From 446e1b03d6d6f69cb5d908b163c2ab017cbce99f Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 11:42:13 -0500 Subject: [PATCH 1/7] Add spell check --- R/auth.R | 11 ++- R/book_txt.R | 6 +- R/get_data.R | 26 +++---- R/github_handling.R | 4 +- R/google_slides.R | 1 - R/leanpub.R | 5 +- R/quiz_formatting.R | 1 - R/spell_check.R | 95 ++++++++++++++++++++++++ R/{token-handlers.R => token_handlers.R} | 0 R/{url-check.R => url_check.R} | 7 +- R/utils.R | 1 - inst/extdata/dictionary.txt | 67 +++++++++++++++++ inst/extdata/exclude_files.txt | 8 ++ inst/extdata/ignore-urls.txt | 5 ++ tests/testthat/test-spell-check.R | 64 ++++++++++++++++ 15 files changed, 264 insertions(+), 37 deletions(-) create mode 100644 R/spell_check.R rename R/{token-handlers.R => token_handlers.R} (100%) rename R/{url-check.R => url_check.R} (98%) create mode 100644 inst/extdata/dictionary.txt create mode 100644 inst/extdata/exclude_files.txt create mode 100644 inst/extdata/ignore-urls.txt create mode 100644 tests/testthat/test-spell-check.R diff --git a/R/auth.R b/R/auth.R index 25339e96..36a96039 100644 --- a/R/auth.R +++ b/R/auth.R @@ -16,7 +16,6 @@ #' authorize("github") #' #' authorize("google") -#' #' } authorize <- function(app_name = NULL, cache = FALSE, @@ -242,11 +241,11 @@ find_scopes <- function(app_name) { ### Declare all the scopes scopes <- list( google = c( - "https://www.googleapis.com/auth/drive", - "https://www.googleapis.com/auth/drive.file", - "https://www.googleapis.com/auth/drive.readonly", - "https://www.googleapis.com/auth/presentations", - "https://www.googleapis.com/auth/presentations.readonly" + "https://www.googleapis.com/auth/drive", + "https://www.googleapis.com/auth/drive.file", + "https://www.googleapis.com/auth/drive.readonly", + "https://www.googleapis.com/auth/presentations", + "https://www.googleapis.com/auth/presentations.readonly" ), github = c("repo") ) diff --git a/R/book_txt.R b/R/book_txt.R index 962a3fb4..a56e8c45 100644 --- a/R/book_txt.R +++ b/R/book_txt.R @@ -1,4 +1,3 @@ - #' Create Book.txt file from files existing in quiz directory #' #' @param path path to the bookdown or quarto course repository, must have a `_bookdown.yml` or `_quarto.yml` file @@ -84,8 +83,7 @@ course_to_book_txt <- function(path = ".", #' @export #' qrmd_files <- function(path = ".") { - - yaml <- list.files(path = path, pattern ="_bookdown.yml|_quarto.yml", full.names = TRUE) + yaml <- list.files(path = path, pattern = "_bookdown.yml|_quarto.yml", full.names = TRUE) spec <- yaml::read_yaml(yaml) @@ -95,7 +93,7 @@ qrmd_files <- function(path = ".") { rmd_files <- spec$rmd_files } if (basename(yaml) == "_quarto.yml") { - qmd_files <- grep(".qmd", unlist(spec$book$chapters), value = TRUE) + qmd_files <- grep(".qmd", unlist(spec$book$chapters), value = TRUE) } if (length(rmd_files) > 0 && length(qmd_files) > 0) stop("Both qmd and rmd files are found. Not sure what format to expect") diff --git a/R/get_data.R b/R/get_data.R index 7d3b8d92..8b600157 100644 --- a/R/get_data.R +++ b/R/get_data.R @@ -46,19 +46,19 @@ setup_ottr_template <- function(dir = ".", type, render = TRUE) { ## Render it if (render) { - if (type == "rmd") bookdown::render_book(output_dir) - if (type == "rmd_website") rmarkdown::render_site(output_dir) - - if (type == "quarto" | type == "quarto_website") { - quarto::quarto_render(output_dir, as_job = FALSE) - } - if (type == "quarto") { - quarto::quarto_render(output_dir, - metadata = list(sidebar = F, toc = F), - quarto_args = c("--output-dir", "docs/no_toc/"), - as_job = FALSE - ) - } + if (type == "rmd") bookdown::render_book(output_dir) + if (type == "rmd_website") rmarkdown::render_site(output_dir) + + if (type == "quarto" | type == "quarto_website") { + quarto::quarto_render(output_dir, as_job = FALSE) + } + if (type == "quarto") { + quarto::quarto_render(output_dir, + metadata = list(sidebar = F, toc = F), + quarto_args = c("--output-dir", "docs/no_toc/"), + as_job = FALSE + ) + } } return(output_dir) } diff --git a/R/github_handling.R b/R/github_handling.R index 0c4c1029..5807060a 100644 --- a/R/github_handling.R +++ b/R/github_handling.R @@ -136,7 +136,6 @@ get_pages_url <- function(repo_name, get_repo_info <- function(repo_name, token = NULL, verbose = FALSE) { - # Try to get credentials other way if (is.null(token)) { # Get auth token @@ -205,8 +204,7 @@ get_repo_info <- function(repo_name, #' #' authorize("github") #' check_git_repo("jhudsl/OTTR_Template") -#' -#'} +#' } check_git_repo <- function(repo_name, token = NULL, silent = TRUE, diff --git a/R/google_slides.R b/R/google_slides.R index 80e41b60..958c262d 100644 --- a/R/google_slides.R +++ b/R/google_slides.R @@ -78,7 +78,6 @@ get_slide_page <- function(url) { #' @param output_dir path to output png #' @param overwrite should the slide PNG be overwritten? gs_png_download <- function(url, output_dir = ".", overwrite = TRUE) { - id <- get_slide_id(url) slide_id <- get_slide_page(url) url <- gs_png_url(url) diff --git a/R/leanpub.R b/R/leanpub.R index b9e51771..b546cbaf 100644 --- a/R/leanpub.R +++ b/R/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 clean_up Should the previous docs and manuscript folder be cleaned up? +#' @param clean_up Should the previous docs and manuscript folder be cleaned up? #' @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 @@ -52,7 +52,6 @@ website_to_embed_leanpub <- function(path = ".", remove_resources_start = FALSE, verbose = TRUE, footer_text = "") { - # Find the OTTR course root_dir <- course_path(path = path) @@ -60,7 +59,6 @@ website_to_embed_leanpub <- function(path = ".", rooted_quiz_dir <- file.path(root_dir, quiz_dir) if (clean_up) { - if (dir.exists(rooted_output_dir)) { message(paste("Clearing out old version of output files:", rooted_output_dir)) @@ -271,7 +269,6 @@ make_embed_markdown <- function(path = ".", get_chapters <- function(path = ".", html_page = file.path("docs", "index.html"), base_url = ".") { - # Put this relative to project path html_page <- file.path(root_dir, html_page) diff --git a/R/quiz_formatting.R b/R/quiz_formatting.R index 7a1956db..be92dd57 100644 --- a/R/quiz_formatting.R +++ b/R/quiz_formatting.R @@ -844,7 +844,6 @@ check_quizzes <- function(path = ".", write_report = TRUE, verbose = TRUE, ignore_coursera = TRUE) { - files <- list.files( pattern = "\\.md", ignore.case = TRUE, diff --git a/R/spell_check.R b/R/spell_check.R new file mode 100644 index 00000000..4e6b37e1 --- /dev/null +++ b/R/spell_check.R @@ -0,0 +1,95 @@ +#' Check spelling of all md,rmd, and qmd files +#' +#' @param path path to the bookdown or quarto course repository, must have a +#' `.github` folder which will be used to establish the top of the repo. +#' @param output_dir A relative file path to the folder (existing or not) that the +#' output check file should be saved to. Default is "check_reports" +#' @param resources_dir A relative file path to the folder (existing or not) that the +#' dictionary.txt file and exclude_files.txt will be found. Default is "resources". +#' If no dictionary.txt file and exclude_files.txt files are found, we will download one. +#' @param file_pattern A file pattern should we be looking for for the files whose +#' spelling should be tested. Default is "md$". Regex interpreted. +#' @return A file will be saved that lists the broken URLs will be saved to the specified output_dir. +#' @export +#' +#' @importFrom magrittr +#' +#' @examples +#' +#' rmd_dir <- setup_ottr_template(dir = ".", type = "rmd", render = FALSE) +#' +#' check_spelling(rmd_dir) +#' +#' # If there are broken URLs they will be printed in a list at "check_reports/url_checks.tsv" +#' +#' qmd_dir <- setup_ottr_template(dir = ".", type = "qmd", render = FALSE) +#' +#' check_spelling(qmd_dir) +#' +check_spelling <- function(path = ".", + output_dir = "check_reports", + resources_dir = "resources", + file_pattern = "md$") { + # Find .git root directory + root_dir <- rprojroot::find_root(path = path, rprojroot::has_dir(".github")) + + resources_dir <- file.path(root_dir, resources_dir) + output_dir <- file.path(root_dir, output_dir) + + if (!dir.exists(output_dir)) { + dir.create(output_dir, recursive = TRUE, showWarnings = FALSE) + } + if (!dir.exists(resources_dir)) { + dir.create(resources_dir, recursive = TRUE, showWarnings = FALSE) + } + + output_file <- file.path(output_dir, "spell_check_results.tsv") + dictionary_file <- file.path(resources_dir, "dictionary.txt") + exclude_file <- file.path(resources_dir, "exclude_files.txt") + + # Read in dictionary file if it exists + if (file.exists(dictionary_file)) { + dictionary <- readLines(dictionary_file) + } else { + dictionary <- "" + } + + # Read in ignore urls file if it exists + if (file.exists(exclude_file)) { + exclude_file <- readLines(exclude_file) + } else { + exclude_file <- "" + } + + # Only declare `.Rmd` files but not the ones in the style-sets directory + files <- list.files(pattern = file_pattern, recursive = TRUE, full.names = TRUE) + + if (exclude_file[1] != "") files <- grep(paste0(exclude_file, collapse = "|"), files, invert = TRUE, value = TRUE) + + tryCatch( + expr = { + # Run spell check + sp_errors <- spelling::spell_check_files(files, ignore = dictionary) + + if (nrow(sp_errors) > 0) { + sp_errors <- sp_errors %>% + data.frame() %>% + tidyr::unnest(cols = found) %>% + tidyr::separate(found, into = c("file", "lines"), sep = ":") + } else { + sp_errors <- data.frame(errors = NA) + } + }, + error = function(e) { + stop("Spell check did not work. Check that your dictionary is formatted correctly. You cannot have special characters (e.g., Diné) in the dictionary.txt file. You need to use HTML formatting (e.g., Diné) for these.") + } + ) + + # Print out how many spell check errors + write(nrow(sp_errors), stdout()) + + # Save spell errors to file temporarily + readr::write_tsv(sp_errors, output_file) + + message(paste0("Saved to: ", output_file)) +} diff --git a/R/token-handlers.R b/R/token_handlers.R similarity index 100% rename from R/token-handlers.R rename to R/token_handlers.R diff --git a/R/url-check.R b/R/url_check.R similarity index 98% rename from R/url-check.R rename to R/url_check.R index a78f625a..5d0944a2 100644 --- a/R/url-check.R +++ b/R/url_check.R @@ -74,9 +74,9 @@ check_urls <- function(path = ".", if (nrow(all_urls_df) > 0) { if (!report_all) { - all_urls_df <- all_urls_df %>% - dplyr::filter(urls_status == "failed") %>% - readr::write_tsv(output_file) + all_urls_df <- all_urls_df %>% + dplyr::filter(urls_status == "failed") %>% + readr::write_tsv(output_file) } } else { all_urls_df <- data.frame(errors = NA) @@ -103,7 +103,6 @@ check_urls <- function(path = ".", #' @importFrom magrittr #' test_url <- function(url, ignore_urls = "") { - if (url %in% ignore_urls) { message(paste0("Ignoring: ", url)) return("ignored") diff --git a/R/utils.R b/R/utils.R index 7c6ee358..e7963b2b 100644 --- a/R/utils.R +++ b/R/utils.R @@ -17,7 +17,6 @@ utils::globalVariables(c( #' @export #' course_path <- function(path = ".") { - # Find .git root directory root_dir <- rprojroot::find_root(has_dir(".github"), path = path) diff --git a/inst/extdata/dictionary.txt b/inst/extdata/dictionary.txt new file mode 100644 index 00000000..1520d003 --- /dev/null +++ b/inst/extdata/dictionary.txt @@ -0,0 +1,67 @@ +AnVIL +Audiographer +Audiography +automagic +BIPOC +Bloomberg +Bookdown +chapt +Coursera +creativecommons +css +Datatrail +DataTrail +DISCOVERABLE +Dockerfile +Dockerhub +dropdown +enforceability +faq +favicon +FirstName +Funder +fyi +GDSCN +Generis +GH +Github +GitHub +https +ies +iframe +immunities +impactful +ITCR +itcrtraining +ITN +LastName +Leanpub +Licensor +LICENSOR +Markua +mentorship +MERCHANTABILITY +Muschelli +NCI +NHGRI +OTTR +ottrpal +ottrproject +Pandoc +png +pre +reproducibility +rmarkdown +RMarkdown +Savonen +sexualized +socio +synched +tada +UE +UE5 +underserved +Videographer +Videography +WIPO +www diff --git a/inst/extdata/exclude_files.txt b/inst/extdata/exclude_files.txt new file mode 100644 index 00000000..5525a403 --- /dev/null +++ b/inst/extdata/exclude_files.txt @@ -0,0 +1,8 @@ +About.Rmd +docs/* +style-sets/* +manuscript/* +CONTRIBUTING.md +LICENSE.md +code_of_conduct.md +README.md diff --git a/inst/extdata/ignore-urls.txt b/inst/extdata/ignore-urls.txt new file mode 100644 index 00000000..66f04c35 --- /dev/null +++ b/inst/extdata/ignore-urls.txt @@ -0,0 +1,5 @@ +https://www.someurl.html +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html][v2.0]. +https://www.contributor-covenant.org/faq][FAQ]. +https://www.contributor-covenant.org/translations][translations]. +https://github.com/jhudsl/OTTR_Template/issues/new/choose)! diff --git a/tests/testthat/test-spell-check.R b/tests/testthat/test-spell-check.R new file mode 100644 index 00000000..70cd88de --- /dev/null +++ b/tests/testthat/test-spell-check.R @@ -0,0 +1,64 @@ + +output_file <- file.path("check_reports", "spell_check_results.tsv") + +test_that("Test spell checks for OTTR main", { + + rmd_dir <- setup_ottr_template(type = "rmd", render = FALSE) + + status <- check_spelling(rmd_dir) + testthat::expect_true(status == 0) + + # Make