Merge branch gh-pages of carpentries/styles

Author: maxim-belkin

.gitignore

@@ -13,4 +13,5 @@ _site
 .bundle/
 .vendor/
 .docker-vendor/
-Gemfile.lock
+Gemfile.lock
+.*history

Makefile

@@ -6,7 +6,6 @@ export SHELL = /bin/bash
 
 # Settings
 MAKEFILES=Makefile $(wildcard *.mk)
-JEKYLL_VERSION=3.8.5
 JEKYLL=bundle install --path .vendor/bundle && bundle update && bundle exec jekyll
 PARSER=bin/markdown_ast.rb
 DST=_site
@@ -54,11 +53,14 @@ site : lesson-md
 
 ## * docker-serve     : use Docker to serve the site
 docker-serve :
-	docker run --rm -it --volume ${PWD}:/srv/jekyll \
-           --volume=${PWD}/.docker-vendor/bundle:/usr/local/bundle \
-           -p 127.0.0.1:4000:4000 \
-           jekyll/jekyll:${JEKYLL_VERSION} \
-           bin/run-make-docker-serve.sh
+	docker pull carpentries/lesson-docker:latest
+	docker run --rm -it \
+		-v $${PWD}:/home/rstudio \
+		-p 4000:4000 \
+		-p 8787:8787 \
+		-e USERID=$$(id -u) \
+		-e GROUPID=$$(id -g) \
+		carpentries/lesson-docker:latest
 
 ## * repo-check       : check repository settings
 repo-check :

_includes/links.md

@@ -35,7 +35,7 @@
 [pandoc]: https://pandoc.org/
 [paper-now]: https://github.com/PeerJ/paper-now
 [python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
-[pyyaml]: https://pypi.python.org/pypi/PyYAML
+[pyyaml]: https://pypi.org/project/PyYAML/
 [r-markdown]: https://rmarkdown.rstudio.com/
 [rstudio]: https://www.rstudio.com/
 [ruby-install-guide]: https://www.ruby-lang.org/en/downloads/

assets/css/lesson.scss

@@ -10,6 +10,7 @@ $color-brand:       #2b3990 !default;
 
 // code boxes
 $color-error:       #bd2c00 !default;
+$color-warning:     #cda01d !default;
 $color-output:      #303030 !default;
 $color-source:      #360084 !default;
 
@@ -36,9 +37,10 @@ $color-testimonial: #fc8dc1 !default;
     border-radius: 4px 0 0 4px;
 }
 
-.error  { @include cdSetup($color-error); }
-.output { @include cdSetup($color-output); }
-.source { @include cdSetup($color-source); }
+.error   { @include cdSetup($color-error); }
+.warning { @include cdSetup($color-warning); }
+.output  { @include cdSetup($color-output); }
+.source  { @include cdSetup($color-source); }
 
 .bash, .language-bash     { @include cdSetup($color-source); }
 .make, .language-make     { @include cdSetup($color-source); }
@@ -48,6 +50,7 @@ $color-testimonial: #fc8dc1 !default;
 .sql, .language-sql       { @include cdSetup($color-source); }
 
 .error::before,
+.warning:before,
 .output::before,
 .source::before,
 .bash::before, .language-bash::before,
@@ -56,13 +59,14 @@ $color-testimonial: #fc8dc1 !default;
 .python::before, .language-python::before,
 .r::before, .language-r::before,
 .sql::before, .language-sql::before {
-  background-color: #f2eff6;
-  display: block;
-  font-weight: bold;
-  padding: 5px 10px;
+    background-color: #f2eff6;
+    display: block;
+    font-weight: bold;
+    padding: 5px 10px;
 }
 
