Add ferx as NLME fitting backend

.gitignore

@@ -8,3 +8,6 @@
 docs
 data-raw/
 .claude
+*.fitrx
+!inst/extdata/**/*.fitrx
+.luna.cache.*

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: luna
 Type: Package
 Title: Light-weight Universal NLME Admininstrator
-Version: 0.1.0
+Version: 0.2.0
 Author: Ron Keizer
 Maintainer: Ron Keizer <ron@insight-rx.com>
 Description: Organizes model development workflows in NONMEM and nlmixr2. The 
@@ -24,10 +24,11 @@ Imports:
     stats,
     job,
     diffr
-Suggests: 
+Suggests:
     httr,
     ellmer,
     nlmixr2,
+    ferx,
     ggplot2,
     xpose,
     vpc,
@@ -41,7 +42,8 @@ Suggests:
     rstudioapi
 Remotes:
     InsightRX/irxutils,
-    InsightRX/pharmr.extra
+    InsightRX/pharmr.extra,
+    ferx=FeRx-NLME/ferx-r
 License: MIT + file LICENSE
 URL: https://github.com/InsightRX/uno, https://insightrx.github.io/uno/, https://insightrx.github.io/luna/
 LazyData: TRUE

NAMESPACE

@@ -11,6 +11,7 @@ export(luna_dataset)
 export(luna_diff)
 export(luna_edit)
 export(luna_edit_project)
+export(luna_ferx_info)
 export(luna_gof)
 export(luna_help)
 export(luna_ind)

R/get_luna_config.R

@@ -16,7 +16,7 @@ get_luna_config <- function(
     proj_conf <- proj_yaml$project$config
     ## use any specified project conf to overwrite env conf
     for(key in names(proj_conf)) {
-      if(is.null(conf[[key]]) || proj_conf[[key]] != conf[[key]]) {
+      if(is.null(conf[[key]]) || !identical(proj_conf[[key]], conf[[key]])) {
         if(verbose)
           cli::cli_alert_info("Overriding global luna setting for `{key}` with project-specific setting")
         conf[[key]] <- proj_conf[[key]]

R/get_status.R

@@ -5,15 +5,26 @@
 #'
 get_status <- function(id, folder = ".") {
   status <- "not run"
+  # NONMEM: check for .lst output file
   tmp <- find_file_with_fallback(
     folder,
     file.path(id, paste0("run", ".lst")),
     fallback = file.path(paste0(id, ".lst")),
     verbose = FALSE,
     abort = FALSE
   )
-  if(!is.null(tmp)) {
+  if (!is.null(tmp)) {
     status <- "finished"
   }
+  # ferx: check for .fitrx result file and convergence
+  rds_path <- file.path(folder, paste0(id, ".fitrx"))
+  if (file.exists(rds_path)) {
+    fit <- tryCatch(ferx::ferx_load_fit(rds_path), error = function(e) NULL)
+    if (!is.null(fit) && isTRUE(fit$converged)) {
+      status <- "finished"
+    } else {
+      status <- "failed"
+    }
+  }
   status
 }

R/luna_check.R

@@ -1,7 +1,8 @@
-#' Syntax-check a NONMEM model
+#' Syntax-check a model
 #'
-#' Uses pharmpy to parse the model. A successful parse indicates the model is
-#' valid. Any pharmpy parse error is reported as a syntax issue.
+#' For NONMEM models (`method = "pharmpy"`, `"psn"`, `"nmfe"`): uses pharmpy
+#' to parse the model file. For ferx models (`method = "ferx"`): verifies the
+#' `.ferx` file exists.
 #'
 #' @inheritParams luna_run
 #'
@@ -12,34 +13,48 @@ luna_check <- function(
     verbose = FALSE,
     ...
 ) {
-  
+
   id <- unlist(lapply(id, validate_id))
   if(length(id) > 1) {
     cli::cli_abort("Sorry, checking multiple runs in batch is not yet supported.")
   }
-  
+
   ## Get cache and config
   is_luna_cache_available(abort = TRUE)
   config <- get_luna_config()
   name <- .luna_cache$get("project")$metadata$name
   if(is.null(folder)) {
     folder <- .luna_cache$get("project")$metadata$folder
   }
-  
+
   ## make sure we're up to date
   luna_load_project(
     name = name,
     folder = folder,
     verbose = FALSE
   )
-  
+
   folder <- normalizePath(folder, mustWork = TRUE)
-
+
+  method <- ifelse0(config$tools$modelfit$method, "pharmpy")
+
+  ## ferx: check file existence only
+  if (method == "ferx") {
+    model_file <- file.path(folder, paste0(id, ".ferx"))
+    if (!file.exists(model_file)) {
+      cli::cli_alert_warning("ferx model file not found: {.file {model_file}}")
+      return(invisible(FALSE))
+    }
+    cli::cli_alert_success("ferx model file found: {.file {model_file}}")
+    return(invisible(TRUE))
+  }
+
+  ## NONMEM path
   model_file <- file.path(folder, paste0(id, ".mod"))
   if (!file.exists(model_file)) {
     cli::cli_abort("Model file for run {id} not found!")
   }
-  
+
   model <- tryCatch(
     pharmr::read_model(model_file),
     error = function(e) {
@@ -48,14 +63,14 @@ luna_check <- function(
       return(invisible(FALSE))
     }
   )
-  
+
   if (isFALSE(model)) return(invisible(FALSE))
-  
+
   if (!inherits(model, "pharmpy.model.model.Model")) {
     cli::cli_alert_warning("Model could not be parsed as a pharmpy model.")
     return(invisible(FALSE))
   }
-  
+
   if (is.null(model$dataset)) {
     cli::cli_alert_warning("Model parsed but dataset could not be loaded. Check the {.field $DATA} path.")
     return(invisible(FALSE))
@@ -65,12 +80,20 @@ luna_check <- function(
 
