 2.13.4 to 2.14.0 (JabRef#9356) Bump tika-core from 2.5.0 to 2.6.0 (JabRef#9358) Refine guideline "Set up a local workspace" (JabRef#9355) Adds missing "requires" statement (JabRef#9354) Bind "Find unlinked files" default directory to the current library (JabRef#9290) Rename "Remote" to "Tele" (JabRef#9270) Fixed display of file field adjusting for the dark theme (JabRef#9343) Update sorting of entries in maintable by special fields immediately (JabRef#9338) New translations JabRef_en.properties (German) (JabRef#9336) Fix Abbreviation for Escaped Ampersand (JabRef#9288) Fix font size preference not updating in preference dialog 8386 (JabRef#9287) New Crowdin updates (JabRef#9333) Refresh example styles Squashed 'buildres/csl/csl-styles/' changes from 4eee79a..13fd98e Bump unirest-java from 3.13.11 to 3.13.12 (JabRef#9330) Bump checkstyle from 10.3.4 to 10.4 (JabRef#9331) Bump gittools/actions from 0.9.14 to 0.9.15 (JabRef#9332) Group context menu presents relevant options depending on number of subgroups (JabRef#9286) Removed BibTeX file type and included HTML and Markdown types (JabRef#9318) ...
yanyanliu1400 · Nov 7, 2022 · e54fcdf · e54fcdf
2 parents b9fa2e0 + b767ed2
commit e54fcdf
Show file tree

Hide file tree

Showing 254 changed files with 4,914 additions and 1,618 deletions.
diff --git a/.github/workflows/GreetingFirstTimeCodeContribution.yml b/.github/workflows/GreetingFirstTimeCodeContribution.yml
@@ -0,0 +1,23 @@
+name: GreetingFirstTimeCodeContribution
+
+on: 
+  issues:
+     types:
+       - labeled
+
+jobs:
+  GreetingFirstTimeCodeContribution:
+    if: ${{ github.event.label.name == 'FirstTimeCodeContribution' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+    - name: GreetingFirstTimeCodeContribution
+      uses: peter-evans/create-or-update-comment@v2
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        issue-number: ${{ github.event.issue.number }}
+        body: |
+            As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.
+            
+            Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's [Gitter](https://gitter.im/JabRef/jabref) chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.
diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -16,12 +16,12 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v2.4.0
+        uses: hmarr/auto-approve-action@v3.1.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.15.3
+        uses: pascalgn/automerge-action@v0.15.5
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -31,7 +31,6 @@ concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
-
 jobs:
   build:
     strategy:
@@ -51,45 +50,58 @@ jobs:
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.13
+        uses: gittools/actions/gitversion/setup@v0.9.15
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.13
+        uses: gittools/actions/gitversion/execute@v0.9.15
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
           java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Setup OSX key chain on OSX for app id cert
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
+        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
+        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         shell: bash
         run: |
           codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
@@ -100,7 +112,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/')
+        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
@@ -157,12 +169,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/setup@v0.9.13
+        uses: gittools/actions/gitversion/setup@v0.9.15
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.13
+        uses: gittools/actions/gitversion/execute@v0.9.15
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -0,0 +1,60 @@
+name: Deploy Jekyll site to Pages
+
+on:
+  pull_request:
+    paths:
+      - 'docs/**'
+      - '.github/workflows/pages.yml'
+  push:
+    paths:
+      - 'docs/**'
+      - '.github/workflows/pages.yml'
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '2.7' # Not needed with a .ruby-version file
+          bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+          cache-version: 1 # Increment this number if you need to re-download cached gems
+          working-directory: docs/
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v2
+      - name: Build with Jekyll
+        run: |
+          cd docs
+          bundle exec jekyll build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/_site/
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1
diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -32,6 +32,7 @@ jobs:
         run: |
           git subtree pull --prefix buildres/csl/csl-styles csl-styles master --squash || true
           cp buildres/csl/csl-styles/acm-siggraph.csl src/main/resources/csl-styles/
+          cp buildres/csl/csl-styles/apa.csl src/main/resources/csl-styles/
           cp buildres/csl/csl-styles/ieee.csl src/main/resources/csl-styles/
           cp buildres/csl/csl-styles/turabian-author-date.csl src/main/resources/csl-styles/
           git add .

