Merge remote-tracking branch 'origin/main' into url_check

.Rbuildignore

@@ -32,5 +32,6 @@ vignettes/.httr-oauth$
 ^package_bundles/leanbuild_0.1.2.tar.gz*
 ^package_bundles/leanbuild_0.1.2.tgz*
 inst/extdata/tmp/default*
+quarto-session*
 
 ^CRAN-SUBMISSION$

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

@@ -12,71 +12,33 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/base_ottr
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        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
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE, force = TRUE)
+          remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("devtools")
           sessionInfo()
         shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Check
         run: |
           options(crayon.enabled = TRUE)
+          devtools::document()
+          devtools::load_all()
           rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
         shell: Rscript {0}
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
 
       - name: Check testthat
-        if: runner.os != 'Windows'
         id: check_check
         run: |
             error_num=$(Rscript --vanilla '.github/workflows/check_testthat.R')

.github/workflows/check_testthat.R

@@ -0,0 +1,48 @@
+# Check up on the testthat results
+# C. Savonen
+# Nov 2023
+
+library(magrittr)
+
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+# Read in the testthat results
+out_file <- list.files(pattern = "testthat.Rout$|Rout.fail$", file.path(root_dir, "check"),
+ recursive = TRUE, full.names = TRUE)
+
+# Extract testhat results
+testthat_check_content <- readLines(out_file)
+testthat_result <- grep("\\[ FAIL", testthat_check_content, value = TRUE)[1]
+testthat_result <- unlist(strsplit(testthat_result, "\\||\\[|\\]"))
+
+# Read in standard check results
+check_content <- readLines(file.path(root_dir, "check", "ottrpal.Rcheck", "00check.log"))
+
+# Extract standard check results
+check_result <- grep("Status\\:", check_content, value = TRUE)
+check_result <- unlist(strsplit(check_result, ","))
+check_result <- stringr::str_remove(check_result, "Status:| ")
+
+# Format the data into a dataframe
+testthat_result_df <- data.frame(result = trimws(testthat_result)) %>%
+  dplyr::filter(result != "") %>%
+  tidyr::separate(result, sep = " ", into = c("test_name", "num")) %>%
+  dplyr::mutate(num = as.numeric(num))
+
+# Do the same for the check results
+check_result_df <- data.frame(result = trimws(check_result)) %>%
+  tidyr::separate(result, sep = " ", into = c("num", "test_name")) %>%
+  dplyr::mutate(num = as.numeric(num)) %>%
+  dplyr::select("test_name", "num")
+
+# We only want warnings or errors or fails
+fail_num <- dplyr::bind_rows(check_result_df, testthat_result_df) %>%
+  dplyr::filter(test_name %in% c("FAIL", "WARN", "WARNINGs", "ERROR")) %>%
+  dplyr::summarize(total = sum(num))
+
+fail_num <- as.character(fail_num$total)
+
+# Spit the number out
+writeLines(fail_num, con = stdout())

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: ottrpal
 Title: Companion Tools for Open-Source Tools for Training Resources (OTTR)
-Version: 1.2.1
+Version: 1.3.0
 Authors@R: c(
     person("Candace", "Savonen", , c("[email protected]","[email protected]"), role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6331-7070")),
@@ -23,7 +23,6 @@ Imports:
     curl,
     dplyr,
     fs,
-    glue,
     httr,
     jsonlite,
     knitr (>= 1.33),
@@ -36,16 +35,19 @@ Imports:
     rprojroot,
     rvest,
     stringr,
+    webshot2,
     xml2,
     yaml
 Suggests:
-    remotes,
-    testthat,
+    testthat (>= 3.0.0),
     tibble,
     utils
+Remotes: 
+    jhudsl/cow
 VignetteBuilder: 
     knitr
 ByteCompile: true
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
+Config/testthat/edition: 3

