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GitHub Actions: check lesson template (#489)
Co-authored-by: Maxim Belkin <[email protected]> Co-authored-by: François Michonneau <[email protected]>
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‎.github/workflows/template.yml‎

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name: Template
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on:
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push:
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branches: gh-pages
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pull_request:
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jobs:
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check-template:
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name: Test lesson template
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if: github.repository == 'carpentries/styles'
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git]
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os: [ubuntu-latest, macos-latest, windows-latest]
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defaults:
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run:
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shell: bash # forces 'Git for Windows' on Windows
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steps:
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- name: Set up Ruby
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uses: actions/setup-ruby@main
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with:
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ruby-version: '2.7.1'
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.x'
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- name: Install GitHub Pages, Bundler, and kramdown gems
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run: |
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gem install github-pages bundler kramdown
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- name: Install Python modules
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run: |
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if [[ $RUNNER_OS == macOS || $RUNNER_OS == Linux ]]; then
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python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
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elif [[ $RUNNER_OS == Windows ]]; then
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python -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
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fi
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- name: Checkout the ${{ matrix.lesson }} lesson
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uses: actions/checkout@master
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with:
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repository: ${{ matrix.lesson }}
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path: lesson
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fetch-depth: 0
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- name: Look for R-markdown files
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id: check-rmd
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working-directory: lesson
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run: |
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echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
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- name: Set up R
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if: steps.check-rmd.outputs.count != 0
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uses: r-lib/actions/setup-r@master
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with:
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r-version: 'release'
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- name: Install needed packages
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if: steps.check-rmd.outputs.count != 0
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run: |
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install.packages(c('remotes', 'rprojroot', 'renv', 'desc'))
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shell: Rscript {0}
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- name: Query dependencies
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if: steps.check-rmd.outputs.count != 0
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working-directory: lesson
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run: |
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source('bin/dependencies.R')
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deps <- identify_dependencies()
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create_description(deps)
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
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uses: actions/cache@v1
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies for R packages
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if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0
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working-directory: lesson
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run: |
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while read -r cmd
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do
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eval $cmd
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done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
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- name: Install R lessons package dependencies
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if: steps.check-rmd.outputs.count != 0
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working-directory: lesson
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run: |
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remotes::install_deps(dependencies = TRUE)
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file.remove("DESCRIPTION")
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shell: Rscript {0}
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- name: Determine the proper reference to use
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id: styles-ref
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run: |
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if [[ -n "${{ github.event.pull_request.number }}" ]]; then
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echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
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else
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echo "::set-output name=ref::gh-pages"
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fi
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- name: Sync lesson with carpentries/styles
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working-directory: lesson
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run: |
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git config --global user.email "[email protected]"
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git config --global user.name "The Carpentries Bot"
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git remote add styles https://github.com/carpentries/styles.git
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git config --local remote.styles.tagOpt --no-tags
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git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref
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git merge -s recursive -Xtheirs --no-commit styles-ref
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git commit -m "Sync lesson with carpentries/styles"
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- run: make site
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working-directory: lesson

‎Makefile‎

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# Controls
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.PHONY : commands clean files
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.PHONY : commands clean files install-rmd-deps
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# Default target
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.DEFAULT_GOAL := commands
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$(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
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${DST}/license/index.html
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## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson
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install-rmd-deps:
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Rscript -e 'source("bin/dependencies.R"); install_dependencies(identify_dependencies())'
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## * lesson-md : convert Rmarkdown files to markdown
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lesson-md : ${RMD_DST}
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_episodes/%.md: _episodes_rmd/%.Rmd
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_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-dependencies
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@mkdir -p _episodes
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@bin/knit_lessons.sh $< $@
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## * lesson-check : validate lesson Markdown

‎bin/dependencies.R‎

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find_root <- function() {
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if (!requireNamespace("rprojroot", quietly = TRUE)) {
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install.packages("rprojroot", lib = lib, repos = repos)
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}
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cfg <- rprojroot::has_file_pattern("^_config.y*ml$")
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root <- rprojroot::find_root(cfg)
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root
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}
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identify_dependencies <- function(lib = NULL, repos = getOption("repos")) {
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if (is.null(lib)) {
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lib <- .libPaths()
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}
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if (!requireNamespace("renv", quietly = TRUE)) {
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install.packages("renv", lib = lib, repos = repos)
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}
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root <- find_root()
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required_pkgs <- unique(c(
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## Packages for episodes
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renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
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## Packages for tools
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renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
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))
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required_pkgs
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}
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install_dependencies <- function(required_pkgs,
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lib = NULL, repos = getOption("repos"),
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update = FALSE, ...) {
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if (missing(lib)) {
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lib <- .libPaths()
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}
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missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
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if (length(missing_pkgs)) {
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message("Installing missing required packages: ",
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paste(missing_pkgs, collapse=", "))
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install.packages(missing_pkgs, lib = lib, repos = repos)
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}
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if (update) {
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update.packages(
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lib.loc = lib, repos = repos,
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ask = FALSE, checkBuilt = TRUE, ...
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)
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}
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if (require("knitr") && packageVersion("knitr") < '1.9.19') {
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stop("knitr must be version 1.9.20 or higher")
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}
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}
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create_description <- function(required_pkgs) {
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require("desc")
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d <- description$new("!new")
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lapply(required_pkgs, function(x) d$set_dep(x))
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d$write("DESCRIPTION")
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}

‎bin/generate_md_episodes.R‎

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generate_md_episodes <- function() {
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if (!requireNamespace("renv", quietly = TRUE)) {
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install.packages("renv", repos = c(CRAN = "https://cloud.r-project.org/"))
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}
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if (!requireNamespace("rprojroot", quietly = TRUE)) {
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install.packages("rprojroot", repos = c(CRAN = "https://cloud.r-project.org/"))
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}
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cfg <- rprojroot::has_file_pattern("^_config.y*ml$")
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root <- rprojroot::find_root(cfg)
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required_pkgs <- unique(c(
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## Packages for episodes
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renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
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## Pacakges for tools
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renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
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))
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missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
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if (length(missing_pkgs)) {
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message("Installing missing required packages: ",
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paste(missing_pkgs, collapse=", "))
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install.packages(missing_pkgs)
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}
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if (require("knitr") && packageVersion("knitr") < '1.9.19')
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stop("knitr must be version 1.9.20 or higher")
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## get the Rmd file to process from the command line, and generate the path
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## for their respective outputs
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args <- commandArgs(trailingOnly = TRUE)

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