1
0
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:
2022-08-28 19:17:12 +02:00
parent 0d67db4f32
commit 71db246d5c
27 changed files with 51 additions and 74 deletions

View File

@ -32,6 +32,9 @@ name: R-code-check-PR
jobs:
R-code-check-PR:
# do not run if we are the authors - the other checks will already run
if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
runs-on: ${{ matrix.config.os }}
continue-on-error: ${{ matrix.config.allowfail }}

View File

@ -131,6 +131,7 @@ jobs:
_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 }}
# this is a required value to run the unit tests:
R_RUN_TINYTEST: true
run: |
cd ..

View File

@ -33,54 +33,30 @@ name: code-coverage
jobs:
code-coverage:
runs-on: macOS-latest
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-r@v2
with:
r-version: release
- uses: r-lib/actions/setup-pandoc@v2
# with:
# pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
# use RStudio Package Manager to quickly install packages
use-public-rspm: true
- name: Query dependencies
# this will change once a week, so it will cache dependency updates
run: |
writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
shell: Rscript {0}
- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
uses: actions/cache@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
- name: Unpack AMR and install R dependencies
run: |
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
shell: bash
- name: Show session info
run: |
options(width = 100)
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
extra-packages: any::covr
- name: Test coverage
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
run: |
install.packages("covr", repos = "https://cran.rstudio.com/")
library(AMR)
library(tinytest)
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"))
print(x)
shell: Rscript {0}

View File

@ -33,34 +33,23 @@ name: lintr
jobs:
lintr:
runs-on: macOS-latest
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-r@v2
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
r-version: release
# use RStudio Package Manager to quickly install packages
use-public-rspm: true
- name: Install dependencies
run: |
install.packages(c("remotes"))
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("lintr")
shell: Rscript {0}
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::lintr
- name: Lint
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"))