@ -43,39 +43,40 @@ jobs:
@@ -43,39 +43,40 @@ jobs:
steps:
- uses : actions/checkout@v2
- uses : r-lib/actions/setup-r@master
- uses : r-lib/actions/setup-r@v1
with:
r-version : release
- uses : r-lib/actions/setup-pandoc@master
- 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
- name : Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
uses : actions/cache@v1
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-
key : macOS-latest-r-release-v4
- name : Install dependencies
- name : Unpack AMR and install R dependencies
run : |
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
Rscript -e "install.packages('covr')"
shell : bash
- name : Show session info
run : |
install.packages(c("remotes", "tinytest"))
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("covr")
remotes::install_local("data-raw/AMR_latest.tar.gz")
options(width = 100)
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell : Rscript {0}
- name : Test coverage
run : |
library(AMR)
library(tinytest)
source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("inst/tinytest", full.names = TRUE)
source_files <- list.files("AMR/ R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("AMR/ inst/tinytest", full.names = TRUE)
cov <- covr::file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), 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"))
attr(cov, which = "package") <- list(path = ". ") # until https://github.com/r-lib/covr/issues/478 is solved
attr(cov, which = "package") <- list(path = "AMR ") # until https://github.com/r-lib/covr/issues/478 is solved
covr::codecov(cov, quiet = FALSE)
shell : Rscript {0}
