Minor features and improvements for next version (#150)

* Feat(vignettes): -added tables of contents to vignettes -added tip for how to edit rda files to a11y vignette -added link to faqs vignette to a11y vignette re: how to edit alt text and captions * fix to incorrect reference in .bib file (#149) * fix incorrect reference * add url to reference fix * remove replicate nmfs palette and add_theme * remove files * Custom template fixes (#143) * update(create_template): comment out skeleton pop up at the end * update(add_section): add functionality for putting new subsection into section * Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child * update(create_template): select only custom_sections when user wants to make a different outline of report custom must = TRUE otherwise copies all files * Fix(create_template): adjust if statement argument for custom_sections * Add nmfspalette package back in * removed add_theme and associated test and documentation * remove static NOAA Fishies in authorship * update NOAA fisheries affiliations Co-authored-by: Schiano-NOAA <[email protected]> --------- Co-authored-by: sbreitbart-NOAA <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <[email protected]> * Fix(create_template): -Fix so that rda files can be added as input, if already created, OR generated if model results are included as an argument. -Update documentation * update(format_quarto): add functionality for html formatting with associated files and changes to create_template (#152) * small comment update * update(create_template): custom_sections adds all selected plus refs, acknow, and tables and figs if desired * Custom template fixes (#143) * update(create_template): comment out skeleton pop up at the end * update(add_section): add functionality for putting new subsection into section * Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child * update(create_template): select only custom_sections when user wants to make a different outline of report custom must = TRUE otherwise copies all files * Fix(create_template): adjust if statement argument for custom_sections * Add nmfspalette package back in * removed add_theme and associated test and documentation * remove static NOAA Fishies in authorship * update NOAA fisheries affiliations Co-authored-by: sbreitbart-NOAA <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <[email protected]> * Inject accessibility (#124) * Custom template fixes (#143) * update(create_template): comment out skeleton pop up at the end * update(add_section): add functionality for putting new subsection into section * Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child * update(create_template): select only custom_sections when user wants to make a different outline of report custom must = TRUE otherwise copies all files * Fix(create_template): adjust if statement argument for custom_sections * Removed captions_alt_text_template.csv because it's not used in asar... only satf. Then updated a11y vignette to reflect where users should look for the file. * changed eval for first chunk to true, and eval for indices table setup chunk to false, re: #102 . Will change eval to true for all chunks once indices table fxn is completed. * feature(add new template partial for accessibility and add fxn) * Update(add_tagging): ability to add alternative text to tex file from rdas * fix(add_taggig): change directory for rda files to arg * fix(add_tagging): change pathing to rda_dir * fix(add-tagging): rename accessibility tex for output * feature(add_accessibility): rename function and load documentation * Initial commit for add_accessibility test - commented out bc unfinished * update(test-add_accessibility): add snapshot for tex file and add proper code for testing * feature(alter accessibility fxns): split up funxtion into two and called both using the add_accessibility function Also adjusted testing function for add_alttext and removed old snapshot - was not working properly * Remove nmfspallete from dependencies temporarily (#139) * Remove nmfs-pallete from dependencies temporarily * Comment out reference to nmfs pallete in add_theme and tests * style and docs: run devtools::document() and styler::style_pkg() (#140) Co-authored-by: Schiano-NOAA <[email protected]> * Add nmfspalette back into package * Merge newer dev branch into old (#148) * Minor grammatical changes just to set up new dev-1.1 branch (changed quarto --> Quarto) * Feat(vignettes): -added tables of contents to vignettes -added tip for how to edit rda files to a11y vignette -added link to faqs vignette to a11y vignette re: how to edit alt text and captions * remove old package from namespace and add in new * add notes for new alttext test * Removed captions_alt_text_template.csv because it's not used in asar... only satf. Then updated a11y vignette to reflect where users should look for the file. * feature(alter accessibility fxns): split up funxtion into two and called both using the add_accessibility function Also adjusted testing function for add_alttext and removed old snapshot - was not working properly * update(create_template): custom_sections adds all selected plus refs, acknow, and tables and figs if desired * add spp_conout.csv to gitignore during testing * feature(add_alttext): add accessibility for user to add alt text to figures inserted into the outline (png) * fix(add_alttext): improve fxning for adding alt text to custom figs either from images or code chunks * feature(add_alttext): add example to function * comment out alttext fxn test * clean up fxns and add examples * add in support_file/accessibilit.tex * fix(create_tables_doc): remove incorrect and duplicate indices table code * update(accessibility fxns): update to fix minor issues with functions and documentation as mentioned by @sbreitbart-NOAA * update documentation * update(test-alttext): change test for alttext to mimic changes to the function - sdoes not work still * update(a11y fxns): improvements to functions as well as tests * update(add_alttext): update example to show to to use rename arg * minor updates and changes to fix test failures and checks * Feat(create_tables_doc): automatically test if tables are wide enough to require changing page orientation from portrait to landscape. Alter the Tables qmd to allow orientation changes for each table, if necessary. * Update orientation-related code for still-in-dev landings table * Extend landscape table width from 7.5 to 8.5"; add page breaks between tables * bug fixes * Started coding new function to handle super wide tables and split into smaller ones * Finished first full draft of function that will render large tables by splitting into multiple tables * Added essential_columns arg to render_lg_table() * Move orientation-detecting code into own function in utils, then update create_tables_doc * Moved render_lg_table fxn to own R script, then updated documentation * Update tests to remove temporary files upon test completion * Add more params to render_lg_table() and ID_pg_orientation(), then update documentation and usage in create_tables_doc() * Added code into create_tables_doc that splits extra-wide tables into multiple smaller tables, but still a bug in render_lg_table (producing "Error" as part of output when testing) * Found a solution for sourcing render_lg_table in 08_tables.qmd and successfully rendering extra-wide table with new solution, but need to check if this will work in other circumstances * found a successful workflow and applied it to indices table. Next step: apply to other tables, and simplify/clarify the new functions * Copied new changes to bnc table, but referencing a chunk with multiple tables will only reference the last table in the chunk, not the first. So next step: make a chunk for each table. Also removed now irrelevant function: ID_split_tbls * Redesigned create_tables_doc so that each table has its own chunk and can be referenced. * Updated landings table code * Removed "-plot" from create_figures/tables_doc chunks * Add note to create_tables_doc explaining why new rda with split tables is made; update documentation * First draft of render_lg_table test; update documentation * Remove code from create_tables_doc that reduces row height in tables * update terminal sb naming to match other conventions * Added Q&A about figure/table order to FAQs vignette * Updated create_tables_doc so that split tables include header values in parentheses after caption (example: <indices caption> (Fleet 6, Fleet 7)) * Updated examples * Clarified comments; renamed some variables to be unique and more clear; removed unnecessary and repetitious code * Add vignette for convert_output fxn (#161) * feature(convert output vignette): initial commit for article describing the convert output function * feature(conout vignette): add in more information including example