Merge pull request #3 from dchiu911/use-ymlthis

Use ymlthis

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: rsf
 Title: Report of Statistical Findings in 'bookdown'
-Version: 0.1.0.9001
+Version: 0.2.0
 Authors@R: 
     person(given = "Derek",
            family = "Chiu",
@@ -17,10 +17,12 @@ URL: https://github.com/dchiu911/rsf,
 BugReports: https://github.com/dchiu911/rsf/issues
 Imports: 
     bookdown,
-    stringr,
+    knitr,
+    magrittr,
+    rlang,
     usethis,
-    whoami,
-    yaml
+    yaml,
+    ymlthis
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -3,3 +3,4 @@
 export(git_ignore_outputs)
 export(use_references)
 export(use_rsf)
+importFrom(magrittr,"%>%")

NEWS.md

@@ -1,4 +1,8 @@
-# rsf 0.1.0.9001
+# rsf 0.2.0
+
+## API changes
+
+* Use the `ymlthis` package for writing YAML
 
 ## LaTeX changes
 

R/git_ignore_outputs.R

@@ -31,16 +31,6 @@ git_ignore_outputs <- function(path = ".", figs_only = TRUE) {
     output_dir <-
       file.path(output_dir, paste0(bookdown_yml[["book_filename"]], "_files"))
   }
-  outputs <- c(output_dir, "_bookdown_files")
-  if (all(outputs %in% git_ignore)) {
-    usethis::ui_done("Outputs already git ignored")
-    return(invisible())
-  }
-  writeLines(text = c(git_ignore, outputs), con = git_ignore_path)
-  usethis::ui_done(paste(
-    "Adding",
-    usethis::ui_value(outputs),
-    "to",
-    usethis::ui_path(".gitignore")
-  ))
+  usethis::write_union(path = git_ignore_path,
+                       lines = c(git_ignore, output_dir, "_bookdown_files"))
 }

R/rsf-package.R

@@ -1,2 +1,7 @@
 #' @keywords internal
 "_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom magrittr %>%
+## usethis namespace: end
+NULL

R/use_references.R

@@ -24,45 +24,59 @@ use_references <- function(path = ".", number = 99) {
     stop("One or more input files are missing.")
   }
 
-  # Check if references already exists
-  if ("bibliography" %in% names(yaml::read_yaml(index_rmd_path))) {
-    usethis::ui_done("References already added")
-    return(invisible())
-  }
-
-  # Create references Rmd source file
+  # Specify references Rmd file path
   src_path <- file.path(path, "src")
-  if (!dir.exists(src_path)) dir.create(src_path)
-  rmd_name <- paste0(stringr::str_pad(number, 2, pad = 0), "-references.Rmd")
-  write_rmd(src_path, "References", rmd_name)
+  rmd_name <- paste0(sprintf("%02d", number), "-references.Rmd")
+  ref_rmd_path <- file.path(src_path, rmd_name)
 
-  # Add header and generate packages.bib
-  header <- "`r if (knitr::is_html_output()) '# References {-}'`\n"
-  chunk_start <- "```{r include=FALSE}"
-  pkg_list <- "knitr::write_bib(c(.packages(), 'bookdown'), 'packages.bib')"
-  chunk_end <- "```"
-  rmd_path <- file.path(src_path, rmd_name)
-  writeLines(text = c(header, chunk_start, pkg_list, chunk_end), con = rmd_path)
-  usethis::ui_done(paste(usethis::ui_path(rmd_path), "added"))
+  if (file.exists(ref_rmd_path)) {
+    # Do nothing if references Rmd already added
+    usethis::ui_done(paste("Already added", usethis::ui_path(ref_rmd_path)))
+    return(invisible())
+  } else {
+    # Rename file if it exists
+    old_ref_rmd_path <-
+      list.files(src_path, "^[0-9]{2}-references\\.Rmd", full.names = TRUE)
+    if (length(old_ref_rmd_path) == 1) {
+      file.rename(old_ref_rmd_path, ref_rmd_path)
+      usethis::ui_done(paste(
+        "Renaming",
+        usethis::ui_path(old_ref_rmd_path),
+        "to",
+        usethis::ui_path(ref_rmd_path)
+      ))
+      return(invisible())
+    } else {
+      # Write header and generate packages.bib otherwise
+      header <- "`r if (knitr::is_html_output()) '# References {-}'`"
+      chunk <- ymlthis::code_chunk(
+        chunk_code = knitr::write_bib(c(.packages(), "bookdown"), "packages.bib"),
+        chunk_args = list(include = FALSE)
+      )
+      if (!dir.exists(src_path)) dir.create(src_path)
+      writeLines(text = c(header, "", chunk), con = ref_rmd_path)
+      usethis::ui_done(paste("Writing", usethis::ui_path(ref_rmd_path)))
+    }
+  }
 
