mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
90 lines
3.7 KiB
YAML
90 lines
3.7 KiB
YAML
# ==================================================================== #
|
|
# 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:
|
|
- development
|
|
- main
|
|
pull_request:
|
|
branches:
|
|
- main
|
|
|
|
name: code-coverage
|
|
|
|
jobs:
|
|
code-coverage:
|
|
runs-on: macOS-latest
|
|
env:
|
|
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
|
|
steps:
|
|
- uses: actions/checkout@v2
|
|
|
|
- uses: r-lib/actions/setup-r@v1
|
|
with:
|
|
r-version: release
|
|
|
|
- uses: r-lib/actions/setup-pandoc@v1
|
|
# with:
|
|
# pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
|
|
|
|
- name: Query dependencies
|
|
# this will change once a week, so it will cache dependency updates
|
|
run: |
|
|
writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$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}
|