From d23855ef312cb147aae9bf05f8039e090cd57e14 Mon Sep 17 00:00:00 2001
From: Kyle Barrett <barrettk@metrumrg.com>
Date: Mon, 15 Jul 2024 15:43:27 -0400
Subject: [PATCH] remove `nm_fdata` from this PR

 - opting to separate this into a separate, more focused PR
---
 NAMESPACE                          |  2 --
 R/aaa.R                            |  1 -
 R/print.R                          | 12 -------
 R/run-nmtran.R                     | 56 +-----------------------------
 man/nmtran.Rd                      | 12 +------
 man/print_bbi.Rd                   |  5 ---
 tests/testthat/test-workflow-bbi.R | 11 ------
 7 files changed, 2 insertions(+), 97 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 7aa7e76e7..6c09f664d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -76,7 +76,6 @@ S3method(print,bbi_nmboot_summary)
 S3method(print,bbi_nonmem_summary)
 S3method(print,bbi_process)
 S3method(print,model_tree_static)
-S3method(print,nmtran_fdata)
 S3method(print,nmtran_process)
 S3method(print_model_files,default)
 S3method(submit_model,bbi_base_model)
@@ -161,7 +160,6 @@ export(new_bootstrap_run)
 export(new_ext)
 export(new_model)
 export(nm_data)
-export(nm_fdata)
 export(nm_file)
 export(nm_file_multi_tab)
 export(nm_grd)
diff --git a/R/aaa.R b/R/aaa.R
index 9f85ce265..105a70fb1 100644
--- a/R/aaa.R
+++ b/R/aaa.R
@@ -210,7 +210,6 @@ CONF_LOG_CLASS <- "bbi_config_log_df"
 SUM_LOG_CLASS <- "bbi_summary_log_df"
 LOG_DF_CLASS <- "bbi_log_df"
 NMTRAN_PROCESS_CLASS <- "nmtran_process"
-NMTRAN_FDATA_CLASS <- "nmtran_fdata"
 
 # YAML keys that are hard-coded
 YAML_YAML_MD5 <- "yaml_md5"
diff --git a/R/print.R b/R/print.R
index 12f9ef99f..292f4375f 100644
--- a/R/print.R
+++ b/R/print.R
@@ -502,18 +502,6 @@ print.nmtran_process <- function(x, ...){
 }
 
 
-#' @describeIn print_bbi Prints the `FDATA`, showing key changes from `nm_data`
-#' @export
-print.nmtran_fdata <- function(x, ...){
-  recs_dropped <- attributes(x)$n_records_dropped
-  cli::cat_bullet(
-    paste("Number of records dropped:", col_blue(recs_dropped)),
-    bullet = "en_dash"
-  )
-  cat("\n")
-  NextMethod()
-}
-
 #' @describeIn print_bbi Draw model tree as a static plot
 #' @param x plot to display
 #' @param newpage Logical (T/F). If `TRUE`, draw new (empty) page first.
diff --git a/R/run-nmtran.R b/R/run-nmtran.R
index 3f989df0f..bfc406c54 100644
--- a/R/run-nmtran.R
+++ b/R/run-nmtran.R
@@ -8,8 +8,7 @@
 #' control stream data and instructions into a form executable by `NONMEM`.
 #'
 #' `run_nmtran()` allows users to test their models ahead of submission to ensure
-#' correct coding, whereas `nm_fdata()` generates and returns the `NM-TRAN`
-#' dataset (`FDATA`) for further analysis and verification.
+#' correct coding.
 #'
 #' @param .mod A `bbr` model object.
 #' @param .config_path Path to a bbi configuration file. If `NULL`, the default,
@@ -28,9 +27,6 @@
 #' # Set the path to an NM-TRAN executable
 #' run_nmtran(mod, nmtran_exe = "/opt/NONMEM/nm75/tr/NMTRAN.exe")
 #'
-#' # Generate and return `FDATA`
-#' fdata <- nm_fdata(mod)
-#'
 #' }
 #' @name nmtran
 NULL
@@ -91,56 +87,6 @@ run_nmtran <- function(
 }
 
