2022-08-20 20:17:14 +02:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
2022-10-05 09:12:22 +02:00
|
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
2022-08-20 20:17:14 +02:00
|
|
|
# #
|
|
|
|
|
# SOURCE #
|
|
|
|
|
# https://github.com/msberends/AMR #
|
|
|
|
|
# #
|
2022-10-05 09:12:22 +02:00
|
|
|
# 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 #
|
|
|
|
|
# #
|
2022-08-20 20:17:14 +02:00
|
|
|
# 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/ #
|
|
|
|
|
# ==================================================================== #
|
|
|
|
|
|
|
|
|
|
# Create a website from the R documentation using pkgdown
|
|
|
|
|
# Git commit and push to the 'gh-pages' branch
|
|
|
|
|
|
|
|
|
|
on:
|
|
|
|
|
push:
|
|
|
|
|
# only on main
|
2022-08-21 16:37:20 +02:00
|
|
|
branches: 'main'
|
2022-08-20 20:17:14 +02:00
|
|
|
|
|
|
|
|
name: Update website
|
|
|
|
|
|
|
|
|
|
jobs:
|
|
|
|
|
update-website:
|
|
|
|
|
runs-on: ubuntu-latest
|
|
|
|
|
continue-on-error: true
|
|
|
|
|
steps:
|
2022-11-12 09:44:36 +01:00
|
|
|
|
2022-08-20 20:17:14 +02:00
|
|
|
- uses: actions/checkout@v3
|
2022-11-12 09:44:36 +01:00
|
|
|
with:
|
|
|
|
|
# this is to keep timestamps, the default fetch-depth: 1 gets the timestamps of the moment of cloning
|
|
|
|
|
fetch-depth: 0
|
|
|
|
|
|
2022-08-20 20:17:14 +02:00
|
|
|
- uses: r-lib/actions/setup-pandoc@v2
|
2022-11-12 09:44:36 +01:00
|
|
|
|
2022-08-20 20:17:14 +02:00
|
|
|
- name: Set up R
|
|
|
|
|
uses: r-lib/actions/setup-r@v2
|
|
|
|
|
with:
|
2022-11-12 09:44:36 +01:00
|
|
|
r-version: "release"
|
|
|
|
|
# use RStudio Package Manager (RSPM) to quickly install packages
|
|
|
|
|
use-public-rspm: true
|
|
|
|
|
|
2022-08-20 20:17:14 +02:00
|
|
|
- name: Set up R dependencies
|
|
|
|
|
uses: r-lib/actions/setup-r-dependencies@v2
|
|
|
|
|
with:
|
|
|
|
|
extra-packages: any::pkgdown
|
|
|
|
|
|
|
|
|
|
# Send updates to repo using GH Actions bot
|
|
|
|
|
- name: Create website in separate branch
|
|
|
|
|
run: |
|
|
|
|
|
git config user.name "github-actions"
|
|
|
|
|
git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
|
|
|
|
|
Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE, install = TRUE, branch = "gh-pages")'
|
