AMR/.github/workflows/codecovr.yaml

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2022 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:
      - development
      - main
  pull_request:
    branches:
      - main

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@v2
        with:
          r-version: release
      
      - uses: r-lib/actions/setup-pandoc@v2
        # with:
        #   pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.

      - name: Query dependencies
        # this will change once a week, so it will cache dependency updates
        run: |
          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
        shell: Rscript {0}
        
      - name: Restore cached R packages
        # this step will add the step 'Post Restore cached R packages' on a succesful run
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-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 }}
          R_RUN_TINYTEST: true
        run: |
          install.packages("covr", repos = "https://cran.rstudio.com/")
          library(AMR)
          library(tinytest)
          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}