Improving 📦 quality (#4)

Author: maelle

.Rbuildignore

@@ -1,2 +1,14 @@
+^appveyor\.yml$
+^codecov\.yml$
+^\.travis\.yml$
+^LICENSE\.md$
+^README\.Rmd$
+^_redirects$
+^config\.toml$
+^content$
+^index\.Rmd$
+^layouts$
+^netlify\.toml$
+^static$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.travis.yml

@@ -0,0 +1,8 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+sudo: false
+cache: packages
+
+after_success:
+    - Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -1,14 +1,38 @@
 Package: learn
 Version: 0.0.0.9000
 Title: RECON LEARN content
-Description: Contains recon learn content
-Authors@R: person("Steph", "Locke", email = "steph@itsalocke.com", role = c("ctr"))
-License: CC-BY-4.0
+Description: Contains RECON learn content and infrastructure to build it.
+Authors@R: c(person("Steph", 
+                    "Locke", 
+                    email = "steph@itsalocke.com", 
+                    role = c("ctr", "aut", "cre")),
+             person("R Epidemics Consortium (RECON)", 
+                    role = c("cph", "fnd"),
+                    email = "thibautjombart@gmail.com",
+                    comment = "https://www.repidemicsconsortium.org/"))
 Encoding: UTF-8
 LazyData: true
 ByteCompile: true
-Imports: knitr,
+Imports: 
+    knitr,
     rmarkdown,
     automagic,
     htmltools,
-    htmlwidgets
+    htmlwidgets,
+    snakecase,
+    yaml,
+    usethis (>= 1.3.0.9000),
+    stringr,
+    glue,
+    jsonlite,
+    fs,
+    magrittr,
+    dplyr,
+    rlang
+RoxygenNote: 6.1.0
+License: MIT + file LICENSE
+Suggests: 
+    testthat,
+    covr
+Remotes:
+    r-lib/usethis

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2018
+COPYRIGHT HOLDER: R Epidemics Consortium (RECON)

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2018 R Epidemics Consortium (RECON)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -0,0 +1,9 @@
+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(create_post)
+export(get_and_update_dependencies)
+export(render_new_rmds_to_md)
+export(save_and_use_widget)
+importFrom(magrittr,"%>%")
+importFrom(rlang,.data)

R/create_post.R

@@ -0,0 +1,94 @@
+#' Create a post from the template
+#' 
+#' @details create a R Markdown file and open it.
+#'
+#' @param title Title for the post
+#' @param slug Short informative slug with words separated by "-"
+#' @param category Either "tutorials", "practicals" or "case studies"
+#' @param author Author as a vector
+#' @param date Date for the post
+#' @param licence_name Name of the license
+#' @param licence_url URL to the license
+#'
+#' @return Used only for side-effects.
+#' @export
+#'
+create_post <- function(title = "A study of Zika and Cholera",
+                        slug = NULL,
+                        category = c("tutorials", "practicals", "case studies"),
+                        author = c("Celina Turchi", "John Snow"),
+                        date = Sys.Date(),
+                        licence_name = "CC-BY",
+                        licence_url = "https://creativecommons.org/licenses/by/3.0/"){
+  if(is.null(slug)){
+    slug <- snakecase::to_any_case(title, case = "snake", 
+                                   sep_out = "-", sep_in = "-")
+  }
+  
+  singular_category <- switch(category[[1]],
+                              "practicals" = "practical",
+                              "tutorials" = "tutorial",
+                              "case studies" = "study")
+  
+  post_path <- file.path("content", "post", 
+                         glue::glue("{singular_category}-{slug}.Rmd"))
+  
+  file.copy(system.file("rmarkdown", "templates",
+                        "skeleton",
+                        "skeleton.Rmd", package = "learn"),
+            post_path,
+            overwrite = TRUE)
+  
+  file.copy(system.file("rmarkdown", "templates",
+                        "resources",
+                        "practical-phylogenetics.bib", package = "learn"),
+            file.path("content", "post", paste0(slug, ".bib")),
+            overwrite = TRUE)
+  
+  file.copy(system.file("rmarkdown", "templates",
+                        "resources",
+                        "placeholder.jpg", package = "learn"),
+            file.path("static","img", "highres", paste0(slug, ".jpg")),
+            overwrite = TRUE)
+  
+  yaml <- rmarkdown::yaml_front_matter(post_path, encoding = "UTF-8")
+  
+  yaml$title <- title
+  yaml$author <- toString(author)
+  yaml$authors <- jsonlite::toJSON(author)
+  yaml$topics <- jsonlite::toJSON(yaml$topics)
+  yaml$categories <- jsonlite::toJSON(category)
+  yaml$date <- as.character(date)
+  yaml$bibliography <- paste0(slug, ".bib")
+  yaml$image <- glue::glue("img/highres/{slug}.jpg")
+  yaml$licenses <- licence_name
+  
+  file_content <- readLines(post_path)
+  i = grep('^---\\s*$', file_content)
+  file_content <- file_content[(i[2]+1):length(file_content)]
+  
+  newyaml <- yaml::as.yaml(yaml)
+  newyaml <- stringr::str_remove_all(newyaml, "'")
+  
+  file_content[grepl("\\- Zulma Cucunuba \\& Pierre Nouvellet\\: initial version", 
+                     file_content)] <-
+    glue::glue("- {toString(author)}: initial version")
+  
+  file_content[grepl("\\[CC-BY\\]\\(htt", file_content)] <-
+    glue::glue("**License**: [{licence_name}]({licence_url})")
+  
+  file_content[grepl("Zulma Cucunuba \\& Pierre Nouvellet, 2017", 
+                     file_content)] <-
+    glue::glue("**Copyright**: {toString(author)}, {format(date, '%Y')}")
+  
+  
+  file_content <- c(c("---"),
+                    newyaml,
+                    c("---"),
+                    file_content)
+  print(post_path)
+  writeLines(file_content, post_path,
+             useBytes = TRUE)
+  usethis::edit_file(post_path)
+  
+}

