Merge pull request #637 from StuartWheater/v6.3.5-dev

Update 'perf' support and fix typo in variable name

Author: StuartWheater

.github/workflows/dsBaseClient_test_suite.yaml

@@ -22,7 +22,7 @@ jobs:
     timeout-minutes: 180
     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.
@@ -33,7 +33,7 @@ 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' }}
@@ -53,7 +53,7 @@ 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 -
@@ -63,7 +63,7 @@ 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
@@ -83,29 +83,29 @@ 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=$(find man -type f | sort -u | xargs cat | md5sum)
@@ -124,7 +124,7 @@ jobs:
           grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
         working-directory: dsBaseClient
         continue-on-error: true
-        
+
       - name: Start Armadillo docker-compose
         run: docker compose -f docker-compose_armadillo.yml up -d --build
         working-directory: dsBaseClient
@@ -144,7 +144,7 @@ jobs:
           sleep 30
           curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
         working-directory: dsBaseClient
-      
+
       - name: Run tests with coverage & JUnit report
         run: |
           mkdir -p logs
@@ -168,11 +168,11 @@ jobs:
               ),
               "coveragelist.csv"
             )'
-          
+
           mv coveragelist.csv logs/
           mv test_* logs/
         working-directory: dsBaseClient
-      
+
       - name: Check for JUnit errors
         run: |
           issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
@@ -190,7 +190,7 @@ jobs:
           echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
           Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ 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/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '([^:]+)' '(?<=::)[^:]+(?=::)'
@@ -202,24 +202,24 @@ jobs:
       - 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:
@@ -245,4 +245,3 @@ jobs:
           R -e 'sessionInfo()'
           sudo apt install tree -y
           tree .
-        

opal_azure-pipelines.yml

@@ -233,7 +233,7 @@ jobs:
     # Install dsBase.
     # If previous steps have failed then don't run.
   - bash: |
-      R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
+      R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
 
       R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"
 

tests/testthat/perf_tests/perf_rate.R

@@ -8,7 +8,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #-------------------------------------------------------------------------------
 
-.perf.reference.filename <- 'perf_files/default_perf_profile.csv'
+.perf.reference.filename      <- 'perf_files/default_perf_profile.csv'
+.perf.reference.save.filename <- NULL
 
 .perf.reference <- NULL
 
@@ -22,7 +23,13 @@ perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance.
 
     .perf.reference[nrow(.perf.reference)+1,] <- c(perf.ref.name, rate, tolerance.lower, tolerance.upper)
 
-    write.csv(.perf.reference, .perf.reference.filename, row.names = FALSE)
+    if (is.null(.perf.reference.save.filename))
+    {
+        .perf.reference.save.filename <<- base::tempfile(pattern = "perf_file_", fileext = ".csv")
+        message(paste0("Additional perf record added to '", .perf.reference.save.filename, "'"))
+    }
+
+    write.csv(.perf.reference, .perf.reference.save.filename, row.names = FALSE)
 
     .perf.reference <<- .perf.reference
 }