Merge pull request #131 from jhudsl/cansavvy/gha

Adding github actions and some reorganizations

.github/check_testthat.R

@@ -0,0 +1,31 @@
+# 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"))
+
+out_file <- list.files(pattern = "testthat.Rout$|Rout.fail$", file.path(root_dir, "check"),
+ recursive = TRUE, full.names = TRUE)
+
+check_content <- readLines(out_file)
+test_result <- grep("\\[ FAIL", check_content, value = TRUE)[1]
+test_result <- unlist(strsplit(test_result, "\\||\\[|\\]"))
+
+# Format the data into a dataframe
+test_result_df <- data.frame(result = trimws(test_result)) %>%
+  dplyr::filter(result != "") %>%
+  tidyr::separate(result, sep = " ", into = c("test_name", "num")) %>%
+  dplyr::mutate(num = as.numeric(num))
+
+fail_num <- test_result_df %>%
+  dplyr::filter(test_name %in% c("FAIL", "WARN")) %>%
+  dplyr::summarize(total = sum(num))
+
+fail_num <- as.character(fail_num$total)
+
+# Spit the number out
+writeLines(fail_num, con = stdout())

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

@@ -4,11 +4,9 @@ on:
   push:
     branches:
       - main
-      - master
   pull_request:
     branches:
       - main
-      - master
 
 name: R-CMD-check
 
@@ -33,13 +31,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -66,18 +64,28 @@ jobs:
 
       - name: Install dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          remotes::install_deps(dependencies = TRUE, force = TRUE)
+          remotes::install_cran("devtools")
+          sessionInfo()
         shell: Rscript {0}
 
       - 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")
+          rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
         shell: Rscript {0}
 
+      - name: Check testthat
+        if: runner.os != 'Windows'
+        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()
         uses: actions/upload-artifact@main

.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

NAMESPACE

@@ -10,7 +10,6 @@ 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)
@@ -20,6 +19,7 @@ export(check_quizzes)
 export(convert_coursera_quizzes)
 export(convert_quiz)
 export(convert_utube_link)
+export(download_ottr_template)
 export(example_repo_cleanup)
 export(example_repo_setup)
 export(extract_meta)

R/bookdown_to_leanpub.R

@@ -1,134 +1,6 @@
 #' Convert Bookdown to Leanpub
 #'
 #' @param path path to the bookdown book, must have a `_bookdown.yml` file
-#' @param output_dir output directory to put files.  It should likely be
-#' relative to path
-#' @param render if `TRUE`, then [bookdown::render_book()] will be run on each Rmd.
-#' @param verbose print diagnostic messages
-#' @param remove_resources_start remove the word `resources/` at the front
-#' of any image path.
-#' @param run_quiz_checks TRUE/FALSE run quiz checks
-#' @param make_book_txt Should [ottrpal::bookdown_to_book_txt()] be run
-#' to create a `Book.txt` in the output directory?
-#' @param quiz_dir directory that contains the quiz .md files that should be
-#' checked and incorporated into the Book.txt file. If you don't have quizzes,
-#' set this to NULL
-#' @param clean_up TRUE/FALSE the old output directory should be deleted and
-#' everything created fresh.
-#' @param footer_text Optionally can add a bit of text that will be added to the
-#' end of each file before the references section.
-#'
-#' @return A list of output files and diagnostics
-#' @export
-#'
-bookdown_to_leanpub <- function(path = ".",
-                                render = TRUE,
-                                output_dir = "manuscript",
-                                make_book_txt = FALSE,
-                                quiz_dir = "quizzes",
-                                run_quiz_checks = FALSE,
-                                remove_resources_start = FALSE,
-                                verbose = TRUE,
-                                footer_text = NULL,
-                                clean_up = FALSE) {
-  # Run the set up
-  set_up_leanpub(
-    path = path,
-    embed = FALSE,
-    clean_up = clean_up,
-    render = render,
-    output_dir = output_dir,
-    make_book_txt = make_book_txt,
-    quiz_dir = quiz_dir,
-    run_quiz_checks = run_quiz_checks,
-    remove_resources_start = remove_resources_start,
-    verbose = verbose,
-    footer_text = footer_text
-  )
-
-  # Establish path
-  path <- bookdown_path(path)
-
-  rmd_regex <- "[.][R|r]md$"
-
-  # Extract the names of the Rmd files (the chapters)
-  rmd_files <- bookdown_rmd_files(path = path)
-
-  bib_files <- list.files(pattern = "[.]bib$")
-
-  if (length(bib_files) > 0) {
-    pandoc_args <- paste0("--bibliography=", path.expand(normalizePath(bib_files)))
-  } else {
-    pandoc_args <- NULL
-  }
-
-  # run_env = new.env()
-  md_files <- sub(rmd_regex, ".md", rmd_files, ignore.case = TRUE)
-  md_files <- file.path(output_dir, basename(md_files))
-
-  for (file in md_files) {
-    if (verbose > 1) {
-      message("Replacing HTML for ", file)
-    }
-    infile <- normalizePath(file)
-
-    infile <- replace_single_html(infile,
-      verbose = verbose > 1,
-      remove_resources_start = remove_resources_start,
-      footer_text = footer_text
-    )
-
-    if (length(bib_files) > 0) {
-      if (verbose > 1) {
-        message("Making references for ", file)
-      }
-      writeLines(simple_references(infile, bib_files, add_reference_header = TRUE),
-        con = infile, sep = "\n"
-      )
-    }
-  }
-  ####################### Book.txt creation ####################################
-  out <- NULL
-  if (make_book_txt) {
-    if (verbose > 1) {
-      message("Running bookdown_to_book_txt")
-    }
-    bookdown_to_book_txt(
-      md_files = rmd_files,
-      output_dir = output_dir,
-      quiz_dir = quiz_dir,
-      verbose = verbose
-    )
-    out <- book_txt_file <- file.path(output_dir, "Book.txt")
-  } else {
-    # If false, look for Book.txt file to copy to output folder.
-    book_txt_file <- file.path(path, "Book.txt")
-
-    if (file.exists(book_txt_file)) {
-      # Copy over an existing book.txt file if it exists
-      file.copy(from = book_txt_file, to = file.path(output_dir, "Book.txt"))
-
-      out <- book_txt_file <- file.path(output_dir, "Book.txt")
-    } else {
-      # If none exists and make_book_txt is false: stop.
-      stop(paste0(
-        "Book.txt file does not exist in the main directory: ", path, "and make_book_txt is set to FALSE.",
-        "There is no Book.txt file. Leanpub needs one. Either make one and place it in the directory path or ",
-        "use make_book_txt = TRUE and one will be generated for you."
-      ))
-    }
-  }
-  ############################# Wrapping up ####################################
-  message(paste(
-    "Leanpub ready files are saved to",
-    output_dir,
-    "Go to https://leanpub.com/ to publish them using the GitHub writing mode."
-  ))
-}
-
-#' Convert Bookdown to Embed version of Leanpub
-#'
-#' @param path path to the bookdown book, must have a `_bookdown.yml` file
 #' @param chapt_img_key File path to a TSV whose contents are the chapter urls (`url`),
 #' the chapter titles (`chapt_title`), the file path to the image to be used for the chapter (`img_path`).
 #' Column names `url`, `chapt_title`, and `img_path` must be used.