R/get_and_update_dependencies.R

@@ -1,7 +1,7 @@
 #' Determine all dependencies in blog posts and install them
 #' 
 #' Using the automagic package, detect requirements in Rmd files
-#' and install them all. Will help you if packages appear to be on Github.
+#' and install them all. Will help you if packages appear to be on GitHub.
 #'
 #' @param dir Directory to search for packages in. Defaults to the blog post location of Hugo.
 #'

R/render_new_rmds_to_md.R

@@ -6,22 +6,57 @@
 #' preview option in Rstudio to quickly see how your md has worked.
 #'
 #' @param dir Directory to search for new Rmds in. Defaults to the blog post location of Hugo.
+#' @param build Selection criteria for which Rmds to convert to md, options are c("all", "old and new", "old", "new")
 #'
 #' @return Used for pure side effect
 #' @export
-render_new_rmds_to_md <- function(dir = "content/post") {
+render_new_rmds_to_md <- function(dir = "content/post", 
+                                  build = "old and new") {
+  match.arg(build, c("all", "old and new", "old", "new"))
   content = dir
-  # Rmds not rendered
-  rmds <- list.files(content, pattern = "\\.Rmd")
-  mds <- list.files(content, pattern = "\\.md")
 
-  to_build <- setdiff(tools::file_path_sans_ext(rmds),
-                      tools::file_path_sans_ext(mds))
+  # get info about all files
+  info <- fs::dir_info(content)
+  rmds <- info[stringr::str_detect(info$path, "\\.[Rr]md"),]
+  mds <- info[stringr::str_detect(info$path, "\\.md"),]
 
-  for (b in to_build) {
-    rmd = file.path(content, paste0(b, ".Rmd"))
-    rmarkdown::render(rmd,
-                      rmarkdown::md_document(variant = "markdown_github",
-                                             preserve_yaml = TRUE))
+  rmds$slug <- fs::path_ext_remove(rmds$path)
+  mds$slug <- fs::path_ext_remove(mds$path)
+  
+  # Rmd without md
+  unbuilt <- rmds$path[!rmds$slug %in% mds$slug]
+  
+  # Rmd with a too old md
+  dplyr::left_join(rmds, mds, by = "slug",
+                   suffix = c("_rmd", "_md")) %>%
+    dplyr::filter(.data$change_time_md < .data$change_time_rmd) %>%
+    dplyr::pull(.data$path_rmd) -> too_old
+    
+  if(build == "all"){
+    to_build <- rmds$path_rmd 
+  }
+  if(build == "old and new"){
+    to_build <- c(too_old, unbuilt)
+  }
+  if(build == "old"){
+    to_build <- too_old
+  }
+  if(build == "new"){
+    to_build <- unbuilt
   }
+  
+  # build only the ones to be built
+  if(length(to_build) > 0){
+
+    for (b in to_build) {
+      rmd <- b
+      rmarkdown::render(rmd,
+                        rmarkdown::md_document(variant = "markdown_github",
+                                               preserve_yaml = TRUE ))
+    }
+  }else{
+    message("Nothing to build, all .md up-to-date")
+  }
+  
+  
 }

R/save_and_use_widget.R

@@ -14,10 +14,9 @@ save_and_use_widget <- function(x, filename) {
   dir.create("widgets", showWarnings = FALSE)
   origwd <- getwd()
   setwd("widgets")
-  f = paste0(name, ".html")
-  htmlwidget::saveWidget(x, f, selfcontained = TRUE)
+  htmlwidgets::saveWidget(x, filename, selfcontained = TRUE)
   setwd(origwd)
-  htmltools::tags$iframe(src = file.path("widgets", f),
+  htmltools::tags$iframe(src = file.path("widgets", filename),
                          width = "100%",
                          height = "500px")
 }

R/utils-pipe.R

@@ -0,0 +1,12 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @importFrom rlang .data
+#' @usage lhs \%>\% rhs
+NULL