dataframe (needs adjustment to code chunk) * minor improvements to convert_output vignette * update(convert output vignette): add links to function and parts of code; add useful functions outside of asar used in function * finish(convert output vignette): add in flowchart and final details * add(conout-vignette): update chunk displatying example data * Update vignettes/convert_output_details.Rmd Co-authored-by: Sophie Breitbart <[email protected]> * Update vignettes/convert_output_details.Rmd Co-authored-by: Sophie Breitbart <[email protected]> * Update vignettes/convert_output_details.Rmd Co-authored-by: Sophie Breitbart <[email protected]> * Update vignettes/convert_output_details.Rmd Co-authored-by: Sophie Breitbart <[email protected]> * fix(conout vignette): clarity to the text per comments made from @sbreitbart-NOAA * update(conout vignette): add finishing touches to convert output vignette * Fix translation of R0 parameter from BAM in convert_output (#163) * fix(convert_output): fix error when parameters containing a number were incorrectly labelled in the final df * First full draft of vignette re: #156 * fix(dev): remove add_accessibility and add_tagging functions since they are still in development until we can make the change to work alt text and tagging together * Converting vignette's option comparison table to flextable * update(add_alttext): change search name for figures to reflect change to rendering naming convention * update(add_alttext): additional line to find old naming conventions from figures processed from quarto * note(add_alttext): add TODO in fxn for rendering to html or docx if applicable down the line --------- Co-authored-by: sbreitbart-NOAA <[email protected]> Co-authored-by: Ian Taylor <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Schiano-NOAA <[email protected]>
nmfs-ost · Feb 24, 2025 · b264b58 · b264b58
1 parent c8db61f
commit b264b58
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diff --git a/.gitignore b/.gitignore
@@ -18,3 +18,4 @@ converted_file_1126.csv
 rda_files
 Meta
 report
+spp_conout.csv
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,13 +32,16 @@ Imports:
     officer,
     openxlsx,
     prodlim,
+    quarto,
     stats,
     stringr,
     svDialogs,
     tibble,
     tidyr,
     tidyselect,
-    utils
+    tinytex,
+    utils,
+    withr
 Suggests: 
     gt,
     kableExtra,
@@ -52,7 +55,6 @@ Suggests:
 VignetteBuilder: 
     knitr
 Remotes:
-    nmfs-fish-tools/nmfspalette,
     nmfs-fish-tools/nmfspalette,
     nmfs-ost/satf,
     r4ss/r4ss

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,10 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+export(add_alttext)
 export(add_base_section)
 export(add_child)
 export(add_chunk)
 export(add_section)
-export(add_theme)
 export(convert_output)
 export(create_citation)
 export(create_figures_doc)
@@ -15,3 +15,4 @@ export(create_title)
 export(create_titlepage_tex)
 export(export_object)
 export(format_quarto)
+export(render_lg_table)
diff --git a/R/add_alttext.r b/R/add_alttext.r
@@ -0,0 +1,212 @@
+#' Add alternative text into latex
+#'
+#' @param x .tex file containing report. Typically produced after initially
+#' rendering the skeleton made from create_template.
+#' @param dir directory where the tex file is located that will be edited
+#' @param rda_dir folder where rda files containing alternative text is located
+#' @param compile Indicate whether the document (X) should be
+#' rendered after these files are changed. Default TRUE.
+#' @param rename Indicate a name for the new tex file produced from this
+#' function. There is no need to include ".tex" in the name. Defaults to current
+#' name and overwrites the current tex file.
+#' @param alttext_csv_dir Directory for the csv file containing alternative
+#' text and captions generated when running satf::exp_all_figs_tables
+#'
+#' @return This function was made to help add in
+#' alternative text to latex documents generated from
+#' quarto. Quarto does not currently contain a way to
+#' add alternative text to PDF documents, so this function
+#' was developed as a work around. The addition of alternative
+#' text needs to be found in either the rda files produced from
+#' satf::exp_all_figs_tables or in the captions_alt_text.csv also produced from
+#' the same function. Users not using this format should create a csv file with
+#' columns containing "label" and "alt_text".