NAMESPACE

@@ -4,12 +4,6 @@ export("%>%")
 export(auth_from_secret)
 export(authorize)
 export(bad_quiz_path)
-export(bookdown_destination)
-export(bookdown_file)
-export(bookdown_path)
-export(bookdown_rmd_files)
-export(bookdown_to_book_txt)
-export(bookdown_to_embed_leanpub)
 export(check_all_questions)
 export(check_question)
 export(check_quiz)
@@ -18,44 +12,43 @@ export(check_quiz_question_attributes)
 export(check_quizzes)
 export(convert_coursera_quizzes)
 export(convert_quiz)
-export(convert_utube_link)
+export(course_path)
+export(course_to_book_txt)
 export(download_ottr_template)
-export(example_repo_cleanup)
-export(example_repo_setup)
 export(extract_meta)
 export(extract_object_id)
 export(extract_quiz)
-export(get_bookdown_spec)
 export(get_chapters)
 export(get_gs_pptx)
 export(get_image_from_slide)
 export(get_image_link_from_slide)
 export(get_object_id_notes)
+export(get_pages_url)
 export(get_slide_id)
 export(get_slide_page)
+export(get_yaml_spec)
 export(good_quiz_path)
 export(gs_id_from_slide)
 export(gs_png_download)
 export(gs_png_url)
 export(include_slide)
-export(leanpub_check)
 export(make_embed_markdown)
+export(make_screenshots)
+export(output_destination)
 export(parse_q_tag)
 export(parse_quiz)
 export(parse_quiz_df)
 export(pptx_notes)
 export(pptx_slide_note_df)
 export(pptx_slide_text_df)
-export(remove_yaml_header)
+export(qrmd_files)
 export(render_without_toc)
-export(replace_html)
-export(replace_single_html)
 export(set_knitr_image_path)
 export(set_up_leanpub)
-export(simple_references)
 export(unzip_pptx)
+export(website_to_embed_leanpub)
 export(xml_notes)
-importFrom(fs,dir_copy)
+import(dplyr)
 importFrom(httr,GET)
 importFrom(httr,accept_json)
 importFrom(httr,config)
@@ -67,10 +60,13 @@ importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(openssl,aes_cbc_decrypt)
 importFrom(readr,write_tsv)
+importFrom(rprojroot,find_root)
+importFrom(rprojroot,has_dir)
 importFrom(utils,download.file)
 importFrom(utils,installed.packages)
 importFrom(utils,menu)
 importFrom(utils,unzip)
+importFrom(webshot2,webshot)
 importFrom(xml2,read_xml)
 importFrom(xml2,xml_find_all)
 importFrom(xml2,xml_text)

R/coursera_and_leanpub.R

@@ -197,9 +197,10 @@ convert_coursera_quizzes <- function(input_quiz_dir = "quizzes",
   )
 }
 
-#' Create TOC-less Bookdown for use in Coursera
+#' Create TOC-less course website for use in Coursera or Leanpub
 #'
-#' Create a version of Leanpub that does not have a TOC and has quizzes in the Coursera yaml format. Requires Bookdown output files including "assets", "resources", and "libs".
+#' Create a version of the course that does not have a TOC and has quizzes in the Coursera yaml format.
+#' This is only needed to be used on Bookdown courses. Quarto has a simple command for this. 
 #'
 #' @param output_dir A folder (existing or not) that the TOC-less Bookdown for Coursera files should be saved. By default is file.path("docs", "coursera")
 #' @param output_yaml A output.yml file to be provided to bookdown. By default is "_output.yml"
@@ -220,8 +221,8 @@ render_without_toc <- function(output_dir = file.path("docs", "no_toc"),
                                input_quiz_dir = "quizzes",
                                output_quiz_dir = "coursera_quizzes",
                                verbose = TRUE) {
-  # Find root directory by finding `_bookdown.yml` file
-  root_dir <- bookdown_path()
+  # Find root directory by finding `.git` folder
+  root_dir <- course_path()
 
   # Output files:
   output_dir <- file.path(root_dir, output_dir)

R/data.R

@@ -19,7 +19,7 @@ download_ottr_template <- function(dir = "inst/extdata", type = "rmd") {
 
   url <- switch(type,
     rmd = "https://github.com/jhudsl/OTTR_Template/archive/refs/heads/main.zip",
-    quarto = "https://github.com/fhdsl/ottr/archive/refs/heads/main.zip",
+    quarto = "https://github.com/fhdsl/OTTR_Quarto/archive/refs/heads/main.zip",
     rmd_website = "https://github.com/jhudsl/OTTR_Template_Website/archive/refs/heads/main.zip",
     quarto_website = "https://github.com/fhdsl/OTTR_Quarto_Website/archive/refs/heads/main.zip"
   )
@@ -37,14 +37,48 @@ download_ottr_template <- function(dir = "inst/extdata", type = "rmd") {
     download.file(url,
       destfile = file_path
     )
+  }
+  output_dir <- stringr::str_remove(file.path(dir, file_name), ".zip")
 
+  if (!dir.exists(output_dir)) {
     unzip(file_path, exdir = dir)
   }
-  output_dir <- stringr::str_remove(file.path(dir, file_name), ".zip")
 
   return(output_dir)
 }
 
+
+#' Path to good example quiz
+#'
+#' @export
+#' @return The file path to an example good quiz included in the package that should pass the quiz checks.
+#'
+good_quiz_path <- function() {
+  list.files(
+    pattern = "quiz_good.md$",
+    recursive = TRUE,
+    system.file("extdata", package = "ottrpal"),
+    full.names = TRUE
+  )
+}
+
+#' Path to bad example quiz
+#'
+#' @export
+#' @return The file path to an example bad quiz included in the package that will fail the quiz checks.
+#'
+#' @examples
+#'
+#' quiz_path <- bad_quiz_path()
+bad_quiz_path <- function() {
+  list.files(
+    pattern = "quiz_bad.md$",
+    recursive = TRUE,
+    system.file("extdata", package = "ottrpal"),
+    full.names = TRUE
+  )
+}
+
 #' Get file path to an key encryption RDS
 key_encrypt_creds_path <- function() {
   list.files(