defaults:
run:
shell: bash # forces 'Git for Windows' on Windows
+ env:
+ RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/bionic/latest'
steps:
- name: Set up Ruby
uses: actions/setup-ruby@main
path: lesson
fetch-depth: 0
+ - name: Determine the proper reference to use
+ id: styles-ref
+ run: |
+ if [[ -n "${{ github.event.pull_request.number }}" ]]; then
+ echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
+ else
+ echo "::set-output name=ref::gh-pages"
+ fi
+
+ - name: Sync lesson with carpentries/styles
+ working-directory: lesson
+ run: |
+ git config --global user.email "team@carpentries.org"
+ git config --global user.name "The Carpentries Bot"
+ git remote add styles https://github.com/carpentries/styles.git
+ git config --local remote.styles.tagOpt --no-tags
+ git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref
+ git merge -s recursive -Xtheirs --no-commit styles-ref
+ git commit -m "Sync lesson with carpentries/styles"
+
- name: Look for R-markdown files
id: check-rmd
working-directory: lesson
- name: Install needed packages
if: steps.check-rmd.outputs.count != 0
run: |
- install.packages(c('remotes', 'rprojroot', 'renv', 'desc'))
+ install.packages(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'))
shell: Rscript {0}
- name: Query dependencies
run: |
while read -r cmd
do
- eval $cmd
+ eval sudo $cmd
done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
- - name: Install R lessons package dependencies
- if: steps.check-rmd.outputs.count != 0
- working-directory: lesson
- run: |
- remotes::install_deps(dependencies = TRUE)
- file.remove("DESCRIPTION")
- shell: Rscript {0}
-
- - name: Determine the proper reference to use
- id: styles-ref
- run: |
- if [[ -n "${{ github.event.pull_request.number }}" ]]; then
- echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
- else
- echo "::set-output name=ref::gh-pages"
- fi
-
- - name: Sync lesson with carpentries/styles
- working-directory: lesson
- run: |
- git config --global user.email "team@carpentries.org"
- git config --global user.name "The Carpentries Bot"
- git remote add styles https://github.com/carpentries/styles.git
- git config --local remote.styles.tagOpt --no-tags
- git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref
- git merge -s recursive -Xtheirs --no-commit styles-ref
- git commit -m "Sync lesson with carpentries/styles"
-
- run: make site
working-directory: lesson
# Controls
-.PHONY : commands clean files install-rmd-deps
+.PHONY : commands clean files
# Default target
.DEFAULT_GOAL := commands
## III. Commands specific to lesson websites
## =================================================
-.PHONY : lesson-check lesson-md lesson-files lesson-fixme
+.PHONY : lesson-check lesson-md lesson-files lesson-fixme install-rmd-deps
# RMarkdown files
RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd)
## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
install-rmd-deps:
- Rscript -e 'source("bin/dependencies.R"); install_dependencies(identify_dependencies())'
+ @${SHELL} bin/install_r_deps.sh
## * lesson-md : convert Rmarkdown files to markdown
lesson-md : ${RMD_DST}
-_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-dependencies
+_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps
@mkdir -p _episodes
@bin/knit_lessons.sh $< $@
-find_root <- function() {
- if (!requireNamespace("rprojroot", quietly = TRUE)) {
- install.packages("rprojroot", lib = lib, repos = repos)
+install_required_packages <- function(lib = NULL, repos = getOption("repos")) {
+
+ if (is.null(lib)) {
+ lib <- .libPaths()
}
+ message("lib paths: ", paste(lib, collapse = ", "))
+ missing_pkgs <- setdiff(
+ c("rprojroot", "desc", "remotes", "renv"),
+ rownames(installed.packages(lib.loc = lib))
+ )
+
+ install.packages(missing_pkgs, lib = lib, repos = repos)
+
+}
+
+find_root <- function() {
+
cfg <- rprojroot::has_file_pattern("^_config.y*ml$")
root <- rprojroot::find_root(cfg)
root
}
-identify_dependencies <- function(lib = NULL, repos = getOption("repos")) {
-
- if (is.null(lib)) {
- lib <- .libPaths()
- }
-
- if (!requireNamespace("renv", quietly = TRUE)) {
- install.packages("renv", lib = lib, repos = repos)
- }
+identify_dependencies <- function() {
root <- find_root()
required_pkgs
}
-install_dependencies <- function(required_pkgs,
- lib = NULL, repos = getOption("repos"),
- update = FALSE, ...) {
-
- if (missing(lib)) {
- lib <- .libPaths()
- }
+create_description <- function(required_pkgs) {
+ d <- desc::description$new("!new")
+ lapply(required_pkgs, function(x) d$set_dep(x))
+ d$write("DESCRIPTION")
+}
- missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
+install_dependencies <- function(required_pkgs, ...) {
- if (length(missing_pkgs)) {
- message("Installing missing required packages: ",
- paste(missing_pkgs, collapse=", "))
- install.packages(missing_pkgs, lib = lib, repos = repos)
- }
-
- if (update) {
- update.packages(
- lib.loc = lib, repos = repos,
- ask = FALSE, checkBuilt = TRUE, ...
- )
- }
+ create_description(required_pkgs)
+ on.exit(file.remove("DESCRIPTION"))
+ remotes::install_deps(dependencies = TRUE, ...)
if (require("knitr") && packageVersion("knitr") < '1.9.19') {
stop("knitr must be version 1.9.20 or higher")
}
}
-
-create_description <- function(required_pkgs) {
- require("desc")
- d <- description$new("!new")
- lapply(required_pkgs, function(x) d$set_dep(x))
- d$write("DESCRIPTION")
-}
--- /dev/null
+Rscript -e "source(file.path('bin', 'dependencies.R')); install_required_packages(); install_dependencies(identify_dependencies())"