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -11,10 +11,8 @@ on:
       - '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/**'
+      - 'src/main/java/org/jabref/logic/importer/fetcher/**'
+      - 'src/test/java/org/jabref/logic/importer/fetcher/**'
       - '.github/workflows/tests-fetchers.yml'
       - 'build.gradle'
   schedule:

diff --git a/.idea/runConfigurations/JabRef_Main.xml b/.idea/runConfigurations/JabRef_Main.xml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,9 +20,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - An SLR can now be started from the SLR itself. [#9131](https://github.com/JabRef/jabref/pull/9131), [koppor#601](https://github.com/koppor/jabref/issues/601)
 - Implement a new ISBN Fetcher ([doi-to-bibtex-converter.herokuapp.com](http://doi-to-bibtex-converter.herokuapp.com) as source). [#9145](https://github.com/JabRef/jabref/pull/9145)
 - We added support for the Ukrainian and Arabic languages. [#9236](https://github.com/JabRef/jabref/pull/9236), [#9243](https://github.com/JabRef/jabref/pull/9243)
+- The default file directory of a library is used as default directory for [unlinked file lookup](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [koppor#546](https://github.com/koppor/jabref/issues/546)
 
 ### Changed
 
+- We disabled the "change case" menu for empty fields [#9214](https://github.com/JabRef/jabref/issues/9214)
 - We disabled the conversion menu for empty fields [#9200](https://github.com/JabRef/jabref/issues/9200)
 - We upgraded to Lucene 9.4 for the fulltext search.
   Thus, the now created search index cannot be read from older versions of JabRef anylonger.
@@ -38,15 +40,25 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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)
 - The fallback directory of the file folder now is the general file directory. In case there was a directory configured for a library and this directory was not found, JabRef placed the PDF next to the .bib file and not into the general file directory.
-- The global default directory for storing PDFs is now the subdirectory "JabRef" in the user's home.
+- The global default directory for storing PDFs is now the documents folder in the user's home.
 - We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 - We simplified the actions to fast-resolve duplicates to 'Keep Left', 'Keep Right', 'Keep Both' and 'Keep Merged'. [#9056](https://github.com/JabRef/jabref/issues/9056)
 - We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
 - When adding or editing a subgroup it is placed w.r.t. to alphabetical ordering rather than at the end. [koppor#577](https://github.com/koppor/jabref/issues/577)
 - We modified the Directory of Open Access Books (DOAB) fetcher so that it will now also fetch the ISBN when possible. [#8708](https://github.com/JabRef/jabref/issues/8708)
+- Groups context menu now shows appropriate options depending on number of subgroups. [koppor#579](https://github.com/koppor/jabref/issues/579)
+- We changed the color of found text from red to high-contrast colors (background: yellow; font color: purple). [koppor#552](https://github.com/koppor/jabref/issues/552)
+- We modified the "Delete file" dialog and add the full file path to the dialog text. The file path in the title was changed to file name only. [koppor#534](https://github.com/koppor/jabref/issues/534)
+- Download from URL now automatically fills with URL from clipboard. [koppor#535](https://github.com/koppor/jabref/issues/535)
+- We added HTML and Markdown files to Find Unlinked Files and removed BibTeX.[koppor#547](https://github.com/koppor/jabref/issues/547)
+- We changed the messages after importing unlinked local files to past tense. [koppor#548](https://github.com/koppor/jabref/issues/548)
+- We fixed an issue where the wrong icon for a successful import of a bib entry was shown [#9308](https://github.com/JabRef/jabref/pull/9308)
 
 ### Fixed
 
+- We fixed the readability of the file field in the dark dark theme [#9340](https://github.com/JabRef/jabref/issues/9340)
+- We fixed that sorting of entries in the maintable by special fields is updated immediately [#9334](https://github.com/JabRef/jabref/issues/9334)
+- We fixed the Cleanup entries dialog is partially visible [#9223](https://github.com/JabRef/jabref/issues/9223)
 - We fixed the display of the "Customize Entry Types" dialogue title [#9198](https://github.com/JabRef/jabref/issues/9198)
 - 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)
@@ -56,6 +68,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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 some visual inconsistencies (round corners of highlighted buttons). [#8806](https://github.com/JabRef/jabref/issues/8806)
 - 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 library 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)
@@ -69,6 +82,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where an exception was not logged correctly. [koppor#627](https://github.com/JabRef/koppor/issues/627)
 - We fixed an issue where hitting enter on the search field within the preferences dialog closed the dialog. [koppor#630](https://github.com/koppor/jabref/issues/630)
 - We fixed a typo within a connection error message. [koppor#625](https://github.com/koppor/jabref/issues/625)
+- We fixed an issue where the 'close dialog' key binding was not closing the Preferences dialog. [#8888](https://github.com/jabref/jabref/issues/8888)
+- We fixed an issue where journal abbreviations would not abbreviate journal titles with escaped ampersands (\\&). [#8948](https://github.com/JabRef/jabref/issues/8948)
+- We fixed an issue where font size preferences did not apply correctly to preference dialog window and the menu bar. [#8386](https://github.com/JabRef/jabref/issues/8386) and [#9279](https://github.com/JabRef/jabref/issues/9279)
+- We fixed an issue when using an unsafe character in the citation key, the auto-linking feature fails to link files. [#9267](https://github.com/JabRef/jabref/issues/9267)
 
 ### Removed