 
-#' @describeIn nmtran Executes `run_nmtran` on a `bbi_nonmem_model` and
-#'  returns the `NM-TRAN` dataset (`FDATA`)
-#' @export
-nm_fdata <- function(
-    .mod,
-    .config_path = NULL,
-    nmtran_exe = NULL
-){
-  nmtran_p <- run_nmtran(.mod, .config_path, nmtran_exe, delete_on_exit = FALSE)
-  on.exit(fs::dir_delete(nmtran_p$run_dir))
-
-  if(nmtran_p$status_val != 0){
-    # trim output
-    output_lines <- nmtran_p$output_lines[!grepl("^\\s+$", nmtran_p$output_lines)]
-    rlang::warn(
-      c(
-        "NM-TRAN was unsuccessful and returned the following messages:",
-        paste(output_lines, collapse = "\n")
-      )
-    )
-  }
-
-  # Attempt to read in FDATA (even if status_val is not 0)
-  #  - FDATA can still be read in in _some scenarios_ where NM-TRAN fails
-  fdata_path <- file.path(nmtran_p$run_dir, "FDATA")
-  if(fs::file_exists(fdata_path)){
-    input_data <- nm_data(.mod) %>% suppressMessages()
-    fdata <- tryCatch({
-      nm_file_impl(fdata_path, skip = 0) %>%
-        stats::setNames(names(input_data))
-    }, error = function(cond){
-      rlang::inform(
-        c("FDATA could not be read in:", cond$parent$message)
-      )
-      return(NULL)
-    })
-
-    if(!is.null(fdata)){
-      attr(fdata, "n_records_dropped") <- nrow(input_data) - nrow(fdata)
-    }
-
-    # assign class and return
-    class(fdata) <- c(NMTRAN_FDATA_CLASS, class(fdata))
-    return(fdata)
-  }else{
-    return(invisible(NULL))
-  }
-}
-
-
 #' Search for and validate existence of an `NM-TRAN` executable
 #'
 #' If `nmtran_exe = NULL`, this will look for a `bbi.yaml` file in the same
diff --git a/man/nmtran.Rd b/man/nmtran.Rd
index 26527871a..fae2bb6bc 100644
--- a/man/nmtran.Rd
+++ b/man/nmtran.Rd
@@ -3,12 +3,9 @@
 \name{nmtran}
 \alias{nmtran}
 \alias{run_nmtran}
-\alias{nm_fdata}
 \title{Interface for running \code{NM-TRAN} on model objects}
 \usage{
 run_nmtran(.mod, .config_path = NULL, nmtran_exe = NULL, delete_on_exit = TRUE)
-
-nm_fdata(.mod, .config_path = NULL, nmtran_exe = NULL)
 }
 \arguments{
 \item{.mod}{A \code{bbr} model object.}
@@ -32,17 +29,13 @@ generate \code{NM-TRAN} datasets (\code{FDATA}).
 control stream data and instructions into a form executable by \code{NONMEM}.
 
 \code{run_nmtran()} allows users to test their models ahead of submission to ensure
-correct coding, whereas \code{nm_fdata()} generates and returns the \code{NM-TRAN}
-dataset (\code{FDATA}) for further analysis and verification.
+correct coding.
 }
 \section{Functions}{
 \itemize{
 \item \code{run_nmtran()}: Run \code{NM-TRAN} on a model object to validate its control
 stream for correct coding before submission.
 
-\item \code{nm_fdata()}: Executes \code{run_nmtran} on a \code{bbi_nonmem_model} and
-returns the \code{NM-TRAN} dataset (\code{FDATA})
-
 }}
 \examples{
 \dontrun{
@@ -52,8 +45,5 @@ run_nmtran(mod)
 # Set the path to an NM-TRAN executable
 run_nmtran(mod, nmtran_exe = "/opt/NONMEM/nm75/tr/NMTRAN.exe")
 
-# Generate and return `FDATA`
-fdata <- nm_fdata(mod)
-
 }
 }
diff --git a/man/print_bbi.Rd b/man/print_bbi.Rd
index a6bc482f3..c9a8aed1c 100644
--- a/man/print_bbi.Rd
+++ b/man/print_bbi.Rd
@@ -7,7 +7,6 @@
 \alias{print.bbi_nonmem_summary}
 \alias{print.bbi_nmboot_summary}
 \alias{print.nmtran_process}
-\alias{print.nmtran_fdata}
 \alias{print.model_tree_static}
 \title{Print methods for bbr objects}
 \usage{
@@ -21,8 +20,6 @@
 
 \method{print}{nmtran_process}(x, ...)
 
-\method{print}{nmtran_fdata}(x, ...)
-
 \method{print}{model_tree_static}(x, newpage = is.null(vp), vp = NULL, ...)
 }
 \arguments{
@@ -68,8 +65,6 @@ will make for prettier formatting, especially of table outputs.
 \item \code{print(nmtran_process)}: Prints the \code{NM-TRAN} evaluation of a \code{bbi_nonmem_model}
 object
 
-\item \code{print(nmtran_fdata)}: Prints the \code{FDATA}, showing key changes from \code{nm_data}
-
 \item \code{print(model_tree_static)}: Draw model tree as a static plot
 
 }}
diff --git a/tests/testthat/test-workflow-bbi.R b/tests/testthat/test-workflow-bbi.R
index 60350a8f1..dbcb7e1e9 100644
--- a/tests/testthat/test-workflow-bbi.R
+++ b/tests/testthat/test-workflow-bbi.R
@@ -402,17 +402,6 @@ withr::with_options(list(
       expect_equal(nmtran_results$status, "NMTRAN successful")
     })
 
-    it("nm_fdata: integration", {
-      fdata <- nm_fdata(mod1)
-
-      expect_equal(names(fdata), names(nm_data(mod1)))
-
-      # Test dropped/renamed columns
-
-      # Test failure: incorrect data path
-      data_path <- "test/this/path/data.csv"
-      modify_data_path_ctl(mod1, data_path)
-    })
   })
 
 }) # closing withr::with_options