Merge branch 'main' into ki/refactor

.Rbuildignore

@@ -32,4 +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

@@ -4,79 +4,49 @@ on:
   push:
     branches:
       - main
-      - master
   pull_request:
     branches:
       - main
-      - master
 
 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@v3
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$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"))')
+      - uses: actions/checkout@v4
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          remotes::install_cran("devtools")
+          sessionInfo()
         shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), check_dir = "check")
+          devtools::document()
+          devtools::load_all()
+          rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
         shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check testthat
+        id: check_check
+        run: |
+            error_num=$(Rscript --vanilla '.github/workflows/check_testthat.R')
+            echo "error_num=$error_num" >> $GITHUB_OUTPUT
+
+      - name: Stop if there are errors!
+        if: ${{ steps.check_check.outputs.error_num != '0' }}
+        run: exit 1
 
       - name: Upload check results
         if: failure()

.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())

.github/workflows/docker-build.yml

@@ -0,0 +1,62 @@
+# Candace Savonen Jan 2024
+
+name: Build Docker
+
+on:
+  workflow_dispatch:
+    inputs:
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: true
+        default: 'false'
+
+jobs:
+  build-docker:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v3
+        with:
+          token: ${{secrets.GH_PAT}}
+          fetch-depth: 0
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Get token
+        run: echo ${{ secrets.GH_PAT }} > ${{ github.workspace }}/inst/extdata/docker/git_token.txt
+
+      # Build docker image
+      - name: Build Docker image
+        uses: docker/build-push-action@v5
+        with:
+          push: false
+          load: true
+          context: inst/extdata/docker
+          tags: cansav09/metricminer
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        run: |
+          docker push cansav09/metricminer

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.2.1
+Date: 2024-01-09 15:20:24 UTC
+SHA: 60a69efa2a507c472471cf7ffb7c8d7d370d66ab

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),
@@ -41,7 +40,7 @@ Imports:
 Suggests:
     remotes,
     cow,
-    testthat,
+    testthat (>= 3.0.0),
     tibble,
     utils
 VignetteBuilder: 
@@ -50,3 +49,4 @@ ByteCompile: true
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
+Config/testthat/edition: 3

NAMESPACE

@@ -4,57 +4,47 @@ 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(bookdown_to_leanpub)
 export(check_all_questions)
 export(check_question)
 export(check_quiz)
 export(check_quiz_attributes)
 export(check_quiz_question_attributes)
 export(check_quizzes)
 export(convert_coursera_quizzes)
-export(convert_footnotes)
 export(convert_quiz)
-export(convert_utube_link)
-export(example_repo_cleanup)
-export(example_repo_setup)
+export(course_path)
+export(course_to_book_txt)
+export(download_ottr_template)
 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_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(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)
 import(bookdown_path)
 import(cow)

R/auth.R

@@ -78,7 +78,6 @@ authorize <- function(token = NULL, cache = FALSE, ...) {
 #' }
 #'
 auth_from_secret <- function(access_token = NULL, refresh_token = NULL) {
-
   # If no tokens are specified, we'll grab the default ones.
   if (is.null(access_token) | is.null(refresh_token)) {
     decrypted <- openssl::aes_cbc_decrypt(