Updates to align with v6.3.5-dev

.Rbuildignore

@@ -19,6 +19,7 @@
 ^docs$
 ^dsBase_6.4.0.tar.gz$
 ^dsBase_6.4.0-permissive.tar.gz$
-^dsDanger_6.3.1.tar.gz$
+^dsDanger_6.3.4.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/dsBaseClient_test_suite.yaml

@@ -0,0 +1,247 @@
+################################################################################
+# 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 * * 6'   # Weekly (on Saturdays @ 0.00)
+
+jobs:
+  dsBaseClient_test_suite:
+    runs-on: ubuntu-latest
+    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.
+    # 'asNumericDS*'    <- Run all asNumericDS tests, i.e. all the arg, etc. tests.
+    # '*_smk_*'         <- Run all the smoke tests for all functions.
+    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: Uninstall default MySQL
+        run: |
+          curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
+          sudo service mysql stop || true
+          sudo apt-get update
+          sudo apt-get remove --purge mysql-client mysql-server mysql-common -y
+          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
+        with:
+          r-version: release
+          http-user-agent: release
+          use-public-rspm: true
+
+      - name: Install R and dependencies
+        run: |
+          sudo apt-get install --no-install-recommends software-properties-common dirmngr -y
+          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
+          sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+          sudo apt-get update -qq
+          sudo apt-get upgrade -y
+          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
+          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y
+          sudo R -q -e "install.packages(c('devtools','covr','fields','meta','metafor','ggplot2','gridExtra','data.table','DSI','DSOpal','DSLite','MolgenisAuth','MolgenisArmadillo','DSMolgenisArmadillo','DescTools','e1071'), repos='https://cloud.r-project.org')"
+          sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'c("Imports")'
+          extra-packages: |
+            any::rcmdcheck
+            cran::devtools
+            cran::git2r
+            cran::RCurl
+            cran::readr
+            cran::magrittr
+            cran::xml2
+            cran::purrr
+            cran::dplyr
+            cran::stringr
+            cran::tidyr
+            cran::quarto
+            cran::knitr
+            cran::kableExtra
+            cran::rmarkdown
+            cran::downlit
+          needs: check
+
+      - name: Check manual updated
+        run: |
+          orig_sum=$(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_6.3.5-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: $issue_count"
+          sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true
+          cat issues.log || true
+          # continue with workflow even when some tests fail
+          exit 0
+        working-directory: dsBaseClient/logs
+
+      - name: Write versions to file
+        run: |
+          echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt
+          echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
+          echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
+          Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ 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 }} '([^:]+)' '(?<=::)[^:]+(?=::)'
+        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 }}/${{ env.WORKFLOW_ID }}/
+          mkdir -p new/docs/${{ 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:
+          name: dsbaseclient-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 .

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,23 +1,27 @@
 Package: dsBaseClient
-Title: DataSHIELD Client Functions
+Title: 'DataSHIELD' Client Side Base Functions
 Version: 6.4.0.9000
-Description: Base DataSHIELD functions for the client side. DataSHIELD is a software package which allows
-    you to do non-disclosive federated analysis on sensitive data. DataSHIELD analytic functions have
+Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows
+    you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
     been designed to only share non disclosive summary statistics, with built in automated output
     checking based on statistical disclosure control. With data sites setting the threshold values for
-    the automated output checks.
+    the automated output checks. For more details, see citation("dsBaseClient").
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-5799-9634")),
              person(given = "Rebecca",
                     family = "Wilson",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0003-2294-593X")),
              person(given = "Olly",
                     family = "Butters",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0003-0354-8461")),
              person(given = "Patricia",
                     family = "Ryser-Welch",
-                    role = c("aut")),
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-0070-0264")),
              person(given = "Alex",
                     family = "Westerberg",
                     role = c("aut")),
@@ -37,6 +41,17 @@ Authors@R: c(person(given = "Paul",
                     role = c("aut"),
                     email = "yannick.marcon@obiba.org",
                     comment = c(ORCID = "0000-0003-0138-2023")),
+             person(given = "Tom",
+                    family = "Bishop",
+                    role = c("aut")),
+             person(given = "Amadou",
+                    family = "Gaye",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0002-1180-2792")),
+             person(given = "Xavier",
+                    family = "Escribà-Montagut",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0003-2888-8948")),
              person(given = "Stuart",
                     family = "Wheater",
                     role = c("aut", "cre"),
@@ -58,12 +73,14 @@ Imports:
 Suggests:
     lme4,
     httr,
+    spelling,
     tibble,
     testthat,
     e1071,
     DescTools,
     DSOpal,
     DSMolgenisArmadillo,
     DSLite
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
+Language: en-GB