library("stringr")

clean_md_file <- function(file_path, re_bib = "^References$") {
  # report
  report <- readr::read_lines(file_path)

  # Ignore the bibliography
  line_references_start <-  report %>%
    str_detect(re_bib) %>%
    which

  # Say the bibliography is last line if it's missing
  if (length(line_references_start) == 0) {
    line_references_start <- length(report)
  }

  main_lines <- report[seq_len(line_references_start)]

  # Ignore lines that aren't prose
  table_lines <- main_lines %>% str_detect("^[|]")
  img_lines <- main_lines %>% str_detect("^[<img]")
  header_lines <- main_lines %>% str_detect("^[-][-]|^[#]")

  do_not_touch <- table_lines | img_lines | header_lines
  lines_to_check <- main_lines[!do_not_touch]

  main_lines[!do_not_touch] <- lines_to_check %>%
    replace_inline_amper

  report[seq_len(line_references_start)] <- main_lines
  report
}



replace_inline_amper <- function(text) {
  # Assume that an inline citation consists of an author's last name followed by a
  # parenthesized year. If we find those, we fix the inline citations with
  # ampersands.

  # Last names are letters and hyphens and spaces.
  re_author <- "[[:alpha:]- ]+"

  re_inline_year <- "[(]\\d{4}[)]"
  re_author_year <- paste(re_author, re_inline_year)
  re_ampersand <- " & "

  re_ampersand_author_year <- sprintf("%s(?=%s)", re_ampersand, re_author_year)
  str_replace_all(text, re_ampersand_author_year, " and ")

  # c("Maggie & Lisa (2005) found...",
  #   "...have been found (Maggie & Lisa, 2005)",
  #   "Jones & Hyphen-Name (2005) found...",
  #   "...have been found (Jones & Hyphen-Name, 2005)",
  #   "Marge, Maggie, & Lisa (2005) found...",
  #   "...have been found (Marge, Maggie, & Lisa, 2005)",
  #   "Jones & Space Name (2005) found...",
  #   "...have been found (Jones & Space Name, 2005)") %>%
  #   replace_inline_amper() -> text
}