+#'
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#'   create_template(
+#'   new_template = TRUE,
+#'   format = "pdf",
+#'   office = "NWFSC",
+#'   region = "U.S. West Coast",
+#'   species = "Dover sole",
+#'   spp_latin = "Microstomus pacificus",
+#'   year = 2010,
+#'   author = c("John Snow", "Danny Phantom", "Patrick Star"),
+#'   include_affiliation = TRUE,
+#'   convert_output = TRUE,
+#'   resdir = "C:/Users/Documents/Example_Files",
+#'   model_results = "Report.sso",
+#'   model = "SS3",
+#'   new_section = "an_additional_section",
+#'   section_location = "after-introduction",
+#'   rda_dir = getwd()
+#'   )
+#'
+#'   path <- getwd()
+#'
+#'   quarto::quarto_render(file.path(path, "report", "SAR_USWC_Dover_sole_skeleton.qmd"))
+#'
+#'   withr::with_dir(
+#'   file.path(path, "report"),
+#'    add_alttext(
+#'      x = "SAR_USWC_Dover_sole_skeleton.tex",
+#'      dir = getwd(),
+#'      alttext_csv_dir = getwd(),
+#'      rda_dir = path,
+#'      compile = TRUE,
+#'      rename = "SAR_Dover_sole_tagged")
+#'    )
+#' }
+#'
+add_alttext <- function(
+    x = list.files(getwd())[grep("skeleton.tex", list.files(getwd()))],
+    dir = getwd(),
+    rda_dir = getwd(),
+    alttext_csv_dir = getwd(),
+    compile = TRUE,
+    rename = NULL
+) {
+  # Read latex file
+  tex_file <- readLines(file.path(dir, x))
+
+  # Check: count instances of pattern
+  # sub_count <- length(
+  #   grep("1",
+  #        stringr::str_count(
+  #          tex_file,
+  #          pattern = stringr::coll("\\pandocbounded{\\includegraphics["))
+  #        )
+  #   )
+
+  # Identify lines with figures
+  # this approach allows us to not mistake the replacement for other figures
+  fig_lines <- grep("fig-([a-z]+|[a-z]+_[a-z]+)-1.pdf", tex_file) # -plot
+  # Find images from previous naming conventions after quarto render
+  fig_lines <- c(fig_lines, grep("fig-([a-z]+|[a-z]+_[a-z]+)-plot-1.pdf", tex_file))
+
+  # TODO:
+  # create check to see if there are any instances where the suffix is not plot-1
+  # Replace instances of macro in the tex file
+  # replace_macro <- gsub(
+  #   "\\pandocbounded",
+  #   "\\pdftooltip",
+  #   tex_file
+  # )
+
+  # TODO:
+  # Create alternative options for render to html or docx
+
+  # Replace pandocbounded with pdftooltip so alt text can be added
+  tex_file[fig_lines] <- lapply(
+    tex_file[fig_lines],
+    function(line) {
+      gsub("\\pandocbounded", "\\pdftooltip", line)
+    }
+  )
+
+  # Check instance of pandocbounded that haven't been replaced
+  # these are the additional images
+  addl_figs <- grep("\\pandocbounded", tex_file)[-1]
+  # ignore line 82 - this is the department of commerce logo
+  # replace as above
+  tex_file[addl_figs] <- lapply(
+    tex_file[addl_figs],
+    function(line) {
+      gsub("\\pandocbounded", "\\pdftooltip", line)
+    }
+  )
+  # Add alt text to custom images
+  # read in alt text csv file to match with labels
+  alttext <- utils::read.csv(file.path(alttext_csv_dir, "captions_alt_text.csv"))
+  for (i in addl_figs) {
+    # Find line label
+    line <- tex_file[i]
+    # Find line following target to extract label
+    matches <- grep("\\label", tex_file)
+    label_line <- matches[matches > i][1]
+    line_label <- stringr::str_extract(tex_file[label_line], "\\\\label\\{([^}]*)\\}") |>
+      stringr::str_remove_all("^\\\\label\\{|\\}$")
+    # Match label name to label in csv and extract alttext
+    alttext_i <- alttext |>
+      dplyr::filter(label == line_label) |>
+      dplyr::pull(alt_text)
+    if (is.na(label_line)) {
+      alttext_i <- ""
+      warning(glue::glue(
+        "No alternative text found for {line_label}."
