Add support for setting up Python through renv

.github/workflows/test-coverage.yaml

@@ -26,7 +26,7 @@ jobs:
       - name: "Set up pandoc"
         uses: r-lib/actions/setup-pandoc@v2
         with:
-          pandoc-version: '2.11' 
+          pandoc-version: '2.11'
 
       - name: "Install sysreqs"
         id: run-apt

DESCRIPTION

@@ -1,20 +1,28 @@
 Package: sandpaper
 Title: Create and Curate Carpentries Lessons
-Version: 0.11.9
+Version: 0.12.0.9000
 Authors@R: c(
     person(given = "Zhian N.",
            family = "Kamvar",
            role = c("aut", "cre"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-1458-7108")),
-    person(given = "François",
-           family = "Michonneau",
+    person(given = "Julien",
+           family = "Colomb",
            role = c("ctb"),
-           email = "[email protected]"),
+           comment = c(ORCID = "0000-0002-3127-5520")),
+    person(given = "Ben",
+           family = "Companjen",
+           role = c("ctb"),
+           comment = c(ORCID = "0000-0002-7023-9047")),
     person(given = "Toby",
            family = "Hodges",
            role = c("ctb"),
            email = "[email protected]"),
+    person(given = "François",
+           family = "Michonneau",
+           role = c("ctb"),
+           email = "[email protected]"),
     person())
 Description: We provide tools to build a Carpentries-themed lesson repository
   into an accessible standalone static website. These include local tools and
@@ -23,7 +31,7 @@ Description: We provide tools to build a Carpentries-themed lesson repository
 License: MIT + file LICENSE
 Imports:
     pkgdown (>= 1.6.0),
-    pegboard (>= 0.2.3),
+    pegboard (>= 0.5.1),
     cli (>= 3.4.0),
     commonmark,
     fs (>= 1.5.0),
@@ -47,27 +55,28 @@ Imports:
     tools
 Suggests:
     testthat (>= 3.0.0),
+    covr,
     markdown,
     brio,
     xml2,
     xslt,
-    covr,
     withr,
     jsonlite,
     sessioninfo,
+    mockr,
     varnish (>= 0.2.1),
-    mockr
+    reticulate
 Additional_repositories: https://carpentries.r-universe.dev/
 Remotes:
   ropensci/tinkr,
   carpentries/pegboard,
-  carpentries/varnish,
-  rstudio/renv
-SystemRequirements: pandoc (>= 1.11.4) - http://pandoc.org
+  carpentries/varnish
+SystemRequirements: pandoc (>= 2.11.4) - https://pandoc.org
 Encoding: UTF-8
 LazyData: true
 Config/testthat/edition: 3
 Config/testthat/parallel: false
+Config/Needs/check: rstudio/renv
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 URL: https://carpentries.github.io/sandpaper/, https://github.com/carpentries/sandpaper/, https://carpentries.github.io/workbench/

NAMESPACE

@@ -24,6 +24,7 @@ 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)
@@ -54,10 +55,12 @@ 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)
 importFrom(rlang,is_interactive)
+importFrom(tools,file_ext)
 importFrom(tools,md5sum)
 importFrom(utils,modifyList)
 importFrom(utils,read.table)

NEWS.md

@@ -1,13 +1,150 @@
-# sandpaper 0.11.9 (in development)
+# sandpaper 0.12.0 (2023-05-19)
 
