# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # # # # 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 more info: https://msberends.github.io/AMR. # # ==================================================================== # on: push: branches: - master pull_request: branches: - master name: code-tested jobs: code-tested: runs-on: macOS-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@master - uses: r-lib/actions/setup-pandoc@master - name: Query dependencies run: | install.packages('remotes') saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") shell: Rscript {0} - name: Cache R packages 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- - name: Install dependencies run: | install.packages(c("remotes")) remotes::install_deps(dependencies = TRUE) remotes::install_cran("covr") shell: Rscript {0} - name: Test coverage run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R")) shell: Rscript {0}