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(v1.7.1.9041) new GH actions, branches rename

development
parent
commit
e8d3ce05d7
  1. 82
      .github/workflows/check.yaml
  2. 157
      .github/workflows/check.yaml.old
  3. 2
      DESCRIPTION
  4. 2
      NEWS.md
  5. BIN
      data-raw/AMR_latest.tar.gz
  6. 13
      data-raw/_install_deps.R
  7. 2
      docs/articles/datasets.html
  8. 8
      docs/news/index.html
  9. 20
      git_development.sh
  10. 30
      git_merge.sh
  11. 26
      git_siteonly.sh

82
.github/workflows/check.yaml

@ -23,16 +23,14 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
on:
push:
branches:
- premaster
- master
- development
- main
pull_request:
branches:
- master
- main
schedule:
# run a schedule everyday at 1 AM.
# this is to check that all dependencies are still available (see R/zzz.R)
@ -81,45 +79,35 @@ jobs:
- {os: windows-latest, r: '3.2', allowfail: false}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
RSPM: ${{ matrix.config.rspm }}
R_REPOSITORIES: "https://cran.rstudio.com"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
R_CHECK_CRAN_INCOMING_: false
R_CHECK_FORCE_SUGGESTS_: false
R_CHECK_DEPENDS_ONLY_: true
R_CHECK_LENGTH_1_CONDITION_: verbose
R_CHECK_LENGTH_1_LOGIC2_: verbose
# during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- name: Install Linux dependencies
if: runner.os == 'Linux'
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
- name: Query dependencies
# this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates
run: |
writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle")
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
- uses: r-lib/actions/setup-r-dependencies@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ matrix.config.os }}-${{ hashFiles('.github/daily-R-bundle') }}-v4
- name: Unpack AMR and install R dependencies
if: always()
run: |
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
shell: bash
extra-packages: rcmdcheck
- name: Show session info
if: always()
run: |
@ -127,31 +115,17 @@ jobs:
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
- name: Run R CMD check
if: always()
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
# during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
run: |
R CMD check --no-manual --run-donttest --run-dontrun AMR
shell: bash
- uses: r-lib/actions/check-r-package@v1
- name: Show unit tests output
if: always()
run: |
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload artifacts
- name: Upload check results
if: always()
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@main
with:
name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
path: AMR.Rcheck
path: check

157
.github/workflows/check.yaml.old

@ -0,0 +1,157 @@
# ==================================================================== #
# 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/ #
# ==================================================================== #
# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
on:
push:
branches:
- premaster
- master
pull_request:
branches:
- master
schedule:
# run a schedule everyday at 1 AM.
# this is to check that all dependencies are still available (see R/zzz.R)
- cron: '0 1 * * *'
name: R-code-check
jobs:
R-code-check:
runs-on: ${{ matrix.config.os }}
continue-on-error: ${{ matrix.config.allowfail }}
name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
# test all systems against all released versions of R >= 3.0, we support them all!
- {os: macOS-latest, r: 'devel', allowfail: true}
- {os: macOS-latest, r: '4.1', allowfail: false}
- {os: macOS-latest, r: '4.0', allowfail: false}
- {os: macOS-latest, r: '3.6', allowfail: false}
- {os: macOS-latest, r: '3.5', allowfail: false}
- {os: macOS-latest, r: '3.4', allowfail: false}
- {os: macOS-latest, r: '3.3', allowfail: false}
- {os: macOS-latest, r: '3.2', allowfail: false}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: windows-latest, r: 'devel', allowfail: true}
- {os: windows-latest, r: '4.1', allowfail: false}
- {os: windows-latest, r: '4.0', allowfail: false}
- {os: windows-latest, r: '3.6', allowfail: false}
- {os: windows-latest, r: '3.5', allowfail: false}
- {os: windows-latest, r: '3.4', allowfail: false}
- {os: windows-latest, r: '3.3', allowfail: false}
- {os: windows-latest, r: '3.2', allowfail: false}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
R_REPOSITORIES: "https://cran.rstudio.com"
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
- name: Install Linux dependencies
if: runner.os == 'Linux'
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
- name: Query dependencies
# this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates
run: |
writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle")
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/daily-R-bundle') }}-v4
- name: Unpack AMR and install R dependencies
if: always()
run: |
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
shell: bash
- name: Show session info
if: always()
run: |
options(width = 100)
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
- name: Run R CMD check
if: always()
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
# during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
R_RUN_TINYTEST: true
run: |
R CMD check --no-manual --run-donttest --run-dontrun AMR
shell: bash
- name: Show unit tests output
if: always()
run: |
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload artifacts
if: always()
uses: actions/upload-artifact@v2
with:
name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
path: AMR.Rcheck

2
DESCRIPTION

@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9040
Version: 1.7.1.9041
Date: 2021-09-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md