-BUG FIX
--------
+## NEW FEATURES
+
+* Aggregate instructor notes now have headings that link back to the source
+  instructor note (reported: @tobyhodges, #463; fixed: @zkamvar, #468)
+* The internal function `sandpaper:::render_html()` now explicitly sets the
+  pandoc version before running the subprocess. This allows lesson developers to
+  use the {pandoc} package to set their pandoc versions. (reported: @zkamvar,
+  #465; fixed: @zkamvar, #465)
+
+## BUG FIX
+
+* Callout block anchor links now point to the correct ID of the block derived
+  from the title of the block (as opposed to the generic ID). 
+  (reported: @debpaul, 
+  https://github.com/datacarpentry/OpenRefine-ecology-lesson/issues/292 and
+  @bencomp, #454; fixed: @zkamvar, #467).
+* Inline images no longer automatically transform to figure blocks
+  (reported: @ostephens, #445; fixed: @zkamvar, #446). This bug was preventing
+  image links (e.g. MyBinder badges) from being rendered as links with images
+  in them. This fixes that issue. It also helps distinguish inline images
+  between figures in the DOM.
+
+# sandpaper 0.11.17 (2023-05-16)
+
+## NEW FEATURES
+
+* `sandpaper::serve()` gains the `quiet` argument, defaulting to `TRUE` for
+  interactive sessions and `FALSE` for command line sessions 
+* `sandpaper::serve()` gains the `...` argument to pass options to 
+  `servr::server_config()` for setting ports and hosts (reported:
+  @twrightsman, https://github.com/carpentries/workbench/issues/50 and #459;
+  fixed: @zkamvar, #461).
+
+## BUG FIX
+
+* Break timing is now included in the overall schedule. (reported: @karenword,
+  #437; fixed: @bencomp, #455).
+
+
+## TEST SUITE
+
+* An upstream feature in {renv}, forcing it to be silent when testing caused
+  some expectations to fail. This has been fixed in specific tests by turning
+  verbosity on in those tests (reported: @zkamvar, #457; fixed: @zkamvar, #458)
+
+# sandpaper 0.11.16 (2023-05-05)
+
+## BUG FIX
+
+* A failure to incrementally build the lesson with `sandpaper::serve()` has been
+  fixed (reported: @zkamvar, #450; fixed: @zkamvar, #451)
+
+## MISC
+
+* Lessons with markdown documents no longer use `callr::r()` as an intermediary
+  (reported: @zkamvar, #442, fixed: @zkamvar, #452)
+
+# sandpaper 0.11.15 (2023-04-05)
+
+## BUG FIX
+
+* The 404 page will now have proper styling applied when the site is deployed
+  via one of the `ci_` functions (reported: @zkamvar, #430; fixed: @zkamvar,
+  #431).
+* `sandpaper::serve()` will no longer error if a different directory is used.
+
+# sandpaper 0.11.14 (2023-04-04)
+
+## BUG FIX
+
+* A 404 page has been added (reported: @fmichonneau, #268; fixed: 
+  @zkamvar, #429)
+
+## DEPENDENCIES
+
+* The minimum version of {pegboard} has been set to 0.5.1
+
+## TEMPLATES
+
+* The README, LICENSE, CONTRIBUTING, and SETUP templates have been fixed to work
+  with {pegboard} version 0.5.1
+* The LICENSE and CONTRIBUTING templates now refer to The Carpentries as a
+  whole and provides correct links to community forums. 
+
+# sandpaper 0.11.13 (2023-03-25)
+
+## WORKAROUND
+
+* Fix an issue for {renv} version 0.17.2 where it was unable to provision
+  packages that were being used in the parent environment. This was a problem
+  in environments where the version of {sandpaper} was controlled by {renv}. 
+  (reported: https://github.com/rstudio/renv/issues/1177, @zkamvar; fixed
+  #423, @zkamvar). Note that this fix is ONLY applicable to {renv} 0.17.2
+  and will be fixed with newer versions of {renv}.
+
+# sandpaper 0.11.12 (2023-03-22)
+
+## CONTINUOUS INTEGRATION
+
+* workflow files now have explicit permissions to comment on pull requests or
+  create new branches when called. This fixes an issue where new lessons would
+  not have the ability to preview pull requests or update workflows.
+  (reported: #420, @zkamvar; fixed #421, @zkamvar)
+* the `create-pull-request` action is now coming from a fork in The Carpentries
+  organisation for security. 
+
+## MISC
+
+* A typo has been fixed in the package cache vignette
+- The CONTRIBUTING boilerplate has been updated to fix formatting issues
+
+# sandpaper 0.11.11 (2023-03-17)
+
+## BUG FIX
+
+* `update_cache()` will now work with {renv} version 0.17.1, which lost a
+  print method for the `renv_updates` class (reported: @zkamvar, #415; 
+  fixed: @zkamvar, #416 and 
+  https://github.com/zkamvar/vise/commit/ee4798701a958ee48429980eb970266885f8265b
+
+# MISC
+
+* @jcolomb has been added as a contributor in the DESCRIPTION.
+
+# sandpaper 0.11.10 (2023-03-16)
+
+## BUG FIX
+
+* New lessons will now provision `learners/resources.md`, which will allow the
+  glossary link to work (reported: @elichad, #404 and 
+  @ManonMarchand,
+  https://github.com/carpentries/workbench-template-md/issues/20; 
+  fixed: @zkamvar, #410)
+- default CONTRIBUTING file is better suited to The Workbench and no longer
+  references the now-defunct lesson-example repository (reported and fixed:
+  @jcolomb, #407)
+
+# sandpaper 0.11.9 (2023-03-14)
+
+## BUG FIX
 
 * Links to assets in instructor view no longer render a 404. (reported:
-  @brownsarahm, #404; fixed: @zkamvar, #408)
+  @brownsarahm, #404; fixed: @zkamvar, #409)
 
-CONTINUOUS INTEGRATION
-----------------------
+## CONTINUOUS INTEGRATION
 
 * Lessons with files that have spaces in their names (e.g as a learning tool)
   no longer fail to comment on pull request previews (reported: @zkamvar, #399;

R/build_404.R

@@ -0,0 +1,39 @@
+build_404 <- function(pkg, quiet) {
+  page_globals <- setup_page_globals()
+  calls <- sys.calls()
+  is_prod <- in_production(calls)
+  if (is_prod) {
+    url  <- page_globals$metadata$get()$url
+    page_globals$instructor$set(c("site", "root"), url)
+    page_globals$learner$set(c("site", "root"), url)
+  }
+  path  <- root_path(pkg$src_path)
+
+  fof <- fs::path_package("sandpaper", "templates", "404-template.txt")
+  html <- xml2::read_html(render_html(fof))
+  if (is_prod) {
+    # make sure index links back to the original root
+    lnk <- xml2::xml_find_first(html, ".//a[@href='index.html']")
+    xml2::xml_set_attr(lnk, "href", url)
+    # update navigation so that we have full URL
+    nav <- page_globals$learner$get()[c("sidebar", "more", "resources")]
+    for (item in names(nav)) {
+      new <- gsub("href='", paste0("href='", url), nav[[item]])
+      page_globals$learner$set(item, new)
+      page_globals$instructor$set(item, new)
+    }
+  }
+  fix_nodes(html)
+
+  this_dat <- list(
+    this_page = "404.html",
+    body = html,
+    pagetitle = "Page not found"
+  )
+  page_globals$instructor$update(this_dat)
+  page_globals$learner$update(this_dat)
+  page_globals$meta$update(this_dat)
+
+  build_html(template = "extra", pkg = pkg, nodes = html,
+    global_data = page_globals, path_md = "404.html", quiet = quiet)
+}