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# ==================================================================== #
# 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}