   # Call packages.bib from index.Rmd
   index_rmd <- readLines(index_rmd_path)
   before_style <- grep("biblio-style", index_rmd) - 1
   index_rmd <- append(index_rmd, "bibliography: packages.bib", before_style)
   writeLines(text = index_rmd, con = index_rmd_path)
-  usethis::ui_done(paste(usethis::ui_path(index_rmd_path), "modified"))
+  usethis::ui_done(paste("Writing", usethis::ui_path(index_rmd_path)))
 
   # Add bib options to bookdown::pdf_book output
   output_yml <- yaml::read_yaml(output_yml_path)
   bib_opts <- list(citation_package = "natbib", toc_bib = TRUE)
   output_yml[["bookdown::pdf_book"]] <-
     c(output_yml[["bookdown::pdf_book"]], bib_opts)
   yaml::write_yaml(x = output_yml, file = output_yml_path)
-  usethis::ui_done(paste(usethis::ui_path(output_yml_path), "modified"))
+  usethis::ui_done(paste("Writing", usethis::ui_path(output_yml_path)))
 
   # Rename Bibliography to References in tex
   preamble_tex <- readLines(preamble_tex_path)
-  bib_rename <- "\n\\renewcommand{\\bibname}{References}"
-  writeLines(text = c(preamble_tex, bib_rename), con = preamble_tex_path)
-  usethis::ui_done(paste(usethis::ui_path(preamble_tex_path), "modified"))
+  bib_rename <- "\\renewcommand{\\bibname}{References}"
+  writeLines(text = c(preamble_tex, "", bib_rename), con = preamble_tex_path)
+  usethis::ui_done(paste("Writing", usethis::ui_path(preamble_tex_path)))
 }

R/use_rsf.R

@@ -20,4 +20,5 @@ use_rsf <- function(path, ...) {
   write_index(path)
   write_src(path)
   write_preamble(path)
+  write_gitignore(path)
 }

R/write_bookdown_yml.R

@@ -1,15 +1,17 @@
-# _bookdown.yml
+#' Write `_bookdown.yml`
+#' @noRd
 write_bookdown_yml <- function(path, params) {
-  bookdown_yml <- c(
-    list(
-      book_filename = paste(basename(path), "RSF", sep = "_"),
-      rmd_subdir = "src",
-      before_chapter_script = "src/utils.R"
-    ),
-    params
-  )
-  yaml::write_yaml(
-    x = bookdown_yml,
-    file = file.path(path, "_bookdown.yml")
+  bookdown_yml <- rlang::exec(
+    ymlthis::yml_bookdown_opts,
+    .yml = ymlthis::yml_empty(),
+    book_filename = paste(basename(path), "RSF", sep = "_"),
+    before_chapter_script = "src/utils.R",
+    rmd_subdir = "src",
+    !!!params
   )
+  # TODO: quiet arg not passed
+  tmp <- utils::capture.output(ymlthis::use_bookdown_yml(bookdown_yml, path, quiet = TRUE))
+  # TODO: extra final line return
+  tmp_path <- gsub(".*'(.*)'.*", "\\1", tmp)
+  writeLines(utils::head(readLines(tmp_path), -1), tmp_path)
 }

R/write_gitignore.R

@@ -0,0 +1,8 @@
+#' Write `.gitignore`
+#' @noRd
+write_gitignore <- function(path) {
+  writeLines(
+    c(".Rproj.user", ".Rhistory", ".RData", ".Ruserdata"),
+    file.path(path, ".gitignore")
+  )
+}

R/write_index.R

@@ -1,19 +1,22 @@
-# index.Rmd
+#' Write `index.Rmd`
+#' @noRd
 write_index <- function(path) {
-  index_yml <- list(
-    title = paste(basename(path), "Report of Statistical Findings", sep = ": "),
-    author = whoami::fullname(fallback = "Author"),
-    date = "`r Sys.Date()`",
-    site = "bookdown::bookdown_site",
-    documentclass = "report",
-    geometry = "margin=1in",
-    `biblio-style` = "apalike",
-    `link-citations` = TRUE,
-    colorlinks = TRUE,
-    lot = TRUE,
-    lof = TRUE
-  )
-  index_yml <- gsub("\n$", "", yaml::as.yaml(index_yml))
-  writeLines(text = c("---", index_yml, "---\n\n# Preface {-}"),
-             con = file.path(path, "index.Rmd"))
+  index_yml <- ymlthis::yml_empty() %>%
+    ymlthis::yml_title(paste(basename(path),
+                             "Report of Statistical Findings", sep = ": ")) %>%
+    ymlthis::yml() %>%
+    ymlthis::yml_bookdown_site() %>%
+    ymlthis::yml_latex_opts(
+      documentclass = "report",
+      geometry = "margin=1in",
+      colorlinks = TRUE,
+      lof = TRUE,
+      lot = TRUE,
+      biblio_style = "apalike"
+    ) %>%
+    ymlthis::yml_citations(link_citations = TRUE)
+  writeLines(
+    text = c(utils::capture.output(print(index_yml)), "\n# Preface {-}"),
+    con = file.path(path, "index.Rmd")
+  )  # TODO: use_rmarkdown() forces index.Rmd to open, use_index_rmd doesn't pass body param
 }

