Merge remote-tracking branch 'origin/ScholarArchiveFetcher' into Scho…

…larArchiveFetcher
liyou969 · Oct 29, 2023 · 951c8b6 · 951c8b6
2 parents 505bcef + 18512df
commit 951c8b6
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -31,9 +31,9 @@
         // Install java.
         // See https://github.com/devcontainers/features/tree/main/src/java#options for details.
         "ghcr.io/devcontainers/features/java:1": {
-            "version": "20.0.2-tem",
+            "version": "21.0.1-librca",
             "installGradle": false,
-            "jdkDistro": "tem"
+            "jdkDistro": "librca"
         }
     }
 }
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.10 (latest release)"
+        - "5.11 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -12,6 +12,7 @@ The title of the PR must not reference an issue, because GitHub does not support
 -->
 
 ### Mandatory checks
+
 - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)

diff --git a/.github/failure-csl-update.md b/.github/failure-csl-update.md
diff --git a/.github/heylogs.java b/.github/heylogs.java
@@ -1,4 +1,4 @@
-//DEPS com.github.nbbrd.heylogs:heylogs-cli:0.6.0
+//DEPS com.github.nbbrd.heylogs:heylogs-cli:0.7.1
 public class heylogs {
     public static void main(String... args) throws Exception {
         nbbrd.heylogs.cli.HeylogsCommand.main(args);

diff --git a/...ows/GreetingFirstTimeCodeContribution.yml → .github/workflows/add-greeting-to-issue.yml b/...ows/GreetingFirstTimeCodeContribution.yml → .github/workflows/add-greeting-to-issue.yml
@@ -1,4 +1,4 @@
-name: GreetingFirstTimeCodeContribution
+name: Add greeting to issues for first time contributors
 
 on: 
   issues:

diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -21,7 +21,7 @@ jobs:
           PR_URL: ${{github.event.pull_request.html_url}}
           GITHUB_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
       - name: Merge PR
-        run: gh pr merge --auto "$PR_URL"
+        run: gh pr merge --auto --squash "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}
           GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}
diff --git a/.github/workflows/deployment-arm64.yml b/.github/workflows/deployment-arm64.yml
@@ -61,23 +61,9 @@ jobs:
       - name: Setup JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 20
-          distribution: 'temurin'
+          java-version: 21.0.1
+          distribution: 'liberica'
           cache: 'gradle'
-      - name: Setup JDK jabref-fix macOS
-        shell: bash
-        run: |
-            mkdir ${{runner.temp}}/jdk
-            wget -qO- https://files.jabref.org/jdks/jdk-macos-aarch64.tar.gz | tar xz -C ${{runner.temp}}/jdk
-            mv ${{runner.temp}}/jdk/jdk-21.jdk ${{runner.temp}}/jdk/jdk-21
-            echo "JDK21=${{runner.temp}}/jdk/jdk-21" >> "$GITHUB_ENV"
-            ls ${{runner.temp}}/jdk
-
-            echo "org.gradle.java.installations.paths=${{runner.temp}}/jdk/jdk-21" >> gradle.properties
-            echo "org.gradle.java.installations.auto-detect=false" >> gradle.properties
-            cat gradle.properties
-
-            sed -i'.bak' -e "s/JavaLanguageVersion.of(20)/JavaLanguageVersion.of(21)/" build.gradle
       - name: Clean up keychain
         run: |
          security delete-keychain signing_temp.keychain ${{runner.temp}}/keychain/notarization.keychain || true
@@ -104,9 +90,9 @@ jobs:
       - name: Build dmg (macOS)
         shell: bash
         run: |
-          ${{env.JDK21}}/Contents/Home/bin/jpackage \
+          jpackage \
           --module org.jabref/org.jabref.cli.Launcher \
-          --module-path ${{env.JDK21}}/Contents/Home/jmods/:build/jlinkbase/jlinkjars \
+          --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
           --app-content buildres/mac/jabrefHost.py \
@@ -128,9 +114,9 @@ jobs:
       - name: Build pkg (macOS)
         shell: bash
         run: |
-          ${{env.JDK21}}/Contents/Home/bin/jpackage \
+          jpackage \
           --module org.jabref/org.jabref.cli.Launcher \
-          --module-path ${{env.JDK21}}/Contents/Home/jmods/:build/jlinkbase/jlinkjars \
+          --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
           --app-content buildres/mac/jabrefHost.py \

