Merge branch 'main' into duplicate-check-test

koppor · Sep 4, 2023 · 3526573 · 3526573
2 parents de6bf07 + eaabae5
commit 3526573
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diff --git a/.gitattributes b/.gitattributes
@@ -12,6 +12,8 @@ gradlew text eol=lf
 
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol
+# Exception: The files used for the http server test - they should have linux line endings
+src/test/resources/org/jabref/http/server/*.bib text eol=lf
 
 # Citavi needs to be LF line ending
 # This overwrites the setting of "*.bib"

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -12,8 +12,7 @@ body:
  attributes:
  label: JabRef version
  options:
- - "5.9 (latest release)"
- - "3.8.2"
+ - "5.10 (latest release)"
  - Latest development branch build (please note build date below)
  - Other (please describe below)
  description: The version as shown in the about dialog.
@@ -42,7 +41,7 @@ body:
 
  - type: checkboxes
  attributes:
- label: Checked with the latest development build
+ label: Checked with the latest development build (copy version output from About dialog)
  description: |
  Please always test if the bug is still reproducible in the latest development version. We are constantly improving JabRef and some bugs may already be fixed. If you already use a development version, ensure that you use the latest one.
  You can download the latest development build at: https://builds.jabref.org/main/ . **Please make a backup of your library before you try out this version.**

diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -1,34 +1,22 @@
-name: Automerge Pull Requests
-on:
- pull_request:
- types:
- - opened
- - synchronize
- - reopened
- - labeled
+name: Dependabot auto-merge
+on: pull_request
+
+permissions:
+ contents: write
+ pull-requests: write
+
 jobs:
- automerge:
- name: Automerge Dependency Updates
+ dependabot:
  runs-on: ubuntu-latest
- if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]' || contains(github.event.pull_request.labels.*.name, 'dependencies')
+ if: ${{ (github.actor == 'dependabot[bot]') || (github.actor == 'koppor' && startsWith(github.event.pull_request.title, '[Bot]')) }}
  steps:
- - name: 'Wait for status checks'
- id: waitforstatuschecks
- uses: "WyriHaximus/github-action-wait-for-status@v1.8.0"
- with:
- ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
- checkInterval: 13
+ - name: Approve PR
+ run: gh pr review --approve "$PR_URL"
  env:
- GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
- - name: Auto approve
- uses: hmarr/auto-approve-action@v3.2.1
- if: steps.waitforstatuschecks.outputs.status == 'success'
- with:
- github-token: "${{ secrets.GITHUB_TOKEN }}"
- - name: Merge pull requests
- uses: pascalgn/automerge-action@v0.15.6
- if: steps.waitforstatuschecks.outputs.status == 'success'
+ PR_URL: ${{github.event.pull_request.html_url}}
+ GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+ - name: Merge PR
+ run: gh pr merge --auto "$PR_URL"
  env:
- MERGE_METHOD: "merge"
- MERGE_LABELS: ""
- GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+ PR_URL: ${{github.event.pull_request.html_url}}
+ GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
diff --git a/.github/workflows/check-links.yaml b/.github/workflows/check-links.yaml
@@ -11,6 +11,8 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - uses: actions/checkout@v3
+ with:
+ show-progress: 'false'
  - uses: gaurav-nelson/github-action-markdown-link-check@v1
  with:
  use-quiet-mode: 'yes'

diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -49,6 +49,8 @@ jobs:
  uses: actions/checkout@v3
  with:
  fetch-depth: 0
+ submodules: 'true'
+ show-progress: 'false'
  - name: Install GitVersion
  uses: gittools/actions/gitversion/setup@v0.10.2
  with:
@@ -143,26 +145,27 @@ jobs:
  --resource-dir buildres/mac \
  --file-associations buildres/mac/bibtexAssociations.properties \
  --jlink-options --bind-services
- - name: Rename files
- shell: pwsh
+ - name: Rename files with arm64 suffix as well
+ shell: bash
  run: |
- get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
- get-childitem -Path build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
+ mv build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.dmg
+ mv build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg
  - name: Notarize dmg
  if: (startsWith(github.ref, 'refs/tags/') || (${{ inputs.notarization }}))
  shell: bash
  run: |
  xcrun notarytool store-credentials "notarytool-profile" --apple-id "vorstand@jabref.org" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}" --keychain ${{runner.temp}}/keychain/notarization.keychain
- xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
- xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg
+ xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.dmg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
+ xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.dmg
  - name: Notarize pkg
  if: (startsWith(github.ref, 'refs/tags/') || (${{ inputs.notarization }}))
  shell: bash
  run: |
  xcrun notarytool store-credentials "notarytool-profile" --apple-id "vorstand@jabref.org" --team-id "6792V39SK3" --password "${{ secrets.OSX_NOTARIZATION_APP_PWD }}" --keychain ${{runner.temp}}/keychain/notarization.keychain
- xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
- xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg
+ xcrun notarytool submit build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg --keychain-profile "notarytool-profile" --keychain ${{runner.temp}}/keychain/notarization.keychain --wait
+ xcrun stapler staple build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-arm64.pkg
  - name: Upload with rsync
+ if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
  shell: bash
  run: |
  mkdir ${{runner.temp}}/sshkey
@@ -172,7 +175,8 @@ jobs:
  fi
  rsync -Pavz --itemize-changes --stats --partial-dir=/tmp/partial --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i ~/.ssh/id_rsa' build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
  - name: Upload to GitHub workflow artifacts store
+ if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
  uses: actions/upload-artifact@v3
  with:
  name: JabRef-${{ matrix.displayName }}
- path: build/distribution
+ path: build/distribution
diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -22,6 +22,7 @@ on:
  - 'docs/**'
  - 'src/test/**'
  - 'README.md'
+ merge_group:
 
 env:
  SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
@@ -73,6 +74,14 @@ jobs:
  uses: actions/checkout@v3
  with:
  fetch-depth: 0
+ submodules: 'true'
+ show-progress: 'false'
+ - name: Install pigz and cache (linux)
+ if: (matrix.os == 'ubuntu-latest')
+ uses: awalsh128/cache-apt-pkgs-action@latest
+ with:
+ packages: pigz
+ version: 1.0
  - name: Install GitVersion
  uses: gittools/actions/gitversion/setup@v0.10.2
  with:
@@ -222,7 +231,7 @@ jobs:
  rm debian-binary control.tar.* data.tar.*
  mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
  - name: Upload to builds.jabref.org (ubuntu)
- if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+ if: (matrix.os == 'ubuntu-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
  uses: Pendect/action-rsyncer@v2.0.0
  env:
  DEPLOY_KEY: ${{ secrets.buildJabRefPrivateKey }}
@@ -233,13 +242,13 @@ jobs:
  src: 'build/distribution/'
  dest: jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/
  - name: Upload to GitHub workflow artifacts store (windows)
- if: (matrix.os == 'windows-latest')
+ if: (matrix.os == 'windows-latest') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
  uses: actions/upload-artifact@v3
  with:
  name: JabRef-${{ matrix.displayName }}
  path: build/distribution
  - name: Upload to GitHub workflow artifacts store (macos)
- if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
+ if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
  uses: actions/upload-artifact@v3
  with:
  # tbn = to-be-notarized
@@ -266,6 +275,8 @@ jobs:
  uses: actions/checkout@v3
  with:
  fetch-depth: 0
+ submodules: 'true'
+ show-progress: 'false'
  - name: Install GitVersion
  if: steps.checksecrets.outputs.secretspresent == 'YES'
  uses: gittools/actions/gitversion/setup@v0.10.2
@@ -300,7 +311,7 @@ jobs:
  shell: bash
  run: ${{ matrix.archivePortable }}
  - name: Upload to GitHub workflow artifacts store
- if: (steps.checksecrets.outputs.secretspresent == 'YES')
+ if: (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
  uses: actions/upload-artifact@v3
  with:
  name: JabRef-macOS
@@ -311,6 +322,7 @@ jobs:
  name: Upload binaries on builds.jabref.org
  runs-on: ubuntu-latest
  needs: [build, notarize]
+ if: ${{ !startsWith(github.ref, 'refs/heads/gh-readonly-queue') }}
  steps:
  - name: Check secrets presence
  id: checksecrets
@@ -326,9 +338,10 @@ jobs:
  - name: Checkout source
  if: steps.checksecrets.outputs.secretspresent == 'YES'
  uses: actions/checkout@v3
- - name: Fetch all history for all tags and branches
- if: steps.checksecrets.outputs.secretspresent == 'YES'
- run: git fetch --prune --unshallow
+ with:
+ fetch-depth: 0
+ submodules: 'true'
+ show-progress: 'false'
  - name: Install GitVersion
  if: steps.checksecrets.outputs.secretspresent == 'YES'
  uses: gittools/actions/gitversion/setup@v0.10.2
@@ -345,7 +358,7 @@ jobs:
  name: JabRef-windows
  path: build/distribution
  - name: Get macOS binaries unsigned
- if: (steps.checksecrets.outputs.secretspresent == 'YES') && (inputs.notarization == false && ! startsWith(github.ref, 'refs/tags/'))
+ if: (steps.checksecrets.outputs.secretspresent == 'YES') && (inputs.notarization == false && !startsWith(github.ref, 'refs/tags/'))
  uses: actions/download-artifact@master
  with:
  name: JabRef-macOS-tbn