R/write_output_yml.R

@@ -1,19 +1,20 @@
-# _output.yml
+#' Write `_output.yml`
+#' @noRd
 write_output_yml <- function(path) {
-  output_yml <- list(
-    `bookdown::gitbook` = list(
+  output_yml <- ymlthis::yml_output(
+    .yml = ymlthis::yml_empty(),
+    bookdown::gitbook(
       lib_dir = "assets",
       split_by = "chapter+number"
     ),
-    `bookdown::pdf_book` = list(
+    bookdown::pdf_book(
       keep_tex = TRUE,
-      includes = list(
-        in_header = "preamble.tex"
-      )
+      includes = ymlthis::includes2(in_header = "preamble.tex")
     )
   )
-  yaml::write_yaml(
-    x = output_yml,
-    file = file.path(path, "_output.yml")
-  )
+  # TODO: quiet arg not passed
+  tmp <- utils::capture.output(ymlthis::use_output_yml(output_yml, path, quiet = TRUE))
+  # TODO: extra final line return
+  tmp_path <- gsub(".*'(.*)'.*", "\\1", tmp)
+  writeLines(utils::head(readLines(tmp_path), -1), tmp_path)
 }

appveyor.yml

@@ -18,7 +18,7 @@ environment:
   # env vars that may need to be set, at least temporarily, from time to time
   # see https://github.com/krlmlr/r-appveyor#readme for details
   # USE_RTOOLS: true
-  # R_REMOTES_STANDALONE: true
+  R_REMOTES_STANDALONE: true
 
 # Adapt as necessary starting from here
 

cran-comments.md

@@ -1,24 +1,8 @@
-## Resubmission
-
-This is a resubmission. In this version I have:
-
-* Renamed installed file '.gitignore to 'gitignore' so it can be found in examples
-* Removed package 'here' from Imports
-* Used files from inst/extdata for examples
-* Improved documentation for use_rsf()
-* Ensured examples are executable by adding conditional checks
-* Reset the working directory at the end of examples
-* Wrapped 'bookdown' and 'YAML' in Description
-* Replaced dontrun{} with donttest{} in examples
-* Written to tempdir() in examples
-
 ## Test environments
-* local OS X install, R 3.5.3
-* ubuntu 14.04 (on travis-ci), R 3.5.3
-* win-builder (devel and release)
+* local macOS install, R 3.5.3
+* ubuntu 16.04 (on travis-ci), R-devel, R 3.6.1
+* win-builder (devel)
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-* This is a new release.
+0 errors | 0 warnings | 0 notes

inst/extdata/_bookdown.yml

@@ -1,4 +1,4 @@
 book_filename: RSF
-output_dir: reports
-rmd_subdir: src
 before_chapter_script: src/utils.R
+rmd_subdir: src
+output_dir: reports

inst/extdata/_output.yml

@@ -2,6 +2,6 @@ bookdown::gitbook:
   lib_dir: assets
   split_by: chapter+number
 bookdown::pdf_book:
-  keep_tex: yes
+  keep_tex: true
   includes:
     in_header: preamble.tex

inst/extdata/index.Rmd

@@ -1,14 +1,15 @@
 ---
 title: 'Report of Statistical Findings'
 author: Derek Chiu
-date: '`r Sys.Date()`'
+date: '`r format(Sys.Date())`'
 site: bookdown::bookdown_site
 documentclass: report
+geometry: margin=1in
+colorlinks: true
+lof: true
+lot: true
 biblio-style: apalike
-link-citations: yes
-colorlinks: yes
-lot: yes
-lof: yes
+link-citations: true
 ---
 
 # Preface {-}

inst/extdata/preamble.tex

@@ -1,12 +1,3 @@
-\usepackage{booktabs}
-\usepackage{pdflscape}
-\newcommand{\blandscape}{\begin{landscape}}
-\newcommand{\elandscape}{\end{landscape}}
-\usepackage{float}
-\floatplacement{figure}{H}
-\floatstyle{ruled}
-\restylefloat{figure}
-
 \let\paragraph\oldparagraph
 \let\subparagraph\oldsubparagraph
 
@@ -23,3 +14,5 @@
   {}
   {0pt}
   {}
+
+\titlespacing*{\chapter}{0pt}{0pt}{40pt}