+      ))
+    }
+    # Add selected alttext onto end of the line
+    tex_file[i] <- paste(tex_file[i], "{", alttext_i, "}", sep = "")
+  }
+
+  # Insert alt text for figures
+  # Call alt text in list with names
+  obj_files <- list.files(file.path(rda_dir, "rda_files"))
+
+  # read all files in obj_files and put into list
+  alt_text_list <- list()
+  for (i in seq_along(obj_files)) {
+    load(file.path(rda_dir, "rda_files", obj_files[i]))
+    # extract name to add into the list for placement
+    rda_name <- stringr::str_replace(obj_files[i], "_figure.rda", "")
+    # if name is >1 word then replace the _ with - to follow naming convention for
+    # figures in tex file
+    if (grepl("_", rda_name)) rda_name <- stringr::str_replace(rda_name, "_", "-")
+    # convert to name in tex file to find where the line is located
+    tex_name <- glue::glue("fig-{rda_name}-plot-1.pdf")
+    # extract alt. text with figure
+    alt_text <- rda$alt_text
+    # names(alt_text) <- tex_name
+    # place obj into list
+    alt_text_list[[tex_name]] <- alt_text
+      # call tex obj name using names()
+      # call alt text using list[[i]]
+    # remove rda file to declutter
+    rm(rda)
+  }
+
+  # Find where figure is located and append the alt. text
+  for (i in seq_along(alt_text_list)) {
+    fig_line <- grep(names(alt_text_list[i]), tex_file)
+    # Check that line we are adding the alt text to is for correct fig
+    if (!grepl(names(alt_text_list[i]), tex_file[fig_line])) {
+      warning(glue::glue("Non-matching object name to tex file line."))
+      next
+    }
+    # Check that selected tex_line contains a marked figure - aka correct placement
+    file_name <- stringr::str_remove(x, ".tex")
+    if (!grepl(glue::glue("{file_name}_files/figure-pdf/fig-"), tex_file[fig_line])) {
+      warning(glue::glue("Improper line for appendment: \n Skipped adding alternative text for {names(alt_text_list[i])}"))
+      next
+    }
+    tex_file[fig_line] <- paste(tex_file[fig_line], "{", alt_text_list[[i]], "}", sep = "")
+    # tex_file[fig_line] <- strwrap(paste(tex_file[fig_line], "{", alt_text_list[[1]], "}", sep = ""))  # remove strwrap if does not render
+  }
+  # tex_file[430] <- paste(tex_file[fig_line], "{", alt_text_list[[1]], "}", sep = "")
+  # strwrap(paste(tex_file[fig_line], "{", alt_text_list[[1]], "}", sep = ""), width = 80)
+
+  # Checks
+  # add check if there are more plots that did not have alt text added
+  # if (length(obj_files) != length(fig_lines)) {
+  #   # Find which ones were not changed
+  #   # figs_miss_alt <-
+  #   warning("Missing alternative text for the followiing figures:")
+  # }
+  # TODO: test case where additional figure is added into the .tex file that is not included in the rda files
+
+  # Save overwrite tex file
+  write(unlist(tex_file), file = file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x)))
+  # utils::capture.output(cat(tex_file), file = file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x)), append = FALSE)
+  message("______Alternative text added to tex file.______")
+  # Render the .tex file after edits
+  if (compile) {
+    message("______Compiling in progress - This can take a while...______")
+    # test if this can be done when skeleton is in different folder than the wd
+    tinytex::lualatex(file.path(dir, ifelse(!is.null(rename), glue::glue("{rename}.tex"), x)))
+    message("______Compiling finished______")
+  }
+}
diff --git a/R/add_section.R b/R/add_section.R
@@ -8,7 +8,9 @@
 #' @return Add an additional section or subsection to the report template
 #' if it is not already present in the default template. This provides
 #' the option to add it as a section before or after an existing section,
-#' or within a section as a child document.
+#' or within a section as a child document. For developers: this function
+#' creates a list of sections that will be added to the skeleton file
+#' made from create_template.
