chore: build image which can be reused to speed up CI #63
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Check failure on line 1 in .github/workflows/dsBaseClient_test_suite.yaml
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| # DataSHIELD GHA test suite - dsBaseClient | ||
| # Adapted from `armadillo_azure-pipelines.yml` by Roberto Villegas-Diaz | ||
| # | ||
| # Inside the root directory $(Pipeline.Workspace) will be a file tree like: | ||
| # /dsBaseClient <- Checked out version of datashield/dsBaseClient | ||
| # /dsBaseClient/logs <- Where results of tests and logs are collated | ||
| # /testStatus <- Checked out version of datashield/testStatus | ||
| # | ||
| # As of Sept. 2025 this takes ~ 95 mins to run. | ||
| ################################################################################ | ||
| name: dsBaseClient tests' suite | ||
| on: | ||
| push: | ||
| schedule: | ||
| - cron: '0 0 * * 0' # Weekly | ||
| - cron: '0 1 * * *' # Nightly | ||
| jobs: | ||
| dsBaseClient_test_suite: | ||
| runs-on: ubuntu-latest | ||
| timeout-minutes: 120 | ||
| permissions: | ||
| contents: read | ||
| # This logic automatically selects the image tag | ||
| container: | ||
| image: >- | ||
| ghcr.io/${{ github.repository_owner }}/ds-base-env:${{ | ||
| startsWith(github.ref_name, 'dev-') && | ||
| replace(github.ref_name, 'dev-', 'v') || | ||
| 'latest' | ||
| }}-dev | ||
| options: --user root -v /var/run/docker.sock:/var/run/docker.sock | ||
| env: | ||
| TEST_FILTER: '_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-' | ||
| _r_check_system_clock_: 0 | ||
| WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }} | ||
| PROJECT_NAME: dsBaseClient | ||
| BRANCH_NAME: ${{ github.head_ref || github.ref_name }} | ||
| REPO_OWNER: ${{ github.repository_owner }} | ||
| R_KEEP_PKG_SOURCE: yes | ||
| GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }} | ||
| steps: | ||
| - name: Checkout dsBaseClient | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| path: dsBaseClient | ||
| - 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: ${{ env.GITHUB_TOKEN }} | ||
| - name: Install PR version of dsBaseClient | ||
| run: R CMD INSTALL dsBaseClient | ||
| - name: Check manual updated | ||
| run: | | ||
| orig_sum=$(find man -type f | sort -u | xargs cat | md5sum) | ||
| R -q -e "devtools::document()" | ||
| new_sum=$(find man -type f | sort -u | xargs cat | md5sum) | ||
| if [ "$orig_sum" != "$new_sum" ]; then | ||
| echo "Your committed man/*.Rd files are out of sync with the R headers." | ||
| exit 1 | ||
| fi | ||
| working-directory: dsBaseClient | ||
| continue-on-error: true | ||
| - name: Devtools checks | ||
| run: | | ||
| R -q -e "devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout | ||
| grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout | ||
| working-directory: dsBaseClient | ||
| continue-on-error: true | ||
| - name: Start Armadillo docker-compose | ||
| run: docker compose -f docker-compose_armadillo.yml up -d --build | ||
| working-directory: dsBaseClient | ||
| - name: Install test datasets | ||
| run: | | ||
| sleep 60 | ||
| R -q -f "molgenis_armadillo-upload_testing_datasets.R" | ||
| working-directory: dsBaseClient/tests/testthat/data_files | ||
| - name: Install dsBase to Armadillo | ||
| run: | | ||
| curl -u admin:admin -X GET http://localhost:8080/packages | ||
| curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_7.0.0-permissive.tar.gz" -X POST http://localhost:8080/install-package | ||
| sleep 60 | ||
| docker restart dsbaseclient-armadillo-1 | ||
| sleep 30 | ||
| curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase | ||
| working-directory: dsBaseClient | ||
| - name: Run tests with coverage & JUnit report | ||
| run: | | ||
| mkdir -p logs | ||
| R -q -e "devtools::reload();" | ||
| R -q -e ' | ||
| write.csv( | ||
| covr::coverage_to_list( | ||
| covr::package_coverage( | ||
| type = c("none"), | ||
| code = c('"'"' | ||
| output_file <- file("test_console_output.txt"); | ||
| sink(output_file); | ||
| sink(output_file, type = "message"); | ||
| junit_rep <- testthat::JunitReporter$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)); | ||
| options("datashield.return_errors" = FALSE, "default_driver" = "ArmadilloDriver"); | ||
| 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/ | ||
| working-directory: dsBaseClient | ||
| - 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: $issue_count" | ||
| sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true | ||
| cat issues.log || true | ||
| exit 0 | ||
| working-directory: dsBaseClient/logs | ||
| - name: Write versions to file | ||
| run: | | ||
| echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt | ||
| echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt | ||
| echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt | ||
| working-directory: dsBaseClient/logs | ||
| - name: Parse results from testthat and covr | ||
| run: | | ||
| Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '([^:]+)' '(?<=::)[^:]+(?=::)' | ||
| working-directory: dsBaseClient | ||
| 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 }}/${{ env.WORKFLOW_ID }}/ | ||
