From d2252b1062babf531ef0eef4e40e93dfaae0a99d Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 5 Oct 2022 08:10:26 +0200 Subject: [PATCH] unit test split --- .github/workflows/check-pr.yaml | 82 ---------------- .github/workflows/check.yaml | 163 -------------------------------- DESCRIPTION | 2 +- NEWS.md | 2 +- R/rsi.R | 2 +- man/as.rsi.Rd | 2 +- 6 files changed, 4 insertions(+), 249 deletions(-) delete mode 100644 .github/workflows/check-pr.yaml delete mode 100644 .github/workflows/check.yaml diff --git a/.github/workflows/check-pr.yaml b/.github/workflows/check-pr.yaml deleted file mode 100644 index 0851f7a46..000000000 --- a/.github/workflows/check-pr.yaml +++ /dev/null @@ -1,82 +0,0 @@ -# ==================================================================== # -# TITLE # -# AMR: An R Package for Working with Antimicrobial Resistance Data # -# # -# SOURCE # -# https://github.com/msberends/AMR # -# # -# CITE AS # -# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # -# (2022). AMR: An R Package for Working with Antimicrobial Resistance # -# Data. Journal of Statistical Software, 104(3), 1-31. # -# doi:10.18637/jss.v104.i03 # -# # -# Developed at the University of Groningen, the Netherlands, in # -# collaboration with non-profit organisations Certe Medical # -# Diagnostics & Advice, and University Medical Center Groningen. # -# # -# This R package is free software; you can freely use and distribute # -# it for both personal and commercial purposes under the terms of the # -# GNU General Public License version 2.0 (GNU GPL-2), as published by # -# the Free Software Foundation. # -# We created this package for both routine data analysis and academic # -# research and it was publicly released in the hope that it will be # -# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # -# # -# Visit our website for the full manual and a complete tutorial about # -# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # -# ==================================================================== # - -on: - pull_request: - # run in each PR in this repo - branches: '**' - -name: R-code-check-PR - -jobs: - R-code-check-PR: - runs-on: ${{ matrix.config.os }} - - continue-on-error: ${{ matrix.config.allowfail }} - - name: ${{ matrix.config.os }} (R-${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macOS-latest, r: 'devel', allowfail: true} - - {os: macOS-latest, r: 'release', allowfail: false} - - {os: ubuntu-latest, r: 'devel', allowfail: true} - - {os: ubuntu-latest, r: 'release', allowfail: false} - - {os: windows-latest, r: 'devel', allowfail: true} - - {os: windows-latest, r: 'release', allowfail: false} - - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - R_KEEP_PKG_SOURCE: yes - - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-pandoc@v2 - - - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - # use RStudio Package Manager to quickly install packages - use-public-rspm: true - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::rcmdcheck - needs: check - - - uses: r-lib/actions/check-r-package@v2 - env: - _R_CHECK_LENGTH_1_CONDITION_: verbose - _R_CHECK_LENGTH_1_LOGIC2_: verbose - # during 'R CMD check', R_LIBS_USER will be overwritten, so: - R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} - R_RUN_TINYTEST: true diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml deleted file mode 100644 index 00d26914d..000000000 --- a/.github/workflows/check.yaml +++ /dev/null @@ -1,163 +0,0 @@ -# ==================================================================== # -# TITLE # -# AMR: An R Package for Working with Antimicrobial Resistance Data # -# # -# SOURCE # -# https://github.com/msberends/AMR # -# # -# CITE AS # -# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # -# (2022). AMR: An R Package for Working with Antimicrobial Resistance # -# Data. Journal of Statistical Software, 104(3), 1-31. # -# doi:10.18637/jss.v104.i03 # -# # -# Developed at the University of Groningen, the Netherlands, in # -# collaboration with non-profit organisations Certe Medical # -# Diagnostics & Advice, and University Medical Center Groningen. # -# # -# This R package is free software; you can freely use and distribute # -# it for both personal and commercial purposes under the terms of the # -# GNU General Public License version 2.0 (GNU GPL-2), as published by # -# the Free Software Foundation. # -# We created this package for both routine data analysis and academic # -# research and it was publicly released in the hope that it will be # -# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # -# # -# Visit our website for the full manual and a complete tutorial about # -# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # -# ==================================================================== # - -on: - push: - # run after a git push on any branch in this repo - branches: '**' - schedule: - # run a schedule everyday at 1 AM. - # this is to check that all dependencies are still available (see R/zzz.R) - - cron: '0 1 * * *' - -name: R-code-check - -jobs: - R-code-check: - runs-on: ${{ matrix.config.os }} - - continue-on-error: ${{ matrix.config.allowfail }} - - name: ${{ matrix.config.os }} (R-${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - # test all systems against all released versions of R >= 3.0, we support them all! - - {os: macOS-latest, r: 'devel', allowfail: true} - - {os: macOS-latest, r: '4.2', allowfail: false} - - {os: macOS-latest, r: '4.1', allowfail: false} - - {os: macOS-latest, r: '4.0', allowfail: false} - - {os: macOS-latest, r: '3.6', allowfail: false} - - {os: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.5.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - - {os: windows-latest, r: 'devel', allowfail: true} - - {os: windows-latest, r: '4.2', allowfail: false} - - {os: windows-latest, r: '4.1', allowfail: false} - - {os: windows-latest, r: '4.0', allowfail: false} - - {os: windows-latest, r: '3.6', allowfail: false} - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - R_REPOSITORIES: "https://cran.rstudio.com" - - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@v2 - - - name: Install Linux dependencies - if: runner.os == 'Linux' - # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). - # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version - # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11 - run: | - sudo apt install -y libssl-dev libxml2-dev libcurl4-openssl-dev - - - name: Restore cached R packages - # this step will add the step 'Post Restore cached R packages' on a succesful run - uses: actions/cache@v2 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4 - - - name: Install R dependencies - if: always() - run: | - Rscript -e "source('data-raw/_install_deps.R')" - shell: bash - - - name: Show session info - if: always() - run: | - options(width = 100) - utils::sessionInfo() - as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] - shell: Rscript {0} - - - name: Remove vignettes on R without knitr support - if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3' - # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite - run: | - rm -rf vignettes - Rscript -e "writeLines(readLines('DESCRIPTION')[!grepl('VignetteBuilder', readLines('DESCRIPTION'))], 'DESCRIPTION2')" - rm DESCRIPTION - mv DESCRIPTION2 DESCRIPTION - shell: bash - - - name: Run R CMD check - if: always() - env: - # see https://rstudio.github.io/r-manuals/r-ints/Tools.html for an overview - _R_CHECK_CRAN_INCOMING_: false - _R_CHECK_DEPENDS_ONLY_: true - _R_CHECK_LENGTH_1_CONDITION_: verbose - _R_CHECK_LENGTH_1_LOGIC2_: verbose - # no check for old R versions - these packages require higher R versions - _R_CHECK_RD_XREFS_: ${{ matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' && matrix.config.r != '3.3' && matrix.config.r != '3.4' }} - _R_CHECK_FORCE_SUGGESTS_: false - R_CHECK_CONSTANTS: 5 - R_JIT_STRATEGY: 3 - # during 'R CMD check', R_LIBS_USER will be overwritten, so: - R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} - # this is a required value to run the unit tests: - R_RUN_TINYTEST: true - run: | - cd .. - R CMD build AMR - R CMD check --as-cran --no-manual --run-donttest --run-dontrun AMR_*.tar.gz - shell: bash - - - name: Show unit tests output - if: always() - run: | - cd ../AMR.Rcheck - find . -name 'tinytest.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Upload artifacts - if: always() - uses: actions/upload-artifact@v2 - with: - name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }} - path: ${GITHUB_WORKSPACE}.Rcheck diff --git a/DESCRIPTION b/DESCRIPTION index db489eba8..8a0f541af 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9031 +Version: 1.8.2.9032 Date: 2022-10-05 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 561a93e4e..7c367597f 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9031 +# AMR 1.8.2.9032 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/rsi.R b/R/rsi.R index 526811c6a..db2aa1d37 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -164,7 +164,7 @@ #' as.rsi() # automatically determines urine isolates #' #' df %>% -#' mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE) +#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE) #' } #' #' # For CLEANING existing R/SI values ------------------------------------ diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index a701909c4..dd947756a 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -229,7 +229,7 @@ if (require("dplyr")) { as.rsi() # automatically determines urine isolates df \%>\% - mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE) + mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE) } # For CLEANING existing R/SI values ------------------------------------