 #' @export
 #'
 #' @examples add_section(
@@ -20,22 +22,35 @@ add_section <- function(
     new_section = NULL,
     section_location = NULL,
     custom_sections = NULL,
+    custom = TRUE,
     subdir = NULL) {
   # Location options
   # before-section
   # after-section
   # in-section (will always append to the end of the section)
   for (i in 1:length(new_section)) {
     section_i_name <- paste0(gsub(" ", "_", tolower(new_section[i])), ".qmd")
-    local_section <- forstringr::str_extract_part(section_location[i], "-", before = FALSE)
-    local_section_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = FALSE)
+    local_section <- forstringr::str_extract_part(
+      section_location[i], "-", before = FALSE
+    )
+    local_section_prev <- forstringr::str_extract_part(
+      section_location[i - 1], "-", before = FALSE
+    )
 
     if (any("TRUE" %in% grepl("-", section_location))) {
-      locality <- forstringr::str_extract_part(section_location[i], "-", before = TRUE)
-      locality_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = TRUE)
+      locality <- forstringr::str_extract_part(
+        section_location[i], "-", before = TRUE
+      )
+      locality_prev <- forstringr::str_extract_part(
+        section_location[i - 1], "-", before = TRUE
+      )
     } else if (any("TRUE" %in% grepl(" ", section_location))) {
-      locality <- forstringr::str_extract_part(section_location[i], " ", before = TRUE)
-      locality_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = TRUE)
+      locality <- forstringr::str_extract_part(
+        section_location[i], " ", before = TRUE
+      )
+      locality_prev <- forstringr::str_extract_part(
+        section_location[i - 1], "-", before = TRUE
+      )
     }
 
     section_i <- paste0(
@@ -45,21 +60,52 @@ add_section <- function(
       "\n",
       add_chunk("# Insert code", label = "example_chunk"), "\n"
     )
-    utils::capture.output(cat(section_i), file = paste0(subdir, "/", section_i_name), append = FALSE)
+    utils::capture.output(
+      cat(section_i),
+      file = paste0(subdir, "/", section_i_name),
+      append = FALSE
+    )
 
     if (locality == "before") {
-      custom_sections <- append(custom_sections, section_i_name, after = (which(grepl(local_section, custom_sections)) - 1))
+      custom_sections <- append(
+        custom_sections,
+        section_i_name,
+        after = (which(grepl(local_section, custom_sections)) - 1)
+      )
     } else if (locality == "after") {
       if (locality %in% locality_prev & local_section %in% local_section_prev) {
-        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(gsub(" ", "_", tolower(new_section[i - 1])), custom_sections)))
+        custom_sections <- append(
+          custom_sections,
+          section_i_name,
+          after = which(grepl(
+            gsub(" ", "_", tolower(new_section[i - 1])),
+            custom_sections)
+          )
+        )
       } else {
-        custom_sections <- append(custom_sections, section_i_name, after = max(which(grepl(local_section, custom_sections))))
+        custom_sections <- append(
+          custom_sections,
+          section_i_name,
+          after = max(which(grepl(local_section, custom_sections)))
+        )
       }
     } else if (locality == "in") {
-      stop("No available option for adding a new section 'in' another quarto document.", call. = FALSE)
+       # stop("No available option for adding a new section 'in' another quarto document.", call. = FALSE)
+        # recognize locality_prev file
+        file_for_subsection <- list.files(file.path(subdir))[grep(local_section, list.files(file.path(subdir)))]
+        # create code for reading in child doc
+        child_sec <- add_child(
+          section_i_name,
+          label = gsub(" ", "_", tolower(new_section[i]))
+        )
+        # append that text to file
+        utils::capture.output(cat(child_sec), file = fs::path(subdir, file_for_subsection), append = TRUE)
+        # section does not need to be added to appended custom sections as stated above
+        # creating qmd is already done in line 48
+
     } else {
       stop("Invalid selection for placement of section. Please name the follow the format 'placement-section_name' for adding a new section.")
     }
-  }
+  } # close for loop
   custom_sections
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,3 +18,4 @@ converted_file_1126.csv @@
     rda_files
     Meta
     report
+    spp_conout.csv