format.R

#!/usr/bin/env Rscript

if (!requireNamespace("stringr", quietly = TRUE))
  stop("Please install the package stringr and re-run")

library(stringr)

args <- commandArgs(trailingOnly = TRUE)
if (length(args) > 1) {
  stop("Usage: Rscript format.R filename")
} else if (length(args) == 1) {
  fname <- args
} else {
  fname <- "workflowr-publication.tex"
}

lines_in <- readLines(fname)
lines_out <- lines_in

# Format function names (brute force b/c getting clever with regex was hard to
# maintain), e.g. wflow_start() -> \texttt{wflow\_start()}
lines_out <- str_replace_all(lines_out,
                             "wflow_start\\(\\)",
                             "\\\\texttt{wflow\\\\_start()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_build\\(\\)",
                             "\\\\texttt{wflow\\\\_build()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_publish\\(\\)",
                             "\\\\texttt{wflow\\\\_publish()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_status\\(\\)",
                             "\\\\texttt{wflow\\\\_status()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_git_push\\(\\)",
                             "\\\\texttt{wflow\\\\_git\\\\_push()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_use_github\\(\\)",
                             "\\\\texttt{wflow\\\\_use\\\\_github()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_use_gitlab\\(\\)",
                             "\\\\texttt{wflow\\\\_use\\\\_gitlab()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_site\\(\\)",
                             "\\\\texttt{wflow\\\\_site()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_git_pull\\(\\)",
                             "\\\\texttt{wflow\\\\_git\\\\_pull()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_html\\(\\)",
                             "\\\\texttt{wflow\\\\_html()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_git_remote\\(\\)",
                             "\\\\texttt{wflow\\\\_git\\\\_remote()}")
lines_out <- str_replace_all(lines_out,
                             "wflow_git_config\\(\\)",
                             "\\\\texttt{wflow\\\\_git\\\\_config()}")
lines_out <- str_replace_all(lines_out,
                             "render\\(\\)",
                             "\\\\texttt{render()}")
lines_out <- str_replace_all(lines_out,
                             "render_site\\(\\)",
                             "\\\\texttt{render\\\\_site()}")
lines_out <- str_replace_all(lines_out,
                             "html_document\\(\\)",
                             "\\\\texttt{html\\\\_document()}")
lines_out <- str_replace_all(lines_out,
                             "sessionInfo\\(\\)",
                             "\\\\texttt{sessionInfo()}")
lines_out <- str_replace_all(lines_out,
                             "set.seed\\(\\)",
                             "\\\\texttt{set.seed()}")

# Replace \verb|| with \texttt{}
# Note: we had started with \verb and then transitioned to \texttt
lines_out <- str_replace_all(lines_out, "\\\\verb\\|([^\\|]+)\\|", "\\\\texttt\\{\\1}")

# Replace # with \# for LaTeX
lines_out <- str_replace_all(lines_out, "#", "\\\\#")

# Replace & with \& for LaTeX
lines_out <- str_replace_all(lines_out, "&", "\\\\&")

# Remove empty [] where figures were in Word document
lines_out <- str_replace_all(lines_out, "^\\[\\]$", "")

# Fix \texttt{\_workflowr.yml} split over 2 lines
lines_out <- str_replace(lines_out, "\\\\texttt\\{\\\\$", "")
lines_out <- str_replace(lines_out, "^_workflowr.yml", "\\\\texttt\\{\\\\_workflowr.yml")

# Reference figures by labels
lines_out <- str_replace_all(lines_out, "FIGURE 1", "Figure \\\\ref\\{fig:start}\\")
lines_out <- str_replace_all(lines_out, "FIGURE 2", "Figure \\\\ref\\{fig:build}\\")
lines_out <- str_replace_all(lines_out, "FIGURE 3", "Figure \\\\ref\\{fig:publish}\\")
lines_out <- str_replace_all(lines_out, "FIGURE 4", "Figure \\\\ref\\{fig:status}\\")

# Bold names of software
software <- c(
  "adapr",
  "archivist",
  "blogdown",
  "bookdown",
  "cacher",
  "callr",
  "checkpoint",
  "conda",
  "devtools",
  "Docker",
  "drake",
  "Git LFS", # Needs to come before Git
  "Git",
  "git2r",
  "glue",
  "GNU Make",
  "Homebrew",
  "knitr",
  "Kubernetes",
  "libgit2",
  "msigdbr",
  "packrat",
  "pandoc",
  "pkgdown",
  "ProjectTemplate",
  "rmarkdown",
  "rprojroot",
  "rrtools",
  "RStudio",
  "RSuite",
  "Seurat",
  "Singularity",
  "Snakemake",
  "Sumatra",
  "switchr",
  "usethis",
  "workflowr",
  "Workflowr"
)

for (s in software) {
 lines_out <- str_replace_all(lines_out,
                              sprintf("[:space:](%s)\\b", s),
                              " \\\\textbf\\{\\1}")
 # Handle the edge case where the package is the start of a new line
 lines_out <- str_replace_all(lines_out,
                              sprintf("^(%s)\\b", s),
                              " \\\\textbf\\{\\1}")
 # Handle the edge case where software is in parentheses
 lines_out <- str_replace_all(lines_out,
                              sprintf("\\((%s)\\b", s),
                              " \\(\\\\textbf\\{\\1}")
}

writeLines(lines_out, con = fname)