Fix crayon bug and ui_bullet issue (#130)

- removed crayon and usethis as
  dependencies in favor of cli
- fixed bug in R version 4.4.1 with ui_bullet
  internal calls within loadAdatsAsList() and
  write_adat()
- Fixes #129

DESCRIPTION

@@ -24,15 +24,13 @@ Depends:
     R (>= 4.1.0)
 Imports:
     cli,
-    crayon,
     dplyr (>= 1.0.6),
     lifecycle (>= 1.0.0),
     magrittr (>= 2.0.1),
     methods,
     readxl (>= 1.3.1),
     tibble (>= 3.1.2),
-    tidyr (>= 1.1.3),
-    usethis (>= 2.0.1)
+    tidyr (>= 1.1.3)
 Suggests:
     Biobase,
     ggplot2,
@@ -42,6 +40,7 @@ Suggests:
     rmarkdown,
     spelling,
     testthat (>= 3.0.0),
+    usethis (>= 2.0.1),
     withr
 VignetteBuilder: 
     knitr
@@ -54,4 +53,4 @@ LazyLoad: true
 Config/testthat/edition: 3
 Config/Needs/website: tidyverse/tidytemplate
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

R/diffAdats.R

@@ -144,7 +144,7 @@ diffAdats <- function(adat1, adat2, tolerance = 1e-06) {
     }
     cat("\n")
     .done(
-      "Continuing on the {.value('*INTERSECT*')} of ADAT columns"
+      "Continuing on the {.val *INTERSECT*} of ADAT columns"
     )
   }
 

R/is-intact-attr.R

@@ -42,14 +42,14 @@ is_intact_attr <- function(adat, verbose = interactive()) {
   if ( !is.soma_adat(adat) ) {
     if ( verbose ) {
       .oops(
-        "The object is not a `soma_adat` class object: {.value(class(adat))}"
+        "The object is not a `soma_adat` class object: {.val {class(adat)}}"
       )
     }
     FALSE
   } else if ( length(atts) <= 3L ) {
     if ( verbose ) {
       .oops(
-        "Attributes has only 3 entries: {.value(names(atts))}"
+        "Attributes has only 3 entries: {.val {names(atts)}}"
       )
     }
     FALSE
@@ -61,19 +61,19 @@ is_intact_attr <- function(adat, verbose = interactive()) {
   } else if ( !all(c("HEADER", "COL_DATA", "ROW_DATA") %in% names(atts$Header.Meta)) ) {
     if ( verbose ) {
       diff <- setdiff(c("HEADER", "COL_DATA", "ROW_DATA"), names(atts$Header.Meta))
-      .oops(paste("Header.Meta is missing:", .value(diff)))
+      .oops("Header.Meta is missing: {.val {diff}}")
     }
     FALSE
   } else if ( !all(col_meta_checks %in% names(atts$Col.Meta)) ) {
     if ( verbose ) {
       diff <- setdiff(col_meta_checks, names(atts$Col.Meta))
-      .oops(paste("Col.Meta is missing:", .value(diff)))
+      .oops("Col.Meta is missing: {.val {diff}}")
     }
     FALSE
   } else if ( !inherits(atts$Col.Meta, "tbl_df") ) {
     if ( verbose ) {
       .oops(
-        "Col.Meta is not a tibble! -> {.value(class(atts$Col.Meta))}"
+        "Col.Meta is not a tibble! -> {.val {class(atts$Col.Meta)}}"
       )
     }
     FALSE

R/loadAdatsAsList.R

@@ -56,12 +56,12 @@
 #' @export
 loadAdatsAsList <- function(files, collapse = FALSE, verbose = interactive(), ...) {
   files <- setNames(files, cleanNames(basename(files)))
-  res <- lapply(files, function(.file) {
-    x <- tryCatch(read_adat(.file, ...), error = function(e) NULL)
+  res <- lapply(files, function(file) {
+    x <- tryCatch(read_adat(file, ...), error = function(e) NULL)
     if ( is.null(x) ) {
-      .oops("Failed to load: {.value(.file)}")
+      .oops("Failed to load: {.val {file}}")
     } else if ( verbose ) {
-      .done("Loading: {.value(.file)}")
+      .done("Loading: {.val {file}}")
     }
     x
   })