@ -1,4 +1,4 @@
# `AMR` 1.7.1.9040
# `AMR` 1.7.1.9041
## <small>Last updated: 29 September 2021</small>
### Breaking changes

BIN
data-raw/AMR_latest.tar.gz

13
data-raw/_install_deps.R

@ -31,7 +31,10 @@ pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
unlist(strsplit(unlist(packageDescription("AMR",
fields = c("Suggests", "Enhances", "LinkingTo"))),
split = ", ?")))
pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
cat("################################################\n")
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
cat("################################################\n")
if (.Platform$OS.type != "unix") {
# no compiling on Windows here
@ -52,6 +55,16 @@ for (i in seq_len(length(to_install))) {
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
tryCatch(install.packages(to_install[i],
type = "binary",
repos = "https://cran.rstudio.com/",
dependencies = c("Depends", "Imports", "LinkingTo"),
quiet = FALSE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
}
}
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)

2
docs/articles/datasets.html

@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9041</span>
</span>
</div>

8
docs/news/index.html

@ -92,7 +92,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9041</span>
</span>
</div>
@ -240,9 +240,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719040" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9040">
<a href="#amr-1719040" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9040</h1>
<div id="amr-1719041" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9041">
<a href="#amr-1719041" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9041</h1>
<div id="last-updated-29-september-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>

20
git_premaster.sh → git_development.sh

@ -24,26 +24,26 @@
# ==================================================================== #
########################################################################
# `git_premaster.sh` takes 3 parameters: #
# `git_development.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with TRUE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# To push new commits to the development branch, run: #
# bash git_development.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful test checks, merge it to the master branch with: #
# After successful test checks, merge it to the main branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
# bash git_development.sh "v1.x.x" FALSE "1.x.x" #
# #
# To only update the website, run: #
# bash git_siteonly.sh #
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
# (which is short for 'bash git_development.sh "website update" FALSE')#
########################################################################
if [ -z "$1" ]; then
@ -56,8 +56,8 @@ else
lazy=$2
fi
# be sure to be on premaster branch
git checkout premaster --quiet
# be sure to be on development branch
git checkout development --quiet
echo "••••••••••••••••••••••••••••••••••••••••••••"
echo "• Updating package date and version number •"
@ -127,7 +127,7 @@ echo "••••••••••••••••••••"
echo "• Building package •"
echo "••••••••••••••••••••"
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)"
rm data-raw/AMR_latest.tar.gz
mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
@ -193,7 +193,7 @@ git add .
git commit -a -m "(v${new_version}) $1" --quiet
git push --quiet
echo "Comparison:"
echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline"
echo "https://github.com/msberends/AMR/compare/main...development?view=inline"
echo
echo "•••••••••"

30
git_merge.sh

@ -24,44 +24,44 @@
# ==================================================================== #
########################################################################
# `git_premaster.sh` takes 3 parameters: #
# `git_development.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with TRUE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# To push new commits to the development branch, run: #
# bash git_development.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful test checks, merge it to the master branch with: #
# After successful test checks, merge it to the main branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
# bash git_development.sh "v1.x.x" FALSE "1.x.x" #
# #
# To only update the website, run: #
# bash git_siteonly.sh #
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
# (which is short for 'bash git_development.sh "website update" FALSE')#
########################################################################
# stash current changes
# git stash --quiet
# go to master
git checkout master --quiet
echo "• changed branch to master"
# go to main
git checkout main --quiet
echo "• changed branch to main"
# import everything from premaster
git merge premaster --quiet
# import everything from development
git merge development --quiet
# and send it to git
git push --quiet
echo "• pushed changes to master"
echo "• pushed changes to main"
# return to premaster
git checkout premaster --quiet
echo "• changed branch back to premaster"
# return to development
git checkout development --quiet
echo "• changed branch back to development"
git status --short
echo

26
git_siteonly.sh

@ -24,35 +24,35 @@
# ==================================================================== #
########################################################################
# `git_premaster.sh` takes 3 parameters: #
# `git_development.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with TRUE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# To push new commits to the development branch, run: #
# bash git_development.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful test checks, merge it to the master branch with: #
# After successful test checks, merge it to the main branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
# bash git_development.sh "v1.x.x" FALSE "1.x.x" #
# #
# To only update the website, run: #
# bash git_siteonly.sh #
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
# (which is short for 'bash git_development.sh "website update" FALSE')#
########################################################################
bash git_premaster.sh "website update" FALSE
bash git_development.sh "website update" FALSE
echo
echo "••••••••••••••••••••••••••••••"
echo "• Uploading to master branch •"
echo "••••••••••••••••••••••••••••••"
git checkout master
git merge premaster
echo "••••••••••••••••••••••••••••"
echo "• Uploading to main branch •"
echo "••••••••••••••••••••••••••••"
git checkout main
git merge development
git push --quiet
git checkout premaster
git checkout development
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