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v1.7.0

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dr. M.S. (Matthijs) Berends
2021-05-24 15:29:17 +02:00
parent e5599bc694
commit ac73a8d849
120 changed files with 1394 additions and 1481 deletions
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24
.github/workflows/codecovr.yaml vendored
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@ -68,16 +68,28 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
# - name: Test coverage
# env:
# CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
# run: |
# library(AMR)
# library(tinytest)
# library(covr)
# source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
# test_files <- list.files("inst/tinytest", full.names = TRUE)
# cov <- 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
# codecov(coverage = cov, quiet = FALSE)
# shell: Rscript {0}
- name: Test coverage
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
R_RUN_TINYTEST: true
run: |
library(AMR)
library(tinytest)
library(covr)
source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("inst/tinytest", full.names = TRUE)
cov <- 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
codecov(coverage = cov, quiet = FALSE)
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"))
shell: Rscript {0}