R/parseCheck.R

@@ -159,8 +159,8 @@ parseCheck <- function(all.tokens) {
   # check col meta match
   if ( !isTRUE(setequal(col_meta, col_meta2)) ) {
     .oops("Mismatch between `^COL_DATA` in header and `Col.Meta` block:")
-    .todo("  In Header:   {.value(col_meta)}")
-    .todo("  In Col.Meta: {.value(col_meta2)}")
+    .todo("  In Header:   {.val {col_meta}}")
+    .todo("  In Col.Meta: {.val {col_meta2}}")
     stop("Stopping check early.", call. = FALSE)
   }
 
@@ -227,8 +227,8 @@ parseCheck <- function(all.tokens) {
         line_col = "blue", right = cr_red("!")
       )
     )
-    .todo("Should be:    {.value(table_width)}")
-    .todo("Currently is: {.value(header_length)}")
+    .todo("Should be:    {.val {table_width}}")
+    .todo("Currently is: {.val {header_length}}")
     # print(all.tokens[[ which_header_row ]])   # nolint: commented_code_linter.
     .oops("Length of the header row is incorrect")
     .oops("Does not match the width of the data table")
@@ -248,7 +248,7 @@ parseCheck <- function(all.tokens) {
     )
     gap_chr <- col_meta2[has_gaps]
     .todo(
-      paste("Visually inspect the following Col.Meta rows:", .value(gap_chr))
+      paste("Visually inspect the following Col.Meta rows: {.val {gap_chr}}")
     )
     if ( identical(Sys.getenv("TESTTHAT"), "true") ||
          isTRUE(getOption("knitr.in.progress")) ) {
@@ -258,7 +258,7 @@ parseCheck <- function(all.tokens) {
     }
     cat(.symb, "They may be missing in: ")
     print(.value(c("Spuriomers", "HybControls")))
-    .todo("This is non-critical in ADATs with new {.value('seq.1234.56')} format.")
+    .todo("This is non-critical in ADATs with new {.val {'seq.1234.56'}} format.")
   }
   writeLines(cli_rule("Parse Diagnostic Complete", line = 2, line_col = "green"))
 }

R/prepHeaderMeta.R

@@ -66,7 +66,7 @@ prepHeaderMeta <- function(data) {
   if ( !("Version" %in% names(x$Header.Meta$HEADER) &&
          x$Header.Meta$HEADER$Version == "1.2") ) {
     x$Header.Meta$HEADER$Version <- "1.2"
-    .done("Updating ADAT version to: {.value('1.2')}")
+    .done("Updating ADAT version to: {.val 1.2}")
   }
 
   if ( "CreatedBy" %in% names(x$Header.Meta$HEADER) ) {

R/utils.R

@@ -1,10 +1,10 @@
 
-# internal helpers similar to `usethis::ui_*()` functions
+# internal helpers similar to `usethis` functions
 .value <- function(x) {
   if ( identical(Sys.getenv("TESTTHAT"), "true") ) {
     paste(encodeString(x, quote = "'"), collapse = ", ")
   } else {
-    usethis::ui_value(x)
+    cli::cli_text("{.val {x}}")
   }
 }
 
@@ -17,22 +17,22 @@
   paste0("\033[90m", encodeString(x, quote = "`"), "\033[39m")
 }
 
