Merge branch 'l2d' into carpentries-main

.Rbuildignore

@@ -17,3 +17,7 @@
 
 ^doc$
 ^Meta$
+
+^\.vscode$
+^dev$
+^\.renovaterc\.json5$

.devcontainer/devcontainer.json

@@ -0,0 +1,10 @@
+{
+    "name": "${localWorkspaceFolderBasename}",
+    "image": "ghcr.io/rocker-org/devcontainer/r-ver:4.3",
+    "mounts": [
+        "source=${localEnv:HOME}/.gitignore_global,target=/home/rstudio/.gitignore_global,readonly",
+        "source=${localEnv:HOME}/.gitconfig,target=/home/rstudio/.gitconfig,readonly",
+        "source=${localEnv:HOME}/.ssh,target=/home/rstudio/.ssh,readonly"
+    ],
+    "postCreateCommand": "Rscript -e 'pak::local_install_dev_deps()'"
+}

.github/pull.yml

@@ -0,0 +1,8 @@
+## Automatically sync fork with upstream
+version: "1"
+rules:
+  - base: carpentries-main
+    upstream: carpentries:main
+    mergeUnstable: false
+label: ":arrow_heading_down: pull"
+conflictLabel: "merge-conflict"

.github/workflows/R-CMD-check.yaml

@@ -6,9 +6,11 @@
 # usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches: [main, master]
+    branches:
+      - main
+      - l2d
   pull_request:
-    branches: [main, master]
+    branches: [main, master, l2d]
   schedule:
     - cron: '0 0 * * 2'
   workflow_dispatch:
@@ -25,53 +27,21 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, cache: '~/Library/Application Support/renv', r: 'release'}
-
-          - {os: windows-latest, r: 'release'}
-
-          # Use 3.6 to trigger usage of RTools35
-          # As of 2024-06, downlit now requires R >4.0.0 so this should be deprecated.
-          # - {os: windows-latest, cache: '~\AppData\Local\renv', r: '3.6'}
-
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
-          - {os: ubuntu-latest, cache: '~/.local/share/renv', r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest, cache: '~/.local/share/renv', r: 'release', cov: 'true'}
-          - {os: ubuntu-latest, cache: '~/.local/share/renv', r: 'oldrel-1'}
-          - {os: ubuntu-latest, cache: '~/.local/share/renv', r: 'oldrel-2'}
-          - {os: ubuntu-latest, cache: '~/.local/share/renv', r: 'oldrel-3'}
-          - {os: ubuntu-latest, cache: '~/.local/share/renv', r: 'oldrel-4'}
+          ## Run CI only on ubuntu-latest as this is the os used to build lessons
+          - {os: ubuntu-latest, r: 'release', cov: 'true'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RENV_PATHS_ROOT: ${{ matrix.config.cache }}
 
     steps:
-      - name: Record Linux Version
-        if: runner.os == 'Linux'
-        run: |
-          echo "OS_VERSION=`lsb_release -sr`" >> $GITHUB_ENV
-          mkdir -p "${{ runner.temp }}/sandbox/"
-          echo "RENV_PATHS_SANDBOX=${{ runner.temp }}/sandbox/" >> $GITHUB_ENV
-
-      - name: "Windows: prevent autocrlf"
-        if: runner.os == 'Windows'
-        run: git config --global core.autocrlf false
-        shell: bash
-
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: "Windows: setup TMPDIR"
-        if: runner.os == 'Windows'
-        run: |
-          git config --global core.autocrlf true # reset setting to prevent errors downstream
-          echo "TMPDIR=${{ runner.temp }}" >> $GITHUB_ENV
-        shell: bash
+      - name: "Set up Chrome" # for PDF rendering
+        uses: browser-actions/[email protected]
 
       - name: "Setup R"
         uses: r-lib/actions/setup-r@v2
@@ -86,25 +56,6 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - name: "Restore {renv} cache"
-        if: runner.os != 'Windows'
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ runner.os }}-${{ env.OS_VERSION }}-renv-${{ runner.r }}-${{ hashFiles('.github/workflows/R-CMD-check.yaml') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ env.OS_VERSION }}-renv-${{ runner.r }}-
-
-      - name: "Prime {renv} Cache"
-        if: runner.os != 'Windows'
-        run: |
-          renv::settings$snapshot.type("explicit")
-          renv::init()
-          system('sudo rm -rf renv.lock renv .Rprofile')
-          system('git clean -fd -e .github')
-          system('git restore .')
-        shell: Rscript {0}
-
       - name: "Session info"
         run: |
           options(width = 100)
@@ -114,17 +65,5 @@ jobs:
 