sure the report exists + testthat::expect_true(file.exists(file.path(rmd_dir, output_file))) + results <- readr::read_tsv(file.path(rmd_dir, output_file)) + + # It should be a data.frame + testthat::expect_true(is.data.frame(results)) + clean_up() +}) + +test_that("Test spell checks for OTTR Quarto main", { + qmd_dir <- setup_ottr_template(type = "qmd", render = FALSE) + + status <- check_spelling(qmd_dir) + testthat::expect_true(status == 0) + + # Make sure the report exists + testthat::expect_true(file.exists(file.path(qmd_dir, output_file))) + results <- readr::read_tsv(file.path(qmd_dir, output_file)) + + # It should be a data.frame + testthat::expect_true(is.data.frame(results)) + clean_up() +}) + +test_that("Test spell checks for OTTR web", { + rmd_web <- setup_ottr_template(type = "rmd_website", render = FALSE) + + status <- check_spelling(rmd_web) + testthat::expect_true(status == 0) + + # Make sure the report exists + testthat::expect_true(file.exists(file.path(rmd_web, output_file))) + results <- readr::read_tsv(file.path(rmd_web, output_file)) + + # It should be a data.frame + testthat::expect_true(is.data.frame(results)) + clean_up() +}) + +test_that("Test spell checks for OTTR Quarto web", { + ## Test spell + qmd_web <- setup_ottr_template(type = "quarto_website", render = FALSE) + + status <- check_spelling(qmd_web) + testthat::expect_true(status == 0) + + # Make sure the report exists + testthat::expect_true(file.exists(file.path(qmd_web, output_file))) + results <- readr::read_tsv(file.path(qmd_web, output_file)) + + # It should be a data.frame + testthat::expect_true(is.data.frame(results)) + clean_up() +}) From 86c034486e7a7eba9e9516237fdfba7c9465dec3 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 11:47:10 -0500 Subject: [PATCH 2/7] Fix spelling --- tests/testthat/test-check-urls.R | 2 +- tests/testthat/test-spell-check.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat/test-check-urls.R b/tests/testthat/test-check-urls.R index ed335b1c..80428796 100644 --- a/tests/testthat/test-check-urls.R +++ b/tests/testthat/test-check-urls.R @@ -19,7 +19,7 @@ test_that("Test URL checks for OTTR main", { }) test_that("Test URL checks for OTTR Quarto main", { - qmd_dir <- setup_ottr_template(type = "qmd", render = FALSE) + qmd_dir <- setup_ottr_template(type = "quarto", render = FALSE) status <- check_urls(qmd_dir) testthat::expect_true(status == 0) diff --git a/tests/testthat/test-spell-check.R b/tests/testthat/test-spell-check.R index 70cd88de..33a6235a 100644 --- a/tests/testthat/test-spell-check.R +++ b/tests/testthat/test-spell-check.R @@ -18,7 +18,7 @@ test_that("Test spell checks for OTTR main", { }) test_that("Test spell checks for OTTR Quarto main", { - qmd_dir <- setup_ottr_template(type = "qmd", render = FALSE) + qmd_dir <- setup_ottr_template(type = "quarto", render = FALSE) status <- check_spelling(qmd_dir) testthat::expect_true(status == 0) From 7e7b57a6b087594e319f1fc9e259835c3c53c205 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 12:20:06 -0500 Subject: [PATCH 3/7] Return num of errors --- R/spell_check.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/spell_check.R b/R/spell_check.R index 4e6b37e1..efc17152 100644 --- a/R/spell_check.R +++ b/R/spell_check.R @@ -92,4 +92,6 @@ check_spelling <- function(path = ".", readr::write_tsv(sp_errors, output_file) message(paste0("Saved to: ", output_file)) + + return(nrow(sp_errors)) } From 5a03e57a6069bb1f93ee41c61ee32a400f2fe804 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 13:27:52 -0500 Subject: [PATCH 4/7] Add a spelling error --- R/spell_check.R | 4 ++-- R/url_check.R | 2 ++ tests/testthat/test-spell-check.R | 20 ++++++++++++++++---- 3 files changed, 20 insertions(+), 6 deletions(-) diff --git a/R/spell_check.R b/R/spell_check.R index efc17152..eabc8143 100644 --- a/R/spell_check.R +++ b/R/spell_check.R @@ -62,7 +62,7 @@ check_spelling <- function(path = ".", } # Only declare `.Rmd` files but not the ones in the style-sets directory - files <- list.files(pattern = file_pattern, recursive = TRUE, full.names = TRUE) + files <- list.files(path = path, pattern = file_pattern, recursive = TRUE, full.names = TRUE) if (exclude_file[1] != "") files <- grep(paste0(exclude_file, collapse = "|"), files, invert = TRUE, value = TRUE) @@ -93,5 +93,5 @@ check_spelling <- function(path = ".", message(paste0("Saved to: ", output_file)) - return(nrow(sp_errors)) + return(as.numeric(nrow(sp_errors))) } diff --git a/R/url_check.R b/R/url_check.R index 5d0944a2..9f5fbdfd 100644 --- a/R/url_check.R +++ b/R/url_check.R @@ -89,6 +89,8 @@ check_urls <- function(path = ".", readr::write_tsv(all_urls_df, output_file) message(paste0("Saved to: ", output_file)) + + return(nrow(all_urls_df)) } diff --git a/tests/testthat/test-spell-check.R b/tests/testthat/test-spell-check.R index 33a6235a..d9913331 100644 --- a/tests/testthat/test-spell-check.R +++ b/tests/testthat/test-spell-check.R @@ -5,8 +5,11 @@ test_that("Test spell checks for OTTR main", { rmd_dir <- setup_ottr_template(type = "rmd", render = FALSE) + # Add in a spelling error + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + status <- check_spelling(rmd_dir) - testthat::expect_true(status == 0) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(rmd_dir, output_file))) @@ -20,8 +23,11 @@ test_that("Test spell checks for OTTR main", { test_that("Test spell checks for OTTR Quarto main", { qmd_dir <- setup_ottr_template(type = "quarto", render = FALSE) + # Add in a spelling error + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + status <- check_spelling(qmd_dir) - testthat::expect_true(status == 0) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(qmd_dir, output_file))) @@ -35,8 +41,11 @@ test_that("Test spell checks for OTTR Quarto main", { test_that("Test spell checks for OTTR web", { rmd_web <- setup_ottr_template(type = "rmd_website", render = FALSE) + # Add in a spelling error + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + status <- check_spelling(rmd_web) - testthat::expect_true(status == 0) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(rmd_web, output_file))) @@ -51,8 +60,11 @@ test_that("Test spell checks for OTTR Quarto web", { ## Test spell qmd_web <- setup_ottr_template(type = "quarto_website", render = FALSE) + # Add in a spelling error + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + status <- check_spelling(qmd_web) - testthat::expect_true(status == 0) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(qmd_web, output_file))) From 61957569251585e716c47524b5588056069eb993 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 13:41:09 -0500 Subject: [PATCH 5/7] Add tests --- inst/extdata/exclude_files.txt | 7 ------- tests/testthat/test-check-urls.R | 20 ++++++++++++++++---- tests/testthat/test-spell-check.R | 6 +++--- 3 files changed, 19 insertions(+), 14 deletions(-) diff --git a/inst/extdata/exclude_files.txt b/inst/extdata/exclude_files.txt index 5525a403..a188e069 100644 --- a/inst/extdata/exclude_files.txt +++ b/inst/extdata/exclude_files.txt @@ -1,8 +1 @@ -About.Rmd docs/* -style-sets/* -manuscript/* -CONTRIBUTING.md -LICENSE.md -code_of_conduct.md -README.md diff --git a/tests/testthat/test-check-urls.R b/tests/testthat/test-check-urls.R index d30d4c4f..12d1caaf 100644 --- a/tests/testthat/test-check-urls.R +++ b/tests/testthat/test-check-urls.R @@ -5,8 +5,11 @@ test_that("Test URL checks for OTTR main", { rmd_dir <- setup_ottr_template(type = "rmd", render = FALSE) + # Add in a URL error + writeLines("A URL error: https://notawebsiteaaaaaaa.com", file.path(rmd_dir, "url_test_error.md")) + status <- check_urls(rmd_dir) - testthat::expect_true(status < 2) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(rmd_dir, output_file))) @@ -21,8 +24,11 @@ test_that("Test URL checks for OTTR main", { test_that("Test URL checks for OTTR Quarto main", { qmd_dir <- setup_ottr_template(type = "quarto", render = FALSE) + # Add in a URL error + writeLines("A URL error: https://notawebsiteaaaaaaa.com", file.path(qmd_dir, "url_test_error.md")) + status <- check_urls(qmd_dir) - testthat::expect_true(status < 2) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(qmd_dir, output_file))) @@ -36,8 +42,11 @@ test_that("Test URL checks for OTTR Quarto main", { test_that("Test URL checks for OTTR web", { rmd_web <- setup_ottr_template(type = "rmd_website", render = FALSE) + # Add in a URL error + writeLines("A URL error: https://notawebsiteaaaaaaa.com", file.path(rmd_web, "url_test_error.md")) + status <- check_urls(rmd_web, report_all = TRUE) - testthat::expect_true(status < 2) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(rmd_web, output_file))) @@ -52,8 +61,11 @@ test_that("Test URL checks for OTTR Quarto web", { ## Test