AMR/.github/workflows/codecovr.yaml

67 lines
3.0 KiB
YAML

# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# 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: '**'
pull_request:
branches: '**'
name: code-coverage
jobs:
code-coverage:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-r@v2
with:
r-version: release
# use RStudio Package Manager to quickly install packages
use-public-rspm: true
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::covr
- name: Test coverage
env:
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
run: |
x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/zz_deprecated.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
print(x)
shell: Rscript {0}