 .error::before  { background-color: #ffebe6; content: "Error"; }
+.warning:before { background-color: #f8f4e8; content:" Warning"; }
 .output::before { background-color: #efefef; content: "Output"; }
 .source::before { content: "Code"; }
 .bash::before, .language-bash::before { content: "Bash"; }

bin/chunk-options.R

@@ -48,16 +48,23 @@ hook_in <- function(x, options) {
 hook_out <- function(x, options) {
   x <- gsub("\n$", "", x)
   stringr::str_c("\n\n~~~\n",
-                 paste0(x, collapse="\n"),
-                 "\n~~~\n{: .output}\n\n")
+    paste0(x, collapse="\n"),
+    "\n~~~\n{: .output}\n\n")
 }
 
 hook_error <- function(x, options) {
   x <- gsub("\n$", "", x)
   stringr::str_c("\n\n~~~\n",
-                 paste0(x, collapse="\n"),
-                 "\n~~~\n{: .error}\n\n")
+    paste0(x, collapse="\n"),
+    "\n~~~\n{: .error}\n\n")
+}
+
+hook_warning <- function(x, options) {
+  x <- gsub("\n$", "", x)
+  stringr::str_c("\n\n~~~\n",
+    paste0(x, collapse = "\n"),
+    "\n~~~\n{: .warning}\n\n")
 }
 
-knit_hooks$set(source = hook_in, output = hook_out, warning = hook_error,
-               error = hook_error, message = hook_out)
+knit_hooks$set(source = hook_in, output = hook_out, warning = hook_warning,
+  error = hook_error, message = hook_out)

bin/generate_md_episodes.R

@@ -1,20 +1,21 @@
 generate_md_episodes <- function() {
 
-  library("methods")
-  
-  if (!require("remotes", quietly = TRUE)) {
-    install.packages("remotes", repos = c(CRAN = "https://cloud.r-project.org/"))
+  if (!requireNamespace("renv", quietly = TRUE)) {
+    install.packages("renv", repos = c(CRAN = "https://cloud.r-project.org/"))
   }
 
-  if (!require("requirements", quietly = TRUE)) {
-    remotes::install_github("hadley/requirements")
+  if (!requireNamespace("rprojroot", quietly = TRUE)) {
+    install.packages("rprojroot", repos = c(CRAN = "https://cloud.r-project.org/"))
   }
 
+  cfg  <- rprojroot::has_file_pattern("^_config.y*ml$")
+  root <- rprojroot::find_root(cfg)
+
   required_pkgs <- unique(c(
     ## Packages for episodes
-    requirements:::req_dir("_episodes_rmd"),
+    renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
     ## Pacakges for tools
-    requirements:::req_dir("bin")
+    renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
   ))
 
   missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
@@ -28,7 +29,8 @@ generate_md_episodes <- function() {
   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
+  ## get the Rmd file to process from the command line, and generate the path
+  ## for their respective outputs
   args  <- commandArgs(trailingOnly = TRUE)
   if (!identical(length(args), 2L)) {
     stop("input and output file must be passed to the script")
@@ -40,20 +42,28 @@ generate_md_episodes <- function() {
   ## knit the Rmd into markdown
   knitr::knit(src_rmd, output = dest_md)
 
-    # Read the generated md files and add comments advising not to edit them
-    vapply(dest_md, function(y) {
-      con <- file(y)
-      mdfile <- readLines(con)
-      if (mdfile[1] != "---")
-        stop("Input file does not have a valid header")
-      mdfile <- append(mdfile, "# Please do not edit this file directly; it is auto generated.", after = 1)
-      mdfile <- append(mdfile, paste("# Instead, please edit",
-                                     basename(y), "in _episodes_rmd/"), after = 2)
-      writeLines(mdfile, con)
-      close(con)
-      return(paste("Warning added to YAML header of", y))
-    },
-    character(1))
+  # Read the generated md files and add comments advising not to edit them
+  add_no_edit_comment <- function(y) {
+    con <- file(y)
+    mdfile <- readLines(con)
+    if (mdfile[1] != "---")
+      stop("Input file does not have a valid header")
+    mdfile <- append(
+      mdfile,
+      "# Please do not edit this file directly; it is auto generated.",
+      after = 1
+    )
+    mdfile <- append(
+      mdfile,
+      paste("# Instead, please edit", basename(y), "in _episodes_rmd/"),
+      after = 2
+    )
+    writeLines(mdfile, con)
+    close(con)
+    return(paste("Warning added to YAML header of", y))
+  }
+
+  vapply(dest_md, add_no_edit_comment, character(1))
 }
 
 generate_md_episodes()