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
@@ -92,52 +92,9 @@ jobs:
       - name: Setup JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 20
-          distribution: 'temurin'
+          java-version: 21.0.1
+          distribution: 'liberica'
           cache: 'gradle'
-      - name: Setup JDK jabref-fix (Windows)
-        if: (matrix.os == 'windows-latest')
-        shell: bash
-        run: |
-         mkdir ${{runner.temp}}\jdk
-         curl -kLsS ${{matrix.eaJDK}} -o temp.zip && 7z x temp.zip -o"$(cygpath -u "$RUNNER_TEMP\jdk")"
-         echo "JDK21=${{runner.temp}}\jdk\jdk-21" >> "$GITHUB_ENV"
-         ls "$(cygpath -u "$RUNNER_TEMP\jdk\jdk-21")"
-
-         echo "org.gradle.java.installations.paths=${{runner.temp}}\jdk\jdk-21" | sed "s/\\\\/\\\\\\\\/g" >> gradle.properties
-         echo "org.gradle.java.installations.auto-detect=false" >> gradle.properties
-         cat gradle.properties
-
-         sed -i "s/JavaLanguageVersion.of(20)/JavaLanguageVersion.of(21)/" build.gradle
-      - name: Setup JDK jabref-fix (linux)
-        if: (matrix.os == 'ubuntu-latest')
-        shell: bash
-        run: |
-          mkdir ${{runner.temp}}/jdk
-          wget -qO- ${{matrix.eaJDK}} | tar xz -C ${{runner.temp}}/jdk
-          echo "JDK21=${{runner.temp}}/jdk/jdk-21" >> "$GITHUB_ENV"
-          ls ${{runner.temp}}/jdk
-
-          echo "org.gradle.java.installations.paths=${{runner.temp}}/jdk/jdk-21" >> gradle.properties
-          echo "org.gradle.java.installations.auto-detect=false" >> gradle.properties
-          cat gradle.properties
-
-          sed -i "s/JavaLanguageVersion.of(20)/JavaLanguageVersion.of(21)/" build.gradle
-      - name: Setup JDK jabref-fix (macOS)
-        if: (matrix.os == 'macos-latest')
-        shell: bash
-        run: |
-          mkdir ${{runner.temp}}/jdk
-          wget -qO- ${{matrix.eaJDK}} | tar xz -C ${{runner.temp}}/jdk
-          mv ${{runner.temp}}/jdk/jdk-21.jdk ${{runner.temp}}/jdk/jdk-21
-          echo "JDK21=${{runner.temp}}/jdk/jdk-21" >> "$GITHUB_ENV"
-          ls ${{runner.temp}}/jdk
-
-          echo "org.gradle.java.installations.paths=${{runner.temp}}/jdk/jdk-21" >> gradle.properties
-          echo "org.gradle.java.installations.auto-detect=false" >> gradle.properties
-          cat gradle.properties
-
-          sed -i'.bak' -e "s/JavaLanguageVersion.of(20)/JavaLanguageVersion.of(21)/" build.gradle
       - name: Prepare merged jars and modules dir (macOS)
         if: (matrix.os == 'macos-latest') || (steps.checksecrets.outputs.secretspresent == 'NO')
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" prepareModulesDir
@@ -160,9 +117,9 @@ jobs:
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
-          ${{env.JDK21}}/Contents/Home/bin/jpackage \
+          jpackage \
           --module org.jabref/org.jabref.cli.Launcher \
-          --module-path ${{env.JDK21}}/Contents/Home/jmods/:build/jlinkbase/jlinkjars \
+          --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
           --app-content buildres/mac/jabrefHost.py \
@@ -185,9 +142,9 @@ jobs:
         if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES')
         shell: bash
         run: |
-          ${{env.JDK21}}/Contents/Home/bin/jpackage \
+          jpackage \
           --module org.jabref/org.jabref.cli.Launcher \
-          --module-path ${{env.JDK21}}/Contents/Home/jmods/:build/jlinkbase/jlinkjars \
+          --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
           --app-content buildres/mac/jabrefHost.py \
@@ -232,7 +189,7 @@ jobs:
           rm debian-binary control.tar.* data.tar.*
           mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
       - name: Setup rsync (macOS)
-        if: (matrix.os == 'macos-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'macos-latest') && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true))) }}
         run: brew install rsync
       - name: Setup rsync (Windows)
         if: (matrix.os == 'windows-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
@@ -241,8 +198,8 @@ jobs:
         # We cannot use "setup-rsync", because that does not work on Windows
         # We do not use egor-tensin/setup-cygwin@v4, because it replaces the default shell
         run: choco install --no-progress rsync
-      - name: Setup ssh key
-        if: (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+      - name: Setup SSH key
+        if: ${{ (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && ((matrix.os != 'macos-latest') || !((startsWith(github.ref, 'refs/tags/') || (inputs.notarization == true)))) }}
         run: |
           echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
           chmod 600 sshkey

diff --git a/.github/workflows/refresh-journal-lists.yml b/.github/workflows/refresh-journal-lists.yml
@@ -30,8 +30,8 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 20
-          distribution: 'temurin'
+          java-version: 21.0.1
+          distribution: 'liberica'
           cache: 'gradle'
       - name: Check whether journal-list.mv can be generated (the "real" generation is done inside JabRef's build process)
         run: |

diff --git a/.github/workflows/tests-fetchers.yml b/.github/workflows/tests-fetchers.yml
@@ -48,8 +48,8 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
-          java-version: 20
-          distribution: 'temurin'
+          java-version: 21.0.1
+          distribution: 'liberica'
           cache: 'gradle'
       - name: Run fetcher tests
         run: ./gradlew fetcherTest