   model_ok <- pharmr.extra::run_nlme(
     model,
+    id = id,
+    path = folder,
+    method = method,
     check_only = TRUE,
     verbose = verbose
   )
 
   if (isFALSE(model_ok)) {
-    cli::cli_alert_warning("Model failed NONMEM compilation check.")
+    cli::cli_alert_warning(
+      "Model failed NONMEM compilation check."
+    )
+    if (!is.null(attr(model_ok, "message"))) {
+      cat(attr(model_ok, "message"))
+    }
     return(invisible(FALSE))
   }
 

R/luna_ferx_info.R

@@ -0,0 +1,44 @@
+#' Show fit results for a ferx model run
+#'
+#' Reads the `{id}.fitrx` file saved by [luna_run()] (when
+#' `method = "ferx"`) and prints a formatted parameter summary.
+#'
+#' @inheritParams luna_run
+#'
+#' @return The `ferx_fit` result object, invisibly.
+#'
+#' @export
+luna_ferx_info <- function(id, folder = NULL) {
+  id <- validate_id(id)
+  if (is.null(folder)) {
+    folder <- .luna_cache$get("project")$metadata$folder
+  }
+  folder <- normalizePath(folder, mustWork = TRUE)
+
+  result_file <- file.path(folder, paste0(id, ".fitrx"))
+  if (!file.exists(result_file)) {
+    cli::cli_abort(
+      c(
+        "No ferx results found for run {.val {id}}.",
+        "i" = "Run {.fn luna_run} first, or check that {.file {result_file}} exists."
+      )
+    )
+  }
+
+  result <- ferx::ferx_load_fit(result_file)
+
+  cli::cli_h1("ferx fit: {id}")
+  cli::cli_alert_info("Method:    {result$method}")
+  cli::cli_alert_info("Converged: {result$converged}")
+  cli::cli_alert_info("OFV:       {round(result$ofv, 4)}")
+  if (!is.null(result$aic))
+    cli::cli_alert_info("AIC:       {round(result$aic, 4)}")
+  if (!is.null(result$bic))
+    cli::cli_alert_info("BIC:       {round(result$bic, 4)}")
+  if (!is.null(result$n_iterations))
+    cli::cli_alert_info("Iterations: {result$n_iterations}")
+  if (!is.null(result$wall_time_secs))
+    cli::cli_alert_info("Wall time:  {round(result$wall_time_secs, 1)} s")
+
+  invisible(result)
+}

