Merge pull request #135 from jhudsl/cansavvy/test-framework

Adding Unit Testing Framework

.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

@@ -12,68 +12,31 @@ 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:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Check testthat
         if: runner.os != 'Windows'

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("cansav09@gmail.com","csavonen@fredhutch.org"), role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6331-7070")),
@@ -40,7 +40,7 @@ Imports:
     yaml
 Suggests:
     remotes,
-    testthat,
+    testthat (>= 3.0.0),
     tibble,
     utils
 VignetteBuilder: 
@@ -49,3 +49,4 @@ ByteCompile: true
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
+Config/testthat/edition: 3

R/bookdown_to_leanpub.R

@@ -6,7 +6,7 @@
 #' Column names `url`, `chapt_title`, and `img_path` must be used.
 #' If no chapter title column supplied, the basename of the url will be used,
 #' If no image column supplied, default image used.
-#' @param bookdown_index The file path of the rendered bookdown index.html file
+#' @param html_page The file path of the rendered index.html file
 #' @param base_url The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
 #' e.g. https://jhudatascience.org/OTTR_Template/coursera
 #' @param default_img A google slide link to the default image to be used for all chapters
@@ -40,7 +40,7 @@
 #' }
 bookdown_to_embed_leanpub <- function(path = ".",
                                       chapt_img_key = NULL,
-                                      bookdown_index = file.path(base_url, "index.html"),
+                                      html_page = file.path(base_url, "index.html"),
                                       base_url = NULL,
                                       clean_up = FALSE,
                                       default_img = NULL,
@@ -79,6 +79,7 @@ bookdown_to_embed_leanpub <- function(path = ".",
     }
     chapt_df <- get_chapters(
       html_page = paste0(base_url, "index.html"),
+      base_url = base_url
     ) %>%
       dplyr::mutate(chapt_title = gsub("\\:|\\?|\\&|\\!|\\'", "", chapt_title))
   }
@@ -293,7 +294,7 @@ make_embed_markdown <- function(url,
 
 #' Make Leanpub file that has embed webpage of a chapter
 #'
-#' @param bookdown_index The file path of the rendered bookdown index.html file
+#' @param html_page The file path of the rendered index.html file. It can be a url
 #' @param base_url The base url of where the chapters are published -- the url to provide to the iframe in Leanpub
 #' e.g. https://jhudatascience.org/OTTR_Template/coursera
 #'
@@ -302,6 +303,7 @@ make_embed_markdown <- function(url,
 #'
 #' @export
 #'
+
 get_chapters <- function(html_page = file.path("docs", "index.html"),
                          base_url = ".") {
   # Read in html

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"
   )
@@ -37,10 +37,12 @@ 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)
 }

R/utils.R

@@ -5,7 +5,8 @@
 
 utils::globalVariables(c(
   "num", "quiz_dir", "type_url", "file_name", "trimmed", "quiz",
-  "quiz_path", "type", "q_num", "verbose", "chapt_title", "data_path", "image_dir"
+  "quiz_path", "type", "q_num", "verbose", "chapt_title", "data_path", "image_dir",
+  "convert_footnotes"
 ))
 
 

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(ottrpal)
+
+test_check("ottrpal")

tests/testthat/test-quarto_leanpub_prep.R

@@ -0,0 +1,34 @@
+test_that("Create Leanpub IFrames for Quarto", {
+
+  dir <- download_ottr_template(dir = ".", type = "quarto")
+
+  quarto::quarto_render(dir,
+                        metadata = list(sidebar = F, toc = F),
+                        quarto_args = c('--output-dir', 'docs/no_toc/'))
+
+  # TODO: This should be functionalized and incorporated into the package
+  # curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R
+  # chapt_urls=$(Rscript --vanilla make_screenshots.R
+  #             --git_pat sys.getEnv("GH_PAT")
+  #             --repo fhdsl/OTTR_Quarto
+  #             --output_dir resources/chapt_screen_images)
+
+  ## TEST HERE:
+  # 1. Does each chapter have screenshot?
+  # 2. Is the file 'resources/chapt_screen_images/chapter_urls.tsv' made fresh?
+  # 2. Does chapter_urls.tsv file made have columns with information that are labeled "url", "chapt_title" and "img_path"
+
+  #ottrpal::bookdown_to_embed_leanpub(
+  #  render = FALSE,
+  #  chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv',
+  #  make_book_txt = TRUE,
+  #  quiz_dir = NULL)
+
+  ## TEST HERE:
+  # 1. Did each chapter get a md in the manuscript folder?
+  # 2. Does each md link to the appropriate sceenshot?
+  # 3. Did the screenshot file path that's in the md lead to the appropriate file path?
+
+  unlink(dir, recursive = TRUE)
+  file.remove(paste0(dir, ".zip"))
+})

