mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 16:02:02 +02:00
unit test fix
This commit is contained in:
3
.github/workflows/check-pr.yaml
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3
.github/workflows/check-pr.yaml
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@ -32,6 +32,9 @@ name: R-code-check-PR
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jobs:
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R-code-check-PR:
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# do not run if we are the authors - the other checks will already run
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if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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1
.github/workflows/check.yaml
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1
.github/workflows/check.yaml
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@ -131,6 +131,7 @@ jobs:
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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# this is a required value to run the unit tests:
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R_RUN_TINYTEST: true
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run: |
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cd ..
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42
.github/workflows/codecovr.yaml
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42
.github/workflows/codecovr.yaml
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@ -33,54 +33,30 @@ name: code-coverage
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jobs:
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code-coverage:
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: release
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- uses: r-lib/actions/setup-pandoc@v2
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# with:
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# pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
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# use RStudio Package Manager to quickly install packages
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use-public-rspm: true
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- name: Query dependencies
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# this will change once a week, so it will cache dependency updates
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run: |
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writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
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shell: Rscript {0}
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
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- name: Unpack AMR and install R dependencies
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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- name: Show session info
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run: |
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options(width = 100)
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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extra-packages: any::covr
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- name: Test coverage
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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run: |
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install.packages("covr", repos = "https://cran.rstudio.com/")
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library(AMR)
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library(tinytest)
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x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
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print(x)
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shell: Rscript {0}
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29
.github/workflows/lintr.yaml
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29
.github/workflows/lintr.yaml
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@ -33,34 +33,23 @@ name: lintr
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jobs:
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lintr:
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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r-version: release
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# use RStudio Package Manager to quickly install packages
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use-public-rspm: true
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- name: Install dependencies
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run: |
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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("lintr")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::lintr
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- name: Lint
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run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
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