R/luna_run.R

@@ -1,10 +1,14 @@
-#' Run a NONMEM model
+#' Run a model
 #'
-#' @param id run id, e.g. `run1`. This will be the folder in which the NONMEM
-#' model is run.
+#' Dispatches to the configured execution backend. Supported methods:
+#' `"pharmpy"` (default), `"psn"`, `"nmfe"` for NONMEM-based workflows, and
+#' `"ferx"` for the ferx-nlme Rust engine.
+#'
+#' @param id run id, e.g. `run1`. This will be the folder in which the model
+#' is run.
 #' @param folder path to folder containing the model file. Default is current directory.
 #' @param as_job run as an RStudio job (async), or in the console. If left `NULL`
-#' will use setting in luna config.
+#' will use setting in luna config. Not yet supported for `method = "ferx"`.
 #'
 #' @export
 luna_run <- function(
@@ -14,12 +18,12 @@ luna_run <- function(
     as_job = NULL,
     ...
 ) {
-  
+
   id <- unlist(lapply(id, validate_id))
   if(length(id) > 1) {
     cli::cli_abort("Sorry, running of multiple runs in batch is not yet supported.")
   }
-  
+
   ## Get cache and config
   is_luna_cache_available(abort = TRUE)
   config <- get_luna_config()
@@ -28,45 +32,51 @@ luna_run <- function(
     folder <- .luna_cache$get("project")$metadata$folder
   }
   as_job <- is_run_as_job(config, as_job)
-  
+
   ## make sure we're up to date
   luna_load_project(
     name = name,
     folder = folder,
     verbose = FALSE
   )
-  
+
   # Transform folder path to absolute path
   folder <- normalizePath(folder, mustWork = TRUE)
-
+
+  ## Detect method early to dispatch non-NONMEM engines
+  method <- ifelse0(config$tools$modelfit$method, "pharmpy")
+
+  if (method == "ferx") {
+    return(luna_run_ferx(id = id, folder = folder, config = config, ...))
+  }
+
   # read the model file with nm_read_model()
   model_file <- file.path(folder, paste0(id, ".mod"))
   if(! file.exists(model_file)) {
     cli::cli_abort("Model file for run {id} not found!")
   }
   model <- pharmr::read_model(model_file)
-  
-  # Some integrity checksa
+
+  # Some integrity checks
   if(! inherits(model, "pharmpy.model.model.Model")) {
     cli::cli_abort("Model is not a pharmpy model. Please check the model file.")
   }
   if(is.null(model$dataset)) {
     cli::cli_abort("Model has no dataset. Please check the model and dataset files.")
   }
   cli::cli_alert_success("Model loaded successfully.")
-  
+
   ## log event
   log_add(
     event = "action",
     action = "modelfit",
     id = id
   )
-  
+
   # Determine nmfe location to use.
   if(is.null(config$tools$modelfit$method)) {
     cli::cli_alert_warning("Default method for modelfit not configured, using pharmpy dispatcher.")
   }
-  method <- ifelse0(config$tools$modelfit$method, "pharmpy")
   console <- ifelse0(config$tools$modelfit$console, TRUE)
   if(is.null(nmfe)) {
     nmfe <- ifelse0(config$tools$modelfit$nmfe, config$tools$nonmem$nmfe)
@@ -93,4 +103,67 @@ luna_run <- function(
     console = console,
     ...
   )
-}
+}
+
+#' Run a ferx model (internal helper for luna_run)
+#'
+#' @inheritParams luna_run
+#' @param config resolved luna config list
+#'
+#' @keywords internal
+luna_run_ferx <- function(id, folder, config, ...) {
+  if (!requireNamespace("ferx", quietly = TRUE)) {
+    cli::cli_abort(c(
+      "The {.pkg ferx} package is required to run ferx models.",
+      "i" = "Install it with: {.code devtools::install_github('FeRx-NLME/ferx-r')}"
+    ))
+  }
+
+  model_file <- file.path(folder, paste0(id, ".ferx"))
+  if (!file.exists(model_file)) {
+    cli::cli_abort("ferx model file {.file {model_file}} not found!")
+  }
+
+  data_path <- config$tools$modelfit$data
+  if (is.null(data_path)) {
+    cli::cli_abort(c(
+      "ferx method requires a data file path.",
+      "i" = "Set {.code tools.modelfit.data} in the project config YAML."
+    ))
+  }
+  if (!file.exists(data_path)) {
+    data_path_abs <- file.path(folder, data_path)
+    if (!file.exists(data_path_abs)) {
+      cli::cli_abort(
+        "Data file {.file {data_path}} not found (also checked relative to project folder)."
+      )
+    }
+    data_path <- data_path_abs
+  }
+
+  ## log event
+  log_add(
+    event = "action",
+    action = "modelfit",
+    id = id
+  )
+
+  cli::cli_alert_info("Running ferx model {.val {id}}...")
+
+  result_file <- file.path(folder, paste0(id, ".fitrx"))
+
+  result <- ferx::ferx_fit(
+    model = model_file, data = data_path, output = result_file, ...
+  )
+
+  if (isTRUE(result$converged)) {
+    cli::cli_alert_success(
+      "ferx run {.val {id}} converged. OFV = {round(result$ofv, 2)}"
+    )
+  } else {
+    cli::cli_alert_warning("ferx run {.val {id}} did not converge.")
+  }
+  cli::cli_alert_info("Results saved to {.file {result_file}}")
+
+  invisible(result)
+}