       - name: "Check"
         uses: r-lib/actions/check-r-package@v2
-        if: runner.os != 'Windows'
-        with:
-          upload-snapshots: true
-
-      - name: "Check"
-        uses: r-lib/actions/check-r-package@v2
-        if: runner.os == 'Windows'
-        env:
-          RENV_PATHS_ROOT: ~
         with:
           upload-snapshots: true
-
-
-

.github/workflows/pkgdown.yaml

@@ -20,7 +20,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pr-commands.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

.github/workflows/test-coverage.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, l2d]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, l2d]
   workflow_dispatch:
 
 name: test-coverage
@@ -14,11 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RENV_PATHS_ROOT: ~/.local/share/renv
       OS_VERSION: 1
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -27,6 +26,9 @@ jobs:
       - name: "Set up pandoc"
         uses: r-lib/actions/setup-pandoc@v2
 
+      - name: "Set up Chrome" # for PDF rendering
+        uses: browser-actions/[email protected]
+
       - name: "Install sysreqs"
         id: run-apt
         shell: bash
@@ -57,23 +59,6 @@ jobs:
           extra-packages: any::covr
           needs: coverage
 
-      - name: Restore {renv} cache
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ runner.os }}-${{ env.OS_VERSION }}-renv-${{ runner.r }}-${{ hashFiles('.github/workflows/R-CMD-check.yaml') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ env.OS_VERSION }}-renv-${{ runner.r }}-
-
-      - name: Prime {renv} Cache
-        run: |
-          renv::settings$snapshot.type("explicit")
-          renv::init()
-          system('rm -rf renv .Rprofile')
-          system('git clean -fd -e .github')
-          system('git restore .')
-        shell: Rscript {0}
-
       - name: Test coverage
         run: |
           covr::codecov(

.github/workflows/update-dots.yaml

@@ -2,7 +2,7 @@ name: Render Dotfiles
 
 on:
   push:
-    paths: 
+    paths:
       - vignettes/articles/img/*dot
       - .github/workflows/update-docs.yaml
 
@@ -11,8 +11,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2.5.0
-      
+      - uses: actions/checkout@v4
+
       - name: Setup Graphviz
         uses: ts-graphviz/setup-graphviz@v1
 

.renovaterc.json5

@@ -0,0 +1,5 @@
+{
+    "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+    "extends": ["github>UCL-ARC/.github//renovate/default-config.json"],
+    "reviewers": ["milanmlft"]
+}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sandpaper
 Title: Create and Curate Carpentries Lessons
-Version: 0.16.5
+Version: 0.16.5.90000-1
 Authors@R: c(
     person(given = "Robert",
            family = "Davey",
@@ -61,6 +61,7 @@ Description: We provide tools to build a Carpentries-themed lesson repository
   those designed to be used in a continuous integration context so that all the
   lesson author needs to focus on is writing the content of the actual lesson.
 License: MIT + file LICENSE
+Depends: R (>= 4.0)
 Imports:
     pkgdown (>= 1.6.0),
     pegboard (>= 0.7.0),
@@ -85,7 +86,8 @@ Imports:
     callr,
     servr,
     utils,
-    tools
+    tools,
+    pagedown,
 Suggests:
     testthat (>= 3.0.0),
     covr,
@@ -96,11 +98,15 @@ Suggests:
     jsonlite,
     sessioninfo,
     mockr,
-    varnish (>= 0.3.0)
+    varnish (>= 0.3.0),
+    reticulate,
+    jupytextR (>= 0.1.0),
+    BiocManager
 Additional_repositories: https://carpentries.r-universe.dev/
 Remotes:
-  carpentries/pegboard,
-  carpentries/varnish
+    carpentries/pegboard,
+    LearnToDiscover/varnish,
+    milanmlft/jupytextR
 SystemRequirements: pandoc (>= 2.11.4) - https://pandoc.org
 Encoding: UTF-8
 LazyData: true
@@ -109,7 +115,7 @@ Config/testthat/parallel: false
 Config/Needs/check: rstudio/renv
 Config/potools/style: explicit
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://carpentries.github.io/sandpaper/, https://github.com/carpentries/sandpaper/, https://carpentries.github.io/workbench/
 BugReports: https://github.com/carpentries/sandpaper/issues/
 VignetteBuilder: knitr

