dsBase tests' suite #192
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| ################################################################################ | |
| # DataSHIELD GHA test suite - dsBase | |
| # Adapted from `azure-pipelines.yml` by Roberto Villegas-Diaz | |
| # | |
| # Inside the root directory $(Pipeline.Workspace) will be a file tree like: | |
| # /dsBase <- Checked out version of datashield/dsBase | |
| # /dsBase/logs <- Where results of tests and logs are collated | |
| # /testStatus <- Checked out version of datashield/testStatus | |
| # | |
| # As of Jul 2025 this takes ~ 9 mins to run. | |
| ################################################################################ | |
| name: dsBase tests' suite | |
| on: | |
| push: | |
| schedule: | |
| - cron: '0 0 * * 0' # Weekly | |
| jobs: | |
| dsBase_test_suite: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 120 | |
| permissions: | |
| contents: write | |
| # 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. | |
| # 'asNumericDS*' <- Run all asNumericDS tests, i.e. all the arg, etc. tests. | |
| # '*_smk_*' <- Run all the smoke tests for all functions. | |
| env: | |
| TEST_FILTER: '*' | |
| _r_check_system_clock_: 0 | |
| WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }} | |
| PROJECT_NAME: dsBase | |
| BRANCH_NAME: ${{ github.ref_name }} | |
| REPO_OWNER: ${{ github.repository_owner }} | |
| R_KEEP_PKG_SOURCE: yes | |
| GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }} | |
| steps: | |
| - name: Checkout dsBase | |
| uses: actions/checkout@v4 | |
| with: | |
| path: dsBase | |
| - name: Checkout testStatus | |
| if: ${{ github.actor != 'nektos/act' }} # for local deployment only | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: ${{ env.REPO_OWNER }}/testStatus | |
| ref: master | |
| path: testStatus | |
| persist-credentials: false | |
| token: ${{ env.GITHUB_TOKEN }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| http-user-agent: release | |
| use-public-rspm: true | |
| - name: Install dsBase | |
| run: | | |
| Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds", "usethis", "devtools"), dependencies = TRUE)' | |
| R CMD INSTALL ./dsBase | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: 'c("Imports")' | |
| extra-packages: | | |
| any::rcmdcheck | |
| cran::devtools | |
| cran::git2r | |
| cran::RCurl | |
| cran::readr | |
| cran::magrittr | |
| cran::xml2 | |
| cran::purrr | |
| cran::dplyr | |
| cran::stringr | |
| cran::tidyr | |
| cran::quarto | |
| cran::knitr | |
| cran::kableExtra | |
| cran::rmarkdown | |
| cran::downlit | |
| needs: check | |
| - name: Check man files up-to-date | |
| run: | | |
| orig_sum=$(find man -type f | sort -u | xargs cat | md5sum) | |
| R -e "devtools::document()" | |
| new_sum=$(find man -type f | sort -u | xargs cat | md5sum) | |
| if [ "$orig_sum" != "$new_sum" ]; then | |
| echo "Your committed manual files (man/*.Rd) are out of sync with the R files. Run devtools::document() locally then commit." | |
| exit 1 | |
| else | |
| echo "Documentation up-to-date." | |
| fi | |
| working-directory: dsBase | |
| continue-on-error: true | |
| - name: Run devtools::check | |
| run: | | |
| R -q -e "library('devtools'); devtools::check(args = c('--no-tests', '--no-examples'))" | tee ../check.Rout | |
| grep -q "^0 errors" ../check.Rout && grep -q " 0 warnings" ../check.Rout && grep -q " 0 notes" ../check.Rout | |
| working-directory: dsBase | |
| continue-on-error: true | |
| - name: Run tests with coverage & JUnit report | |
| run: | | |
| mkdir -p logs | |
| R -q -e "devtools::reload();" | |
| R -q -e ' | |
| write.csv( | |
| covr::coverage_to_list( | |
| covr::package_coverage( | |
| type = c("none"), | |
| code = c('"'"' | |
| output_file <- file("test_console_output.txt"); | |
| sink(output_file); | |
| sink(output_file, type = "message"); | |
| junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml")); | |
| progress_rep <- testthat::ProgressReporter$new(max_failures = 999999); | |
| multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep)); | |
| testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"' | |
| ) | |
| ) | |
| ), | |
| "coveragelist.csv" | |
| )' | |
| mv coveragelist.csv logs/ | |
| mv test_* logs/ | |
| grep -q " FAIL 0 " logs/test_console_output.txt | |
| working-directory: dsBase | |
| - name: Check for JUnit errors | |
| run: | | |
| issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true) | |
| echo "Number of testsuites with issues: $issue_count" | |
| sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true | |
| cat issues.log || true | |
| exit $issue_count | |
| working-directory: dsBase/logs | |
| - name: Write versions to file | |
| run: | | |
| echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt | |
| echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt | |
| echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt | |
| Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ env.WORKFLOW_ID }}.txt | |
| working-directory: dsBase/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 }} '[^-:.]+' '(?<=::)[^:]+(?=::)' | |
| working-directory: dsBase | |
| env: | |
| PROJECT_NAME: ${{ env.PROJECT_NAME }} | |
| BRANCH_NAME: ${{ env.BRANCH_NAME }} | |
| - name: Render report | |
| run: | | |
| cd testStatus | |
| mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ | |
| mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/ | |
| # Copy logs to new logs directory location | |
| cp -rv ../${{ env.PROJECT_NAME }}/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/ | |
| cp -rv ../${{ env.PROJECT_NAME }}/logs/${{ 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 }}/latest/index.html | |
| 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: | |
| name: dsbase-logs | |
| path: testStatus/new | |
| - name: Dump environment info | |
| run: | | |
| echo -e "\n#############################" | |
| echo -e "ls /: ######################" | |
| ls -al . | |
| echo -e "\n#############################" | |
| echo -e "lscpu: ######################" | |
| lscpu | |
| echo -e "\n#############################" | |
| echo -e "memory: #####################" | |
| free -m | |
| echo -e "\n#############################" | |
| echo -e "env: ########################" | |
| env | |
| echo -e "\n#############################" | |
| echo -e "R sessionInfo(): ############" | |
| R -e 'sessionInfo()' | |
| sudo apt install tree -y | |
| tree . | |