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Merge pull request datashield#613 from villegar/v6.3.5-dev
Add test suite workflow - similar to dsBase
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‎.github/workflows/dsBaseClient_test_suite.yaml‎

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################################################################################
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# DataSHIELD GHA test suite - dsBaseClient
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# Adapted from `armadillo_azure-pipelines.yml` by Roberto Villegas-Diaz
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#
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# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
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# /dsBaseClient <- Checked out version of datashield/dsBaseClient
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# /dsBaseClient/logs <- Where results of tests and logs are collated
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# /testStatus <- Checked out version of datashield/testStatus
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#
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# As of Sept. 2025 this takes ~ 95 mins to run.
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################################################################################
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name: dsBaseClient tests' suite
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on:
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push:
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schedule:
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- cron: '0 0 * * 0' # Weekly
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- cron: '0 1 * * *' # Nightly
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jobs:
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dsBaseClient_test_suite:
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runs-on: ubuntu-latest
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timeout-minutes: 120
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permissions:
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contents: read
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# These should all be constant, except TEST_FILTER. This can be used to test
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# subsets of test files in the testthat directory. Options are like:
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# '*' <- Run all tests.
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# 'asNumericDS*' <- Run all asNumericDS tests, i.e. all the arg, etc. tests.
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# '*_smk_*' <- Run all the smoke tests for all functions.
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env:
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TEST_FILTER: '_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-'
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_r_check_system_clock_: 0
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WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
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PROJECT_NAME: dsBaseClient
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BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
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REPO_OWNER: ${{ github.repository_owner }}
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R_KEEP_PKG_SOURCE: yes
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GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}
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steps:
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- name: Checkout dsBaseClient
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uses: actions/checkout@v4
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with:
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path: dsBaseClient
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- name: Checkout testStatus
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if: ${{ github.actor != 'nektos/act' }} # for local deployment only
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uses: actions/checkout@v4
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with:
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repository: ${{ env.REPO_OWNER }}/testStatus
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ref: master
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path: testStatus
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persist-credentials: false
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token: ${{ env.GITHUB_TOKEN }}
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- name: Uninstall default MySQL
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run: |
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curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
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sudo service mysql stop || true
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sudo apt-get update
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sudo apt-get remove --purge mysql-client mysql-server mysql-common -y
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sudo apt-get autoremove -y
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sudo apt-get autoclean -y
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sudo rm -rf /var/lib/mysql/
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: release
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http-user-agent: release
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use-public-rspm: true
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- name: Install R and dependencies
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run: |
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sudo apt-get install --no-install-recommends software-properties-common dirmngr -y
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wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
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sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
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sudo apt-get update -qq
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y
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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')"
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sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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dependencies: 'c("Imports")'
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extra-packages: |
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any::rcmdcheck
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cran::devtools
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cran::git2r
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cran::RCurl
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cran::readr
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cran::magrittr
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cran::xml2
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cran::purrr
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cran::dplyr
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cran::stringr
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cran::tidyr
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cran::quarto
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cran::knitr
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cran::kableExtra
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cran::rmarkdown
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cran::downlit
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needs: check
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- name: Check manual updated
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run: |
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orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
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R -q -e "devtools::document()"
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new_sum=$(find man -type f | sort -u | xargs cat | md5sum)
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if [ "$orig_sum" != "$new_sum" ]; then
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echo "Your committed man/*.Rd files are out of sync with the R headers."
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exit 1
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fi
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working-directory: dsBaseClient
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continue-on-error: true
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- name: Devtools checks
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run: |
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R -q -e "devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout
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grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
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working-directory: dsBaseClient
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continue-on-error: true
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- name: Start Armadillo docker-compose
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run: docker compose -f docker-compose_armadillo.yml up -d --build
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working-directory: dsBaseClient
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- name: Install test datasets
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run: |
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sleep 60
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R -q -f "molgenis_armadillo-upload_testing_datasets.R"
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working-directory: dsBaseClient/tests/testthat/data_files
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- name: Install dsBase to Armadillo
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run: |
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curl -u admin:admin -X GET http://localhost:8080/packages
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curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
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sleep 60
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docker restart dsbaseclient-armadillo-1
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sleep 30
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curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
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working-directory: dsBaseClient
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- name: Run tests with coverage & JUnit report
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run: |
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mkdir -p logs
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R -q -e "devtools::reload();"
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R -q -e '
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write.csv(
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covr::coverage_to_list(
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covr::package_coverage(
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type = c("none"),
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code = c('"'"'
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output_file <- file("test_console_output.txt");
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sink(output_file);
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sink(output_file, type = "message");
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junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml"));
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progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
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multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
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options("datashield.return_errors" = FALSE, "default_driver" = "ArmadilloDriver");
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testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
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)
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)
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),
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"coveragelist.csv"
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)'
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mv coveragelist.csv logs/
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mv test_* logs/
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working-directory: dsBaseClient
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- name: Check for JUnit errors
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run: |
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issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
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echo "Number of testsuites with issues: $issue_count"
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sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true
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cat issues.log || true
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# continue with workflow even when some tests fail
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exit 0
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working-directory: dsBaseClient/logs
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- name: Write versions to file
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run: |
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echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt
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echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
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echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
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working-directory: dsBaseClient/logs
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- name: Parse results from testthat and covr
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run: |
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Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
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working-directory: dsBaseClient
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- name: Render report
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run: |
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cd testStatus
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mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/
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# Copy logs to new logs directory location
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cp -rv ../dsBaseClient/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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cp -rv ../dsBaseClient/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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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))'
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mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
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cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest
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env:
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PROJECT_NAME: ${{ env.PROJECT_NAME }}
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BRANCH_NAME: ${{ env.BRANCH_NAME }}
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WORKFLOW_ID: ${{ env.WORKFLOW_ID }}
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- name: Upload test logs
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uses: actions/upload-artifact@v4
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with:
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name: dsbaseclient-logs
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path: testStatus/new
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- name: Dump environment info
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run: |
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echo -e "\n#############################"
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echo -e "ls /: ######################"
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ls -al .
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echo -e "\n#############################"
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echo -e "lscpu: ######################"
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lscpu
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echo -e "\n#############################"
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echo -e "memory: #####################"
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free -m
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echo -e "\n#############################"
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echo -e "env: ########################"
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env
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echo -e "\n#############################"
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echo -e "R sessionInfo(): ############"
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R -e 'sessionInfo()'
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sudo apt install tree -y
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tree .
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