diff --git a/.github/workflows/gource.yml b/.github/workflows/gource.yml
@@ -12,7 +12,7 @@ on:
 concurrency:
  group: gource
  cancel-in-progress: true
- 
+
 jobs:
  action:
  runs-on: ubuntu-latest
@@ -21,6 +21,7 @@ jobs:
  uses: actions/checkout@v3
  with:
  fetch-depth: 0
+ show-progress: 'false'
  - name: 'Development history of current build'
  uses: BoundfoxStudios/action-gource@v2
  with:

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -28,6 +28,8 @@ jobs:
  steps:
  - name: Checkout
  uses: actions/checkout@v3
+ with:
+ show-progress: 'false'
  - name: Setup Ruby
  uses: ruby/setup-ruby@v1
  with:

diff --git a/.github/workflows/refresh-csl-subtrees.yml b/.github/workflows/refresh-csl-subtrees.yml
@@ -2,7 +2,6 @@ name: Refresh Citation Style Language Files
 
 on:
  schedule:
- # run on 1st and 15th of each month
  - cron: '1 2 1,15 * *'
  workflow_dispatch:
 
@@ -13,43 +12,48 @@ jobs:
  publish:
  name: Refresh Citation Style Language Files
  runs-on: ubuntu-latest
- if: github.repository == 'JabRef/jabref'
+ permissions:
+ contents: write # for peter-evans/create-pull-request to create branch
+ pull-requests: write # for peter-evans/create-pull-request to create a PR
+ if: (github.repository == 'JabRef/jabref' || github.repository == 'koppor/jabref')
  steps:
- - name: Checkout source
- uses: actions/checkout@v3
+ - uses: actions/checkout@v3
  with:
- ref: main
+ persist-credentials: true
  fetch-depth: 0
+ submodules: 'true'
+ show-progress: 'false'
  - name: Initialize git
  run: |
- git checkout main
  git config --local core.editor /usr/bin/cat
- git config user.name "github actions"
- git config user.email "jabrefmail+webfeedback@gmail.com"
- - name: Add csl-styles remote
- run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
- - name: Update csl-styles
+ git config user.name 'github-actions[bot]'
+ git config user.email 'github-actions[bot]@users.noreply.github.com'
+ - name: Update buildres/csl/csl-styles
  run: |
- git subtree pull --prefix buildres/csl/csl-styles csl-styles master --squash || true
+ cd buildres/csl/csl-styles
+ git checkout master
+ git pull
+ cd ..
+ cd ..
+ cd ..
  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 .
- git commit -m"Refresh example styles" || true
- - name: Add csl-locales remote
- run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
- - name: Update csl-locales
+ - name: Update buildres/csl/csl-locales
  run: |
- git subtree pull --prefix buildres/csl/csl-locales csl-locales master --squash || true
+ cd buildres/csl/csl-locales
+ git checkout master
+ git pull
+ cd ..
+ cd ..
+ cd ..
  cp buildres/csl/csl-locales/locales.json src/main/resources/csl-locales/
  cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
- git add .
- git commit -m"Refresh example styles" || true
  - uses: peter-evans/create-pull-request@v5
  with:
- token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
+ token: ${{ secrets.GITHUB_TOKEN }}
  branch: refresh-csl
- commit-message: Update CSL styles
  title: "[Bot] Update CSL styles"
+ commit-message: Update CSL styles
  labels: dependencies