tests/testthat/test-quizzes.R

@@ -0,0 +1,28 @@
+test_that("Quiz checks", {
+  # Using good quiz md example
+
+  quiz_path <- good_quiz_path()
+  good_quiz <- readLines(quiz_path)
+  good_quiz_specs <- parse_quiz(good_quiz)
+  good_quiz_checks <- check_all_questions(good_quiz_specs)
+
+  # Using bad quiz md example
+  bad_quiz <- readLines(bad_quiz_path())
+  bad_quiz_specs <- parse_quiz(bad_quiz)
+
+  # THe following checks *should fail* because we're giving it a bad quiz.
+  bad_quiz_checks <- suppressWarnings(check_all_questions(bad_quiz_specs))
+
+  ## Make a temporary quiz directory
+  quiz_dir <- dirname(good_quiz_path())
+
+  ## Now check the quizzes in that directory
+  # The following checks *should also fail* because the bad quiz is in there
+  all_quiz_results <- suppressWarnings(check_quizzes(quiz_dir = quiz_dir))
+
+  ## TEST HERE:
+  # 1. quiz_error_report.tsv should be made
+  # 2. bad quiz should have errors
+  # 3. good quiz should pass!
+
+})

tests/testthat/test-rendering.R

@@ -0,0 +1,54 @@
+test_that("Rmd Rendering", {
+  rmd_dir <- download_ottr_template(dir = ".", type = "rmd")
+
+  dir.exists(rmd_dir)
+
+  bookdown::render_book(rmd_dir)
+
+  unlink(rmd_dir, recursive = TRUE)
+  file.remove(paste0(rmd_dir, ".zip"))
+})
+
+test_that("Quarto Rendering", {
+  quarto_dir <- download_ottr_template(dir = ".", type = "quarto")
+
+  dir.exists(quarto_dir)
+
+  # Render it normal
+  quarto::quarto_render(quarto_dir, as_job = FALSE)
+
+  # Render it a different way
+  quarto::quarto_render(quarto_dir,
+                        metadata = list(sidebar = F, toc = F),
+                        quarto_args = c("--output-dir", "docs/no_toc/"),
+                        as_job = FALSE
+
+  )
+  unlink(quarto_dir, recursive = TRUE)
+  file.remove(paste0(quarto_dir, ".zip"))
+})
+
+test_that("Rmd Website Rendering", {
+  rmd_web_dir <- download_ottr_template(dir = ".", type = "rmd_website")
+
+  dir.exists(rmd_web_dir)
+
+  rmarkdown::clean_site(rmd_web_dir, preview = FALSE)
+
+  rmarkdown::render_site(rmd_web_dir)
+
+  unlink(rmd_web_dir, recursive = TRUE)
+  file.remove(paste0(rmd_web_dir, ".zip"))
+})
+
+
+test_that("Quarto Website Rendering", {
+  quarto_web_dir <- download_ottr_template(dir = ".", type = "quarto_website")
+
+  dir.exists(quarto_web_dir)
+
+  quarto::quarto_render(quarto_web_dir, as_job = FALSE)
+
+  unlink(quarto_web_dir, recursive = TRUE)
+  file.remove(paste0(quarto_web_dir, ".zip"))
+})

tests/testthat/test-rmd_leanpub_prep.R

@@ -0,0 +1,35 @@
+
+test_that("Create Leanpub IFrames for Rmd", {
+
+  dir <- download_ottr_template(dir = ".", type = "rmd")
+
+  dir.exists(dir)
+
+  bookdown::render_book(dir)
+
+  # TODO: This should be functionalized and incorporated into the package
+  # curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R
+  # Rscript --vanilla make_screenshots.R
+  #             --git_pat sys.getEnv("GH_PAT")
+  #             --repo fhdsl/OTTR_Template
+  #             --output_dir resources/chapt_screen_images)
+
+  ## TEST HERE:
+  # 1. Does each chapter have screenshot?
+  # 2. Is the file 'resources/chapt_screen_images/chapter_urls.tsv' made fresh?
+  # 2. Does chapter_urls.tsv file made have columns with information that are labeled "url", "chapt_title" and "img_path"
+
+  #ottrpal::bookdown_to_embed_leanpub(
+  #  render = FALSE,
+  #  chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv',
+  #  make_book_txt = TRUE,
+  #  quiz_dir = NULL)
+
+  ## TEST HERE:
+  # 1. Did each chapter get a md in the manuscript folder?
+  # 2. Does each md link to the appropriate sceenshot?
+  # 3. Did the screenshot file path that's in the md lead to the appropriate file path?
+
+  unlink(dir, recursive = TRUE)
+  file.remove(paste0(dir, ".zip"))
+})