GitHub Actions: check lesson template (#489)

Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com>
Co-authored-by: François Michonneau <francois.michonneau@gmail.com>

diff --git a/.github/workflows/template.yml b/.github/workflows/template.yml
new file mode 100644 (file)
index 0000000..80a68aa
--- /dev/null
+++ b/.github/workflows/template.yml
@@ -0,0 +1,124 @@
+name: Template
+on:
+  push:
+    branches: gh-pages
+  pull_request:
+jobs:
+  check-template:
+    name: Test lesson template
+    if: github.repository == 'carpentries/styles'
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    defaults:
+      run:
+        shell: bash # forces 'Git for Windows' on Windows
+    steps:
+      - name: Set up Ruby
+        uses: actions/setup-ruby@main
+        with:
+          ruby-version: '2.7.1'
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install GitHub Pages, Bundler, and kramdown gems
+        run: |
+          gem install github-pages bundler kramdown
+
+      - name: Install Python modules
+        run: |
+          if [[ $RUNNER_OS == macOS || $RUNNER_OS == Linux ]]; then
+            python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
+          elif [[ $RUNNER_OS == Windows ]]; then
+            python -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
+          fi
+
+      - name: Checkout the ${{ matrix.lesson }} lesson
+        uses: actions/checkout@master
+        with:
+          repository: ${{ matrix.lesson }}
+          path: lesson
+          fetch-depth: 0
+
+      - name: Look for R-markdown files
+        id: check-rmd
+        working-directory: lesson
+        run: |
+          echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})"
+
+      - name: Set up R
+        if: steps.check-rmd.outputs.count != 0
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+
+      - name: Install needed packages
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          install.packages(c('remotes', 'rprojroot', 'renv', 'desc'))
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
+        run: |
+          source('bin/dependencies.R')
+          deps <- identify_dependencies()
+          create_description(deps)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies for R packages
+        if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0
+        working-directory: lesson
+        run: |
+          while read -r cmd
+          do
+            eval $cmd
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
+
+      - name: Install R lessons package dependencies
+        if: steps.check-rmd.outputs.count != 0
+        working-directory: lesson
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          file.remove("DESCRIPTION")
+        shell: Rscript {0}
+
+      - name: Determine the proper reference to use
+        id: styles-ref
+        run: |
+          if [[ -n "${{ 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

diff --git a/Makefile b/Makefile
index b585662ce1d299f5bca302fb53c12a623f9ea536..1407962ca27c9a35a384463d41647f304bad7e9b 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -32,7 +32,7 @@ endif
 
 
 # Controls
-.PHONY : commands clean files
+.PHONY : commands clean files install-rmd-deps
 
 # Default target
 .DEFAULT_GOAL := commands
@@ -119,10 +119,15 @@ HTML_DST = \
   $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \
   ${DST}/license/index.html
 
+## * 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())'
+
 ## * lesson-md        : convert Rmarkdown files to markdown
 lesson-md : ${RMD_DST}
 
-_episodes/%.md: _episodes_rmd/%.Rmd
+_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-dependencies
+       @mkdir -p _episodes
        @bin/knit_lessons.sh $< $@
 
 ## * lesson-check     : validate lesson Markdown

diff --git a/bin/dependencies.R b/bin/dependencies.R
new file mode 100644 (file)
index 0000000..b710558
--- /dev/null
+++ b/bin/dependencies.R
@@ -0,0 +1,68 @@
+find_root <- function() {
+  if (!requireNamespace("rprojroot", quietly = TRUE)) {
+    install.packages("rprojroot", lib = lib, repos = repos)
+  }
+
+  cfg  <- rprojroot::has_file_pattern("^_config.y*ml$")
+  root <- rprojroot::find_root(cfg)
+
+  root
+}
+
+identify_dependencies <- function(lib = NULL, repos = getOption("repos")) {
+
+  if (is.null(lib)) {
+    lib <- .libPaths()
+  }
+
+  if (!requireNamespace("renv", quietly = TRUE)) {
+    install.packages("renv", lib = lib, repos = repos)
+  }
+
+  root <- find_root()
+
+  required_pkgs <- unique(c(
+    ## Packages for episodes
+    renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
+    ## Packages for tools
+    renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
+  ))
+
+  required_pkgs
+}
+
+install_dependencies <- function(required_pkgs,
+                                 lib = NULL, repos = getOption("repos"),
+                                 update = FALSE, ...) {
+
+  if (missing(lib))  {
+    lib <- .libPaths()
+  }
+
+  missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
+
+  if (length(missing_pkgs)) {
+    message("Installing missing required packages: ",
+      paste(missing_pkgs, collapse=", "))
+    install.packages(missing_pkgs, lib = lib, repos = repos)
+  }
+
+  if (update) {
+    update.packages(
+      lib.loc = lib, repos = repos,
+      ask = FALSE, checkBuilt = TRUE, ...
+    )
+  }
+
+  if (require("knitr") && packageVersion("knitr") < '1.9.19') {
+    stop("knitr must be version 1.9.20 or higher")
+  }
+
+}
+
+create_description <- function(required_pkgs) {
+  require("desc")
+  d <- description$new("!new")
+  lapply(required_pkgs, function(x) d$set_dep(x))
+  d$write("DESCRIPTION")
+}

diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
index 7c137d765ca2062288ef331e9b80d4b879150812..ce9e8aa63bd0a295ccb76a25150629e383aefba5 100644 (file)
--- a/bin/generate_md_episodes.R
+++ b/bin/generate_md_episodes.R
@@ -1,34 +1,5 @@
 generate_md_episodes <- function() {
 
-  if (!requireNamespace("renv", quietly = TRUE)) {
-    install.packages("renv", repos = c(CRAN = "https://cloud.r-project.org/"))
-  }
-
-  if (!requireNamespace("rprojroot", quietly = TRUE)) {
-    install.packages("rprojroot", repos = c(CRAN = "https://cloud.r-project.org/"))
-  }
-
-  cfg  <- rprojroot::has_file_pattern("^_config.y*ml$")
-  root <- rprojroot::find_root(cfg)
-
-  required_pkgs <- unique(c(
-    ## Packages for episodes
-    renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
-    ## Pacakges for tools
-    renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
-  ))
-
-  missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
-
-  if (length(missing_pkgs)) {
-    message("Installing missing required packages: ",
-            paste(missing_pkgs, collapse=", "))
-    install.packages(missing_pkgs)
-  }
-
-  if (require("knitr") && packageVersion("knitr") < '1.9.19')
-    stop("knitr must be version 1.9.20 or higher")
-
   ## get the Rmd file to process from the command line, and generate the path
   ## for their respective outputs
   args  <- commandArgs(trailingOnly = TRUE)