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(v1.7.1.9000) ab_class update, unit tests

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dr. M.S. (Matthijs) Berends
2021-06-04 21:07:55 +02:00
parent 7e70403efb
commit 1908e7cc7a
34 changed files with 365 additions and 1368 deletions
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19
.github/workflows/codecovr.yaml vendored
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@@ -50,7 +50,7 @@ jobs:
- name: Restore cached R packages
# this step will add the step 'Post Restore cached R packages' on a succesful run
uses: actions/cache@v1
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: macOS-latest-r-release-v5-codecovr
@@ -68,20 +68,6 @@ 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 }}
@@ -89,5 +75,6 @@ jobs:
run: |
library(AMR)
library(tinytest)
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"))
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}