Add ferx as NLME fitting backend

.gitignore

@@ -6,3 +6,7 @@
 .Rproj.user
 .DS_Store
 docs
+data-raw/
+.claude
+*-fit.rds
+.luna.cache.*

DESCRIPTION

@@ -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/create_cache.R

@@ -32,12 +32,11 @@ create_cache <- function(
     "project", project
   )
 
-  ## read pharmpy configuration
-  if(verbose)
-    cli::cli_alert_info("Reading Pharmpy settings into cache")
-  .luna_cache$set(
-    "pharmpy_conf", get_pharmpy_conf()
-  )
+  ## Note: pharmpy configuration (previously read here via get_pharmpy_conf())
+  ## is intentionally not read at cache creation. Reading it eagerly required
+  ## pharmpy to be installed for all users, causing luna_load_project() to fail
+  ## for PSN and nlmixr2 users. Pharmpy config is now read lazily inside
+  ## pharmpy-specific functions (luna_run(), luna_check(), etc.).
 
   ## read / update models and results
   update_cache(project)

R/get_luna_config.R

@@ -12,11 +12,11 @@ get_luna_config <- function(
   }
   conf <- read_yaml_safe(global_conf_file)
   if(is_luna_cache_available(abort = FALSE)) {
-    proj_yaml <- .luna_cache$get("yaml")
+    proj_yaml <- .luna_cache$get("project")$yaml
     proj_conf <- proj_yaml$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

@@ -5,14 +5,19 @@
 #'
 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 -fit.rds result file
+  if (file.exists(file.path(folder, paste0(id, "-fit.rds")))) {
     status <- "finished"
   }
   status

R/luna_check.R

@@ -1,13 +1,17 @@
-#' Syntax-check a NONMEM model
+#' Syntax-check a model
+#'
+#' 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
 #'
 #' @export
 luna_check <- function(
-  id,
-  folder = NULL,
-  verbose = FALSE,
-  ...
+    id,
+    folder = NULL,
+    verbose = FALSE,
+    ...
 ) {
 
   id <- unlist(lapply(id, validate_id))
@@ -30,42 +34,61 @@ luna_check <- function(
     verbose = FALSE
   )
 
-  # Transform folder path to absolute path
   folder <- normalizePath(folder, mustWork = TRUE)
 
-  # read the model file with nm_read_model()
+  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)) {
+  if (!file.exists(model_file)) {
     cli::cli_abort("Model file for run {id} not found!")
   }
-  model <- pharmr::read_model(model_file)
 
-  # Some integrity checksa
-  if(! inherits(model, "pharmpy.model.model.Model")) {
-    cli::cli_abort("Model is not a pharmpy model. Please check the model file.")
+  model <- tryCatch(
+    pharmr::read_model(model_file),
+    error = function(e) {
+      cli::cli_alert_warning("Model has a syntax error:")
+      message(conditionMessage(e))
+      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$dataset)) {
-    cli::cli_abort("Model has no dataset. Please check the model and dataset files.")
+
+  if (is.null(model$dataset)) {
+    cli::cli_alert_warning("Model parsed but dataset could not be loaded. Check the {.field $DATA} path.")
+    return(invisible(FALSE))
   }
+
   cli::cli_alert_success("Model loaded successfully.")
 
   model_ok <- pharmr.extra::run_nlme(
-    model = model,
-    id = id,
-    path = folder,
-    method = "nmfe",
-    as_job = as_job,
-    check_only = TRUE, # !! don't run the model, only check it using NM-TRAN
-    console = FALSE,
-    verbose = verbose,
-    ...
+    model,
+    check_only = TRUE,
+    verbose = verbose
   )
 
-  if(model_ok) {
-    cli::cli_alert_success("Model syntax OK!")
-  } else {
-    cli::cli_alert_warning("Model seems to have syntax error")
-    cat(attr(model_ok, "message"))
+  if (isFALSE(model_ok)) {
+    cli::cli_alert_warning("Model failed NONMEM compilation check.")
+    return(invisible(FALSE))
   }
 
+  cli::cli_alert_success("Model syntax OK!")
+  invisible(TRUE)
 }

R/luna_ferx_info.R

@@ -0,0 +1,44 @@
+#' Show fit results for a ferx model run
+#'
+#' Reads the `{id}-fit.rds` 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$folder
+  }
+  folder <- normalizePath(folder, mustWork = TRUE)
+
+  result_file <- file.path(folder, paste0(id, "-fit.rds"))
+  if (!file.exists(result_file)) {
+    cli::cli_abort(
+      c(
+        "No ferx results found for run {.val {id}}.",
+        "i" = "Run {.fn luna_run} first, or check that {.file {result_file}} exists."
+      )
+    )
+  }
+
+  result <- readRDS(result_file)
+
+  cli::cli_h1("ferx fit: {id}")
+  cli::cli_alert_info("Method:    {result$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_load_project.R

@@ -39,11 +39,21 @@ luna_load_project <- function(
   )
   class(project) <- c("luna.project", class(project))
 
-  if(dir.exists(paste0(".luna.cache.", name))) {
+  cache_folder <- file.path(folder, paste0(".luna.cache.", name))
+  if(dir.exists(cache_folder)) {
     is_cache_available <- is_luna_cache_available(abort = FALSE)
-    if(!is_cache_available) {
+    cached_folder <- if(
+      is_cache_available && .luna_cache$exists("folder")
+    ) .luna_cache$get("folder") else NULL
+    cached_name <- if(
+      is_cache_available && .luna_cache$exists("name")
+    ) .luna_cache$get("name") else NULL
+    if(
+      !is_cache_available ||
+      !identical(cached_folder, folder) ||
+      !identical(cached_name, name)
+    ) {
       if(verbose) cli::cli_alert_info("Reloading luna project cache")
-      cache_folder <- file.path(folder, paste0(".luna.cache.", name))
       .luna_cache <<- cachem::cache_disk(dir = cache_folder)
     }
     if(verbose) cli::cli_alert_info("Updating luna project cache")