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Update to align with V6.3.5 dev changes
Update to align with V6.3.5 dev changes
2 parents 195e4b5 + 3563df7 commit a4cf3a7

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‎.Rbuildignore‎

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^data$
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^docs$
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^pkgdown$
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^\.circleci$
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^\.circleci/config\.yml$
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^\.github$
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^cran-comments\.md$

‎.circleci/config.yml‎

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# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
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version: 2.1
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jobs:
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dsbase:
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docker:
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- image: cimg/base:current
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resource_class: small
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steps:
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- checkout
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- setup_remote_docker:
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docker_layout_caching: true
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- run: |
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echo "Building"
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echo " Repo Name: " $CIRCLE_PROJECT_REPONAME
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echo " Branch: " $CIRCLE_BRANCH
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echo " Tag: " $CIRCLE_TAG
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- run:
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command: |
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sudo apt-get update -y
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sudo apt-get install -y r-base-core cmake
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- run:
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command: |
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sudo apt-get install -y libxml2-dev
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- run:
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command: |
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echo "options(Ncpus=4)" >> ~/.Rprofile
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sudo Rscript -e "install.packages('RANN', dependencies=TRUE)"
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sudo Rscript -e "install.packages('stringr', dependencies=TRUE)"
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sudo Rscript -e "install.packages('lme4', dependencies=TRUE)"
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sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
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sudo Rscript -e "install.packages('reshape2', dependencies=TRUE)"
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sudo Rscript -e "install.packages('polycor', dependencies=TRUE)"
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sudo Rscript -e "install.packages('splines', dependencies=TRUE)"
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sudo Rscript -e "install.packages('gamlss', dependencies=TRUE)"
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sudo Rscript -e "install.packages('gamlss.dist', dependencies=TRUE)"
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sudo Rscript -e "install.packages('mice', dependencies=TRUE)"
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sudo Rscript -e "install.packages('childsds', dependencies=TRUE)"
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sudo Rscript -e "install.packages('xml2', dependencies=TRUE)"
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sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
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sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
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sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
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- run:
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command: |
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sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'")'
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workflows:
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build:
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jobs:
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- dsbase

‎.github/.gitignore‎

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*.html

‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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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: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'

‎.github/workflows/dsBase_test_suite.yaml‎

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################################################################################
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# DataSHIELD GHA test suite - dsBase
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# Adapted from `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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# /dsBase <- Checked out version of datashield/dsBase
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# /dsBase/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 Jul 2025 this takes ~ 9 mins to run.
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################################################################################
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name: dsBase 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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dsBase_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: write
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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: '*'
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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: dsBase
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BRANCH_NAME: ${{ 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 dsBase
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uses: actions/checkout@v4
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with:
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path: dsBase
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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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- 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 dsBase
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run: |
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Rscript -e 'install.packages(c("RANN", "stringr", "lme4", "dplyr", "reshape2", "polycor", "gamlss", "gamlss.dist", "mice", "childsds", "usethis", "devtools"), dependencies = TRUE)'
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R CMD INSTALL ./dsBase
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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 man files up-to-date
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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 -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 manual files (man/*.Rd) are out of sync with the R files. Run devtools::document() locally then commit."
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exit 1
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else
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echo "Documentation up-to-date."
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fi
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working-directory: dsBase
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continue-on-error: true
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- name: Run devtools::check
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run: |
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R -q -e "library('devtools'); devtools::check(args = c('--no-tests', '--no-examples'))" | tee ../check.Rout
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grep -q "^0 errors" ../check.Rout && grep -q " 0 warnings" ../check.Rout && grep -q " 0 notes" ../check.Rout
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working-directory: dsBase
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continue-on-error: true
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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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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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grep -q " FAIL 0 " logs/test_console_output.txt
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working-directory: dsBase
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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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exit $issue_count
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working-directory: dsBase/logs
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- name: Write versions to file
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run: |
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echo "branch:${{ 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)" >> ${{ env.WORKFLOW_ID }}.txt
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working-directory: dsBase/logs
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- name: Parse results from testthat and covr
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run: |
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Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
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working-directory: dsBase
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- name: Render report
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run: |
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cd testStatus
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mkdir -p new/logs/${{ 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 }}/${{ env.BRANCH_NAME }}/latest/
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# Copy logs to new logs directory location
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cp -rv ../${{ env.PROJECT_NAME }}/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
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cp -rv ../${{ env.PROJECT_NAME }}/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: dsbase-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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‎.github/workflows/pkgdown.yaml‎

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

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