URL qmd_web <- setup_ottr_template(type = "quarto_website", render = FALSE) + # Add in a URL error + writeLines("A URL error: https://notawebsiteaaaaaaa.com", file.path(qmd_web, "url_test_error.md")) + status <- check_urls(qmd_web, report_all = TRUE) - testthat::expect_true(status < 2) + testthat::expect_true(status > 0) # Make sure the report exists testthat::expect_true(file.exists(file.path(qmd_web, output_file))) diff --git a/tests/testthat/test-spell-check.R b/tests/testthat/test-spell-check.R index d9913331..d61c4df6 100644 --- a/tests/testthat/test-spell-check.R +++ b/tests/testthat/test-spell-check.R @@ -6,7 +6,7 @@ test_that("Test spell checks for OTTR main", { rmd_dir <- setup_ottr_template(type = "rmd", render = FALSE) # Add in a spelling error - writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(rmd_dir, "spell_test_error.md")) status <- check_spelling(rmd_dir) testthat::expect_true(status > 0) @@ -24,7 +24,7 @@ test_that("Test spell checks for OTTR Quarto main", { qmd_dir <- setup_ottr_template(type = "quarto", render = FALSE) # Add in a spelling error - writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_dir, "spell_test_error.md")) status <- check_spelling(qmd_dir) testthat::expect_true(status > 0) @@ -42,7 +42,7 @@ test_that("Test spell checks for OTTR web", { rmd_web <- setup_ottr_template(type = "rmd_website", render = FALSE) # Add in a spelling error - writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(qmd_web, "spell_test_error.md")) + writeLines("A spelling error: sauibguiabsduvbasuidbv", file.path(rmd_web, "spell_test_error.md")) status <- check_spelling(rmd_web) testthat::expect_true(status > 0) From 37195cb40ebede51dd1eee670f4d97f3802fbe11 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 13:47:38 -0500 Subject: [PATCH 6/7] Simplify check --- .github/workflows/R-CMD-check.yaml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c77e8a3a..390f4821 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -32,14 +32,6 @@ jobs: remotes::install_cran("rcmdcheck") shell: Rscript {0} - - name: Check - env: - GH_PAT: ${{ secrets.GH_PAT }} - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), check_dir = "check") - shell: Rscript {0} - - name: Check package uses: r-lib/actions/check-r-package@v2 with: From 7205c38764473bdcef62ebca2c95590e4454161f Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 20 Dec 2024 13:55:25 -0500 Subject: [PATCH 7/7] Update docs --- NAMESPACE | 11 +++++++++ R/spell_check.R | 6 ++++- R/url_check.R | 29 ++++++++++++++++++++--- man/authorize.Rd | 1 - man/cache_secrets_folder.Rd | 2 +- man/check_git_repo.Rd | 1 - man/check_spelling.Rd | 46 +++++++++++++++++++++++++++++++++++++ man/check_urls.Rd | 46 +++++++++++++++++++++++++++++++++++++ man/get_urls.Rd | 26 +++++++++++++++++++++ man/setup_ottr_template.Rd | 4 +++- man/supported_endpoints.Rd | 2 +- man/test_url.Rd | 31 +++++++++++++++++++++++++ 12 files changed, 196 insertions(+), 9 deletions(-) create mode 100644 man/check_spelling.Rd create mode 100644 man/check_urls.Rd create mode 100644 man/get_urls.Rd create mode 100644 man/test_url.Rd diff --git a/NAMESPACE b/NAMESPACE index b87daad8..71d667a5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -11,6 +11,8 @@ export(check_quiz) export(check_quiz_attributes) export(check_quiz_question_attributes) export(check_quizzes) +export(check_spelling) +export(check_urls) export(clean_up) export(convert_coursera_quizzes) export(convert_quiz) @@ -30,6 +32,7 @@ export(get_pages_url) export(get_repo_info) export(get_slide_id) export(get_slide_page) +export(get_urls) export(good_quiz_path) export(gs_id_from_slide) export(gs_png_download) @@ -46,10 +49,12 @@ export(pptx_slide_text_df) export(qrmd_files) export(render_without_toc) export(setup_ottr_template) +export(test_url) export(unzip_pptx) export(website_to_embed_leanpub) export(xml_notes) import(dplyr) +import(stringr) importFrom(gitcreds,gitcreds_get) importFrom(httr,GET) importFrom(httr,accept_json) @@ -64,7 +69,13 @@ importFrom(magrittr,"%>%") importFrom(readr,write_tsv) importFrom(rprojroot,find_root) importFrom(rprojroot,has_dir) +importFrom(rvest,html_attr) +importFrom(rvest,html_nodes) +importFrom(rvest,read_html) +importFrom(spelling,spell_check_files) importFrom(stringr,str_to_title) +importFrom(tidyr,separate) +importFrom(tidyr,unnest) importFrom(utils,browseURL) importFrom(utils,download.file) importFrom(utils,installed.packages) diff --git a/R/spell_check.R b/R/spell_check.R index eabc8143..e4f328be 100644 --- a/R/spell_check.R +++ b/R/spell_check.R @@ -12,7 +12,11 @@ #' @return A file will be saved that lists the broken URLs will be saved to the specified output_dir. #' @export #' -#' @importFrom magrittr +#' @importFrom magrittr %>% +#' @importFrom spelling spell_check_files +#' @importFrom rprojroot find_root has_dir +#' @importFrom tidyr unnest separate +#' @importFrom readr write_tsv #' #' @examples #' diff --git a/R/url_check.R b/R/url_check.R index 9f5fbdfd..56c03065 100644 --- a/R/url_check.R +++ b/R/url_check.R @@ -12,7 +12,10 @@ #' @return A file will be saved that lists the broken URLs will be saved to the specified output_dir. #' @export #' -#' @importFrom magrittr +#' @importFrom magrittr %>% +#' @importFrom rprojroot find_root has_dir +#' @importFrom tidyr unnest separate +#' @importFrom readr write_tsv #' #' @examples #' @@ -102,7 +105,18 @@ check_urls <- function(path = ".", #' @return a logical TRUE/FALSE for whether the URL is legitimate. #' @export #' -#' @importFrom magrittr +#' @importFrom magrittr %>% +#' @importFrom httr GET +#' +#' @examples /dontrun { +#' +#' # This should print out "failed" +#' test_url("https://notawebsiteaaaaaaa.com") +#' +#' +#' # This should print out "success" +#' test_url("https://github.com") +#' } #' test_url <- function(url, ignore_urls = "") { if (url %in% ignore_urls) { @@ -134,7 +148,16 @@ test_url <- function(url, ignore_urls = "") { #' @return a data.frame of all the URLs identified in the given rmd/qmd/md file #' @export #' -#' @importFrom magrittr +#' @importFrom magrittr %>% +#' @importFrom rvest html_nodes read_html html_attr +#' @import stringr +#' +#' @examples +#' +#' # Add in a URL error +# writeLines("A URL error: https://notawebsiteaaaaaaa.com", "url_test_error.md") +#' +#' get_urls("url_test_error.md") #' get_urls <- function(file, ignore_urls = "") { message(paste("##### Testing URLs from file:", file)) diff --git a/man/authorize.Rd b/man/authorize.Rd index 89799f4f..538c48c9 100644 --- a/man/authorize.Rd +++ b/man/authorize.Rd @@ -27,6 +27,5 @@ authorize() authorize("github") authorize("google") - } } diff --git a/man/cache_secrets_folder.Rd b/man/cache_secrets_folder.Rd index 5679b29c..55a7d980 100644 --- a/man/cache_secrets_folder.Rd +++ b/man/cache_secrets_folder.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/token-handlers.R +% Please edit documentation in R/token_handlers.R \name{cache_secrets_folder} \alias{cache_secrets_folder} \title{See where your cached secrets are being stored} diff --git a/man/check_git_repo.Rd b/man/check_git_repo.Rd index dfa35389..60819167 100644 --- a/man/check_git_repo.Rd +++ b/man/check_git_repo.Rd @@ -38,6 +38,5 @@ Given a repository name, check with git ls-remote whether the repository exists authorize("github") check_git_repo("jhudsl/OTTR_Template") - } } diff --git a/man/check_spelling.Rd b/man/check_spelling.Rd new file mode 100644 index 00000000..ba8ae893 --- /dev/null +++ b/man/check_spelling.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/spell_check.R +\name{check_spelling} +\alias{check_spelling} +\title{Check spelling of all md,rmd, and qmd files} +\usage{ +check_spelling( + path = ".", + output_dir = "check_reports", + resources_dir = "resources", + file_pattern = "md$" +) +} +\arguments{ +\item{path}{path to the bookdown or quarto course repository, must have a +`.github` folder which will be used to establish the top of the repo.} + +\item{output_dir}{A relative file path to the folder (existing or not) that the +output check file should be saved to. Default is "check_reports"} + +\item{resources_dir}{A relative file path to the folder (existing or not) that the +dictionary.txt file and exclude_files.txt will be found. Default is "resources". +If no dictionary.txt file and exclude_files.txt files are found, we will download one.} + +\item{file_pattern}{A file pattern should we be looking for for the files whose +spelling should be tested. Default is "md$". Regex interpreted.