Minor tidyup

Author: StuartWheater

.github/workflows/dsBaseClient_test_suite.yaml

@@ -23,7 +23,7 @@ jobs:
     timeout-minutes: 120
     permissions:
       contents: read
-    
+
     # These should all be constant, except TEST_FILTER. This can be used to test 
     # subsets of test files in the testthat directory. Options are like:
     # '*'               <- Run all tests.
@@ -34,7 +34,7 @@ jobs:
       _r_check_system_clock_: 0
       WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
       PROJECT_NAME: dsBaseClient
-      BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
       REPO_OWNER: ${{ github.repository_owner }}
       R_KEEP_PKG_SOURCE: yes
       GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}
@@ -54,7 +54,7 @@ jobs:
           path: testStatus
           persist-credentials: false
           token: ${{ env.GITHUB_TOKEN }}
-          
+
       - name: Uninstall default MySQL
         run: |
           curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
@@ -64,7 +64,7 @@ jobs:
           sudo apt-get autoremove -y
           sudo apt-get autoclean -y
           sudo rm -rf /var/lib/mysql/
-          
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -84,29 +84,29 @@ jobs:
           sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y
           sudo R -q -e "install.packages(c('devtools','covr','fields','meta','metafor','ggplot2','gridExtra','data.table','DSI','DSOpal','DSLite','MolgenisAuth','MolgenisArmadillo','DSMolgenisArmadillo','DescTools','e1071'), repos='https://cloud.r-project.org')"
           sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"
-      
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: 'c("Imports")'
-          extra-packages: | 
-            any::rcmdcheck 
-            cran::devtools 
-            cran::git2r 
-            cran::RCurl 
-            cran::readr 
-            cran::magrittr 
-            cran::xml2 
-            cran::purrr 
-            cran::dplyr 
-            cran::stringr 
-            cran::tidyr 
-            cran::quarto 
-            cran::knitr 
-            cran::kableExtra 
-            cran::rmarkdown 
-            cran::downlit 
+          extra-packages: |
+            any::rcmdcheck
+            cran::devtools
+            cran::git2r
+            cran::RCurl
+            cran::readr
+            cran::magrittr
+            cran::xml2
+            cran::purrr
+            cran::dplyr
+            cran::stringr
+            cran::tidyr
+            cran::quarto
+            cran::knitr
+            cran::kableExtra
+            cran::rmarkdown
+            cran::downlit
           needs: check
-          
+
       - name: Check manual updated
         run: |
           orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
@@ -125,7 +125,7 @@ jobs:
           grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
         working-directory: dsBaseClient
         continue-on-error: true
-        
+
       - name: Start Armadillo docker-compose
         run: docker compose -f docker-compose_armadillo.yml up -d --build
         working-directory: dsBaseClient
@@ -145,7 +145,7 @@ jobs:
           sleep 30
           curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
         working-directory: dsBaseClient
-      
+
       - name: Run tests with coverage & JUnit report
         run: |
           mkdir -p logs
@@ -169,11 +169,11 @@ jobs:
               ),
               "coveragelist.csv"
             )'
-          
+
           mv coveragelist.csv logs/
           mv test_* logs/
         working-directory: dsBaseClient
-      
+
       - name: Check for JUnit errors
         run: |
           issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
@@ -190,33 +190,33 @@ jobs:
           echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
           echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
         working-directory: dsBaseClient/logs
-        
+
       - name: Parse results from testthat and covr
         run: |
           Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
         working-directory: dsBaseClient
-        
+
       - name: Render report
         run: |
           cd testStatus
-          
+
           mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
           mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
           mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/
-          
+
           # Copy logs to new logs directory location
           cp -rv ../dsBaseClient/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
           cp -rv ../dsBaseClient/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
-          
+
           R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
           mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
           cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest
-          
+
         env:
           PROJECT_NAME: ${{ env.PROJECT_NAME }}
           BRANCH_NAME: ${{ env.BRANCH_NAME }}
           WORKFLOW_ID: ${{ env.WORKFLOW_ID }}
-        
+
       - name: Upload test logs
         uses: actions/upload-artifact@v4
         with:
@@ -242,4 +242,3 @@ jobs:
           R -e 'sessionInfo()'
           sudo apt install tree -y
           tree .
-