# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # on: push: branches: - premaster - master pull_request: branches: - master name: code-coverage jobs: code-coverage: runs-on: macOS-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@v1 with: r-version: release - uses: r-lib/actions/setup-pandoc@master - 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: macOS-latest-r-release-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} - 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}