} +} +\value{ +A file will be saved that lists the broken URLs will be saved to the specified output_dir. +} +\description{ +Check spelling of all md,rmd, and qmd files +} +\examples{ + +rmd_dir <- setup_ottr_template(dir = ".", type = "rmd", render = FALSE) + +check_spelling(rmd_dir) + +# If there are broken URLs they will be printed in a list at "check_reports/url_checks.tsv" + +qmd_dir <- setup_ottr_template(dir = ".", type = "qmd", render = FALSE) + +check_spelling(qmd_dir) + +} diff --git a/man/check_urls.Rd b/man/check_urls.Rd new file mode 100644 index 00000000..9259829b --- /dev/null +++ b/man/check_urls.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/url_check.R +\name{check_urls} +\alias{check_urls} +\title{Check URLs of all md,rmd, and qmd files} +\usage{ +check_urls( + path = ".", + output_dir = "check_reports", + resources_dir = "resources", + report_all = FALSE +) +} +\arguments{ +\item{path}{path to the bookdown or quarto course repository, must have a +`.github` folder which will be used to establish the top of the repo.} + +\item{output_dir}{A relative file path to the folder (existing or not) that the +output check file should be saved to. Default is "check_reports"} + +\item{resources_dir}{A relative file path to the folder (existing or not) that the +ignore_urls.txt file and exclude_files.txt will be found. Default is "resources". +If no ignore_urls.txt file and exclude_files.txt files are found, we will download one.} + +\item{report_all}{Should all URLs that were tested be returned? Default is FALSE +meaning only broken URLs will be reported in the url_checks.tsv file.} +} +\value{ +A file will be saved that lists the broken URLs will be saved to the specified output_dir. +} +\description{ +Check URLs of all md,rmd, and qmd files +} +\examples{ + +rmd_dir <- setup_ottr_template(dir = ".", type = "rmd", render = FALSE) + +check_urls(rmd_dir) + +# If there are broken URLs they will be printed in a list at "check_reports/url_checks.tsv" + +qmd_dir <- setup_ottr_template(dir = ".", type = "qmd", render = FALSE) + +check_urls(qmd_dir) + +} diff --git a/man/get_urls.Rd b/man/get_urls.Rd new file mode 100644 index 00000000..b6c56cec --- /dev/null +++ b/man/get_urls.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/url_check.R +\name{get_urls} +\alias{get_urls} +\title{Identify and collect URLs in a single rmd/qmd/md file} +\usage{ +get_urls(file, ignore_urls = "") +} +\arguments{ +\item{file}{A file path to a rmd/qmd/md file that contains URLs to be check} + +\item{ignore_url}{A vector of URLs which to ignore.} +} +\value{ +a data.frame of all the URLs identified in the given rmd/qmd/md file +} +\description{ +Identify and collect URLs in a single rmd/qmd/md file +} +\examples{ + +# Add in a URL error + +get_urls("url_test_error.md") + +} diff --git a/man/setup_ottr_template.Rd b/man/setup_ottr_template.Rd index a0fee5b6..d4a981cb 100644 --- a/man/setup_ottr_template.Rd +++ b/man/setup_ottr_template.Rd @@ -4,12 +4,14 @@ \alias{setup_ottr_template} \title{Download and render files from main OTTR_Template to test} \usage{ -setup_ottr_template(dir = "inst/extdata", type) +setup_ottr_template(dir = ".", type, render = TRUE) } \arguments{ \item{dir}{What relative file path should the files be downloaded} \item{type}{Which OTTR repo are we downloading? Options are "rmd", "quarto", "rmd_website", "quarto_website"} + +\item{render}{Should the OTTR repo be rendered after downloading? Default is TRUE} } \value{ This downloads the main branch repo files from the respective repo for testing purposes diff --git a/man/supported_endpoints.Rd b/man/supported_endpoints.Rd index 7a74d439..bdf2c943 100644 --- a/man/supported_endpoints.Rd +++ b/man/supported_endpoints.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/token-handlers.R +% Please edit documentation in R/token_handlers.R \name{supported_endpoints} \alias{supported_endpoints} \title{Supported endpoints} diff --git a/man/test_url.Rd b/man/test_url.Rd new file mode 100644 index 00000000..605534e5 --- /dev/null +++ b/man/test_url.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/url_check.R +\name{test_url} +\alias{test_url} +\title{Test a URL} +\usage{ +test_url(url, ignore_urls = "") +} +\arguments{ +\item{url}{A single URL that will be checked whether it is real.} + +\item{ignore_url}{A vector of URLs which to ignore.} +} +\value{ +a logical TRUE/FALSE for whether the URL is legitimate. +} +\description{ +Test a URL +} +\examples{ +/dontrun { + +# This should print out "failed" +test_url("https://notawebsiteaaaaaaa.com") + + +# This should print out "success" +test_url("https://github.com") +} + +}