Updated gradle, yml, rDNA tests+check

Author: leifeld

.github/workflows/DNA build.yml renamed to .github/workflows/build-and-check.yml

@@ -3,41 +3,74 @@ name: build
 on: [push, pull_request, workflow_dispatch]
 
 jobs:
-  Bibliography:
+  install-dependencies:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: r-lib/actions/setup-tinytex@v2
+      - uses: actions/checkout@v3
 
-    - name: Install LaTeX packages
-      run: tlmgr install urlbst
+      - name: Restore System Dependencies Cache
+        uses: actions/cache@v3
+        id: system-deps-cache
+        with:
+          path: |
+            /usr/local/texlive
+            /usr/local/bin/pandoc
+            /usr/local/texlive/texmf-var
+            /usr/local/texlive/tlpkg/texlive.tlpdb
+          key: ${{ runner.os }}-system-deps-v1
+
+      - name: Install System Dependencies
+        if: steps.system-deps-cache.outputs.cache-hit != 'true'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y texlive-latex-base texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended texlive-bibtex-extra pandoc pandoc-citeproc
+
+      - uses: actions/cache@v3
+        id: r-packages-cache
+        with:
+          path: |
+            ~/.cache/R
+            /usr/local/texlive
+            /usr/local/bin/pandoc
+            /usr/local/texlive/texmf-var
+          key: ${{ runner.os }}-r-${{ hashFiles('**/DESCRIPTION') }}-v1
 
-    - uses: gradle/wrapper-validation-action@v1
-    - uses: actions/cache@v3
-      id: pandoc
-      with:
-        path: pandoc-2.19.2-1
-        key: pandoc-2.19.2-1
-    - name: Download pandoc-2.19.2-1-amd64.deb
-      if: steps.pandoc.outputs.cache-hit != 'true'
-      run: |
-        mkdir pandoc-2.19.2-1
-        cd pandoc-2.19.2-1
-        wget https://github.com/jgm/pandoc/releases/download/2.19.2/pandoc-2.19.2-1-amd64.deb
-    - name: Install pandoc
-      run: |
-        cd pandoc-2.19.2-1
-        sudo dpkg -i pandoc-2.19.2-1-amd64.deb
+      - uses: r-lib/actions/setup-r@v2
 
-    - name: Check pandoc version
-      run: pandoc --version
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 2
+          working-directory: rDNA/rDNA
+          extra-packages: |
+            any::devtools
+            any::testthat
+            any::ggplot2
+            any::roxygen2
+            any::igraph
+            any::ggraph
+            any::askpass
+            any::cluster
+            any::sna
+            any::ggrepel
+            any::coda
+            any::MCMCpack
+            any::tidygraph
+            any::heatmaply
+            any::factoextra
+            any::MASS
+            any::pbmcapply
 
+  Bibliography:
+    needs: install-dependencies
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: r-lib/actions/setup-tinytex@v2
+    - uses: gradle/wrapper-validation-action@v1
     - name: Setup Gradle
       uses: gradle/[email protected]
-
     - name: Execute Gradle build for bibliography
       run: ./gradlew :bibliography:build
-
     - name: Store artifacts
       uses: actions/upload-artifact@v3
       with:
@@ -68,33 +101,16 @@ jobs:
         path: build/*.jar
 
   rDNA:
+    needs: [DNA, install-dependencies]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-
     - uses: r-lib/actions/setup-r@v2
-
-    - uses: r-lib/actions/setup-r-dependencies@v2
-      with:
-        cache-version: 2
-        working-directory: rDNA/rDNA
-        extra-packages: |
-          any::ggplot2
-          any::roxygen2
-          any::igraph
-          any::ggraph
-          any::askpass
-          any::cluster
-          any::sna
-
     - uses: gradle/wrapper-validation-action@v1
-
     - name: Setup Gradle
       uses: gradle/[email protected]
-
     - name: Execute Gradle build for rDNA
       run: ./gradlew :rDNA:build
-
     - name: Store artifacts
       uses: actions/upload-artifact@v3
       with:
@@ -103,9 +119,8 @@ jobs:
 
   rDNA-check:
     runs-on: ${{ matrix.config.os }}
-
+    needs: rDNA
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
     strategy:
       fail-fast: false
       matrix:
@@ -115,29 +130,39 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-
     steps:
       - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
           working-directory: rDNA/rDNA
-
       - uses: r-lib/actions/check-r-package@v2
         with:
           working-directory: rDNA/rDNA
           upload-snapshots: true
+
+  rDNA-test:
+    runs-on: ubuntu-latest
+    needs: [rDNA, install-dependencies]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: gradle/wrapper-validation-action@v1
+      - name: Setup Gradle
+        uses: gradle/[email protected]
+      - name: Execute Gradle rDNATest Task
+        run: ./gradlew :rDNA:rDNATest
+      - name: Store test results
+        uses: actions/upload-artifact@v3
+        with:
+          name: rDNA-Test-Results
+          path: build/reports/tests

bibliography/bibliography.bib

@@ -2828,6 +2828,15 @@ @article{starke2023green
   doi={10.1016/j.jclepro.2023.139058}
 }
 
+@article{steemers2024united,
+  title={The {U}nited {K}ingdom's {R}ejoin Movement: A Post-{B}rexit Analysis of Framing Strategies},
+  author={Steemers, Kai},
+  journal={British Journal of Politics and International Relations},
+  year={2024},
+  doi={10.1177/13691481241269308},
+  note={Forthcoming}
+}
+
 @article{steinfeld2016f,
   title={The {F}-Campaign: A Discourse Network Analysis of Party Leaders' Campaign Statements on {F}acebook},
   author={Steinfeld, Nili},

bibliography/build.gradle

@@ -1,3 +1,7 @@
+plugins {
+    id 'base'
+}
+
 task bibliographyMarkdown {
     inputs.dir '.'
     doLast {
@@ -47,7 +51,7 @@ task bibliographyPdflatex {
     }
 }
 
-task build {
+build {
     dependsOn bibliographyMarkdown
     dependsOn bibliographyPdflatex
     inputs.dir '.'
@@ -56,3 +60,25 @@ task build {
 
     doLast {}
 }
+
+clean {
+    doFirst {
+        println "Attempting to delete bibliography files..."
+
+        def filesToDelete = fileTree(dir: "$rootDir/build", include: '**/bibliography.*').files
+        if (filesToDelete.isEmpty()) {
+            println "No bibliography files found to delete."
+        } else {
+            println "Found bibliography files to delete: "
+            filesToDelete.each { file ->
+                println file.absolutePath
+            }
+        }
+    }
+
+    delete fileTree(dir: "$rootDir/build", include: '**/bibliography.*')
+
+    doLast {
+        println "Bibliography files have been removed."
+    }
+}