-# borrow from usethis, cli, and crayon for internal use
+# borrow from cli for internal use
 # without explicitly importing the package in NAMESPACE file
 # avoid R CMD check NOTE:
 #   "Namespace in Imports field not imported from: 'pkg'"
-.todo <- usethis::ui_todo
-.done <- usethis::ui_done
-.oops <- usethis::ui_oops
+.todo <- cli::cli_alert
+.done <- cli::cli_alert_success
+.oops <- cli::cli_alert_danger
 # -------------------------- #
 cli_rule  <- cli::rule
 # -------------------------- #
-cr_bold   <- crayon::bold
-cr_green  <- crayon::green
-cr_cyan   <- crayon::cyan
-cr_red    <- crayon::red
-cr_blue   <- crayon::blue
-cr_yellow <- crayon::yellow
+cr_bold   <- cli::style_bold
+cr_green  <- cli::col_green
+cr_cyan   <- cli::col_cyan
+cr_red    <- cli::col_red
+cr_blue   <- cli::col_blue
+cr_yellow <- cli::col_yellow
 
 
 # wrapper around padding; default to right side padding

R/write-adat.R

@@ -47,7 +47,7 @@ write_adat <- function(x, file) {
 
   if ( !grepl("\\.adat$", file) ) {
     warning(
-      "File extension is not `*.adat` (", .value(file), "). ",
+      "File extension is not `*.adat` ('", file, "'). ",
       "Are you sure this is the correct file extension?",
       call. = FALSE
     )
@@ -103,7 +103,7 @@ write_adat <- function(x, file) {
     if ( n_meta < 1L ) {
       warning(
         "\nYou are writing an ADAT without any meta data.\n",
-        "This may cause this file (", .value(file), ") ",
+        "This may cause this file ('", file, "') ",
         "to be unreadable via `read_adat()`.\n",
         "Suggest including at least one column of meta data (e.g. 'sample_id').",
         call. = FALSE
@@ -139,7 +139,7 @@ write_adat <- function(x, file) {
       fileEncoding = "UTF-8"
     )
   }
-  .done("ADAT written to: {.value(file)}")
+  .done("ADAT written to: {.val {file}}")
   invisible(x)
 }
 

README.Rmd

@@ -109,14 +109,12 @@ file):
 
 * [R (>= 4.1.0)](https://cran.r-project.org/)
 * [cli](https://cran.r-project.org/package=cli)
-* [crayon](https://cran.r-project.org/package=crayon)
 * [dplyr](https://cran.r-project.org/package=dplyr)
 * [lifecycle](https://cran.r-project.org/package=lifecycle)
 * [magrittr](https://cran.r-project.org/package=magrittr)
 * [readxl](https://cran.r-project.org/package=readxl)
 * [tibble](https://cran.r-project.org/package=tibble)
 * [tidyr](https://cran.r-project.org/package=tidyr)
-* [usethis](https://cran.r-project.org/package=usethis)
 
 
 #### Biobase
@@ -141,7 +139,7 @@ Information about Bioconductor can be found here:
 
 #### Loading
 
-Upon _successful_ installation, load the `SomaDataIO` as normal:
+Upon _successful_ installation, load `SomaDataIO` as normal:
 
 ```{r load-somadataio, eval = FALSE}
 library(SomaDataIO)

README.md

@@ -87,14 +87,12 @@ file):
 
 - [R (\>= 4.1.0)](https://cran.r-project.org/)
 - [cli](https://cran.r-project.org/package=cli)
-- [crayon](https://cran.r-project.org/package=crayon)
 - [dplyr](https://cran.r-project.org/package=dplyr)
 - [lifecycle](https://cran.r-project.org/package=lifecycle)
 - [magrittr](https://cran.r-project.org/package=magrittr)
 - [readxl](https://cran.r-project.org/package=readxl)
 - [tibble](https://cran.r-project.org/package=tibble)
 - [tidyr](https://cran.r-project.org/package=tidyr)
-- [usethis](https://cran.r-project.org/package=usethis)
 
 #### Biobase
 
@@ -117,7 +115,7 @@ Information about Bioconductor can be found here:
 
 #### Loading
 
-Upon *successful* installation, load the `SomaDataIO` as normal:
+Upon *successful* installation, load `SomaDataIO` as normal:
 
 ``` r
 library(SomaDataIO)