NAMESPACE

@@ -25,6 +25,7 @@ export(move_episode)
 export(no_package_cache)
 export(package_cache_trigger)
 export(pin_version)
+export(py_install)
 export(renv_diagnostics)
 export(reset_episodes)
 export(reset_site)
@@ -37,6 +38,7 @@ export(set_instructors)
 export(set_learners)
 export(set_profiles)
 export(strip_prefix)
+export(template_citation)
 export(template_conduct)
 export(template_config)
 export(template_contributing)
@@ -55,6 +57,7 @@ export(update_cache)
 export(update_github_workflows)
 export(update_varnish)
 export(use_package_cache)
+export(use_python)
 export(validate_lesson)
 export(work_with_cache)
 importFrom(assertthat,validate_that)

R/build_episode.R

@@ -144,6 +144,7 @@ get_nav_data <- function(path_md, path_src = NULL, home = NULL,
     minutes       = as.integer(yaml$teaching) + as.integer(yaml$exercises),
     file_source   = fs::path_rel(path_src, start = home),
     this_page     = fs::path_file(this_page),
+    this_page_pdf = fs::path_file(as_pdf(this_page)),
     page_back     = page_back,
     back_title    = pb_title,
     page_forward  = page_forward,
@@ -206,6 +207,7 @@ build_episode_md <- function(path, hash = NULL, outdir = path_built(path),
   md <- fs::path_ext_set(fs::path_file(path), "md")
   outpath <- fs::path(outdir, md)
 
+  # Set up the arguments
   # shortcut if we have a markdown file
   if (file_ext(path) == "md") {
     file.copy(path, outpath, overwrite = TRUE)
@@ -233,7 +235,9 @@ build_episode_md <- function(path, hash = NULL, outdir = path_built(path),
   # ==========================================================
   #
   # Note that this process can NOT use any internal functions
+
   sho <- !(quiet || identical(Sys.getenv("TESTTHAT"), "true"))
+
   callr::r(
     func = callr_build_episode_md,
     args = args,
@@ -246,3 +250,41 @@ build_episode_md <- function(path, hash = NULL, outdir = path_built(path),
 
   invisible(outpath)
 }
+
+
+#' Convert a single episode to a Jupyter notebook
+#'
+#' @param path path to the RMarkdown file.
+#' @param outdir the directory to write to/
+#' @param quiet if `TRUE`, output is suppressed, default is `TRUE` so we can use better
+#'   formatting elsewhere.
+#'
+#' @return the path to the output, invisibly
+#' @keywords internal
+build_episode_ipynb <- function(path, outdir = path_built(path),
+                                profile = "lesson-requirements", quiet = TRUE) {
+
+  if (!rlang::is_installed("jupytextR", version = "0.1.0")) {
+    rlang::inform("jupytextR is not installed, attempting to install it.")
+    BiocManager::install("milanmlft/jupytextR")
+  }
+
+  outfile <- fs::path_ext_set(fs::path_file(path), "ipynb")
+  outpath <- fs::path(outdir, outfile)
+
+  args <- list(input = path, output = outpath, quiet = quiet)
+  sho <- !(quiet || identical(Sys.getenv("TESTTHAT"), "true"))
+
+  callr::r(
+    func = function(input, output, quiet) {
+      jupytextR::jupytext(input = input, to = "ipynb", output = output, quiet = quiet)
+    },
+    args = args,
+    show = !quiet,
+    spinner = sho,
+    env = c(callr::rcmd_safe_env(),
+            "RENV_PROFILE" = profile,
+            "RENV_CONFIG_CACHE_SYMLINKS" = renv_cache_available())
+  )
+  invisible(outpath)
+}