Fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hyperion
 Title: Pharmaceutical Model Development and Workflow Tools
-Version: 0.5.0
+Version: 0.4.2.9000
 Authors@R: c(
     person("Matt", "Smith", , "matthews@a2-ai.com", role = c("aut", "cre")),
     person("Vincent", "Prouillet", ,"vincent@a2-ai.com", role = c("aut")),
@@ -18,6 +18,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/rextendr/version: 0.5.0
+Config/PharosVersion: 0.5.0
 Config/build/never-clean: true
 Config/build/extra-sources: src/rust/Cargo.lock
 SystemRequirements: Cargo (Rust's package manager), rustc >= 1.65.0, xz

R/utils.R

@@ -393,6 +393,38 @@ print_data_table_knit <- function(formatted_data, title) {
   return(output)
 }
 
+#' Detect the installed pharos CLI and its version
+#'
+#' Locates the `pharos` executable on the user's PATH via [Sys.which()] and
+#' parses the version reported by `pharos --version`.
+#'
+#' @return A list with elements:
+#'   \itemize{
+#'     \item `path` — absolute path to the pharos binary, or `NA_character_` if not found
+#'     \item `version` — installed version string (e.g. `"0.4.2"`), or `NA_character_` if not found or unparseable
+#'   }
+#' @keywords internal
+#' @noRd
+detect_pharos <- function() {
+  path <- unname(Sys.which("pharos"))
+  if (!nzchar(path)) {
+    return(list(path = NA_character_, version = NA_character_))
+  }
+
+  out <- tryCatch(
+    suppressWarnings(system2(path, "--version", stdout = TRUE, stderr = TRUE)),
+    error = function(e) NULL
+  )
+  if (is.null(out) || !length(out)) {
+    return(list(path = path, version = NA_character_))
+  }
+
+  match <- regmatches(out[1], regexpr("[0-9]+\\.[0-9]+\\.[0-9]+", out[1]))
+  version <- if (length(match)) match else NA_character_
+
+  list(path = path, version = version)
+}
+
 #' Generates a tidyverse-esque onAttach message for hyperion options
 #'
 #' @return a message to display on attach
@@ -456,6 +488,13 @@ hyperion_options_message <- function() {
   # Check pharos config file status
   pharos_config_status <- find_pharos_config_file()
 
+  # Detect installed pharos CLI and compare against expected version
+  pharos_cli <- detect_pharos()
+  expected_pharos <- utils::packageDescription(
+    "hyperion",
+    fields = "Config/PharosVersion"
+  )
+
   # Format .onAttach message
   msg <- "\n\n"
 
@@ -468,24 +507,55 @@ hyperion_options_message <- function() {
     "\n"
   )
 
-  # Show the hyperion.config_dir override status first since it controls
-  # where pharos.toml gets resolved from.
-  config_dir_value <- getOption("hyperion.config_dir")
-  if (!is.null(config_dir_value) && nzchar(config_dir_value)) {
+  # Pharos CLI: absent, mismatched, or matched
+  if (is.na(pharos_cli$path)) {
     msg <- paste0(
       msg,
-      cli::col_green(cli::symbol$tick),
+      cli::col_red(cli::symbol$cross),
       " ",
-      "hyperion.config_dir : ",
-      config_dir_value,
+      cli::col_red("pharos CLI not found on PATH"),
+      "\n"
+    )
+  } else if (is.na(pharos_cli$version)) {
+    msg <- paste0(
+      msg,
+      cli::col_red(cli::symbol$cross),
+      " ",
+      cli::col_red(paste0(
+        "pharos CLI found at ",
+        pharos_cli$path,
+        " but version could not be determined"
+      )),
+      "\n"
+    )
+  } else if (
+    !is.na(expected_pharos) && !identical(pharos_cli$version, expected_pharos)
+  ) {
+    msg <- paste0(
+      msg,
+      cli::col_red(cli::symbol$cross),
+      " ",
+      cli::col_red(paste0(
+        "pharos CLI version mismatch: installed ",
+        pharos_cli$version,
+        ", expected ",
+        expected_pharos,
+        " (",
+        pharos_cli$path,
+        ")"
+      )),
       "\n"
     )
   } else {
     msg <- paste0(
       msg,
-      cli::symbol$info,
+      cli::col_green(cli::symbol$tick),
       " ",
-      cli::style_dim("hyperion.config_dir : (unset)"),
+      "pharos CLI: ",
+      pharos_cli$version,
+      " (",
+      pharos_cli$path,
+      ")",
       "\n"
     )
   }
@@ -509,6 +579,24 @@ hyperion_options_message <- function() {
     )
   }
 
+  # hyperion.config_dir is shown as a sub-detail of pharos.toml resolution
+  # since it controls where pharos.toml is looked up from.
+  config_dir_value <- getOption("hyperion.config_dir")
+  if (!is.null(config_dir_value) && nzchar(config_dir_value)) {
+    msg <- paste0(
+      msg,
+      "    \u2514 hyperion.config_dir : ",
+      config_dir_value,
+      "\n"
+    )
+  } else {
+    msg <- paste0(
+      msg,
+      cli::style_dim("    \u2514 hyperion.config_dir : (unset)"),
+      "\n"
+    )
+  }
+
   # Add general options section
   if (length(set_general_options)) {
     msg <- paste0(

src/rust/Cargo.toml

@@ -38,10 +38,10 @@ serde = { workspace = true }
 extendr-api = { version = "0.9.0", features = ["serde"] }
 
 # Pharos components
-nonmem = { git = "https://github.com/a2-ai/pharos", package = "nonmem", tag = "v0.5.0" }
-nmparser = { git = "https://github.com/a2-ai/pharos", package = "nonmem-parser", tag = "v0.5.0" }
-config = { git = "https://github.com/a2-ai/pharos", package = "config", tag = "v0.5.0" }
-scheduler = { git = "https://github.com/a2-ai/pharos", package = "scheduler", tag = "v0.5.0" }
+nonmem = { git = "https://github.com/a2-ai/pharos", package = "nonmem", tag = "v0.5.1" }
+nmparser = { git = "https://github.com/a2-ai/pharos", package = "nonmem-parser", tag = "v0.5.1" }
+config = { git = "https://github.com/a2-ai/pharos", package = "config", tag = "v0.5.1" }
+scheduler = { git = "https://github.com/a2-ai/pharos", package = "scheduler", tag = "v0.5.1" }
 
 # Core utilities
 anyhow = "1.0.100"

src/rust/nonmem/src/model/copy.rs

@@ -175,7 +175,7 @@ pub fn copy_model_wrap(
                     .ok_or_extendr_err("Could not determine parent directory")?
                     .join(&model_stem);
                 let content = fs::read_to_string(&from_path).map_to_extendr_err("")?;
-                let model = Model::parse(&content)
+                let model = Model::parse(&from_path, &content)
                     .map_err(|_| extendr_err!("Failed to parse model: {}", from_path.display()))?;
                 resolve_ext_path(&model, &run_dir, &model_stem)
             }

src/rust/nonmem/src/model/mod.rs

@@ -123,17 +123,11 @@ pub fn read_model(path: &str) -> Result<Robj> {
     let mod_path = validate_model_path(path)?;
     let content = fs::read_to_string(&mod_path).map_to_extendr_err("")?;
 
-    let mut model = match Model::parse(&content) {
+    let mut model = match Model::parse(path, &content) {
         Ok(model) => model,
-        Err(diags) => {
-            let msg = diags
-                .iter()
-                .map(|d| d.render(mod_path.as_path(), &content))
-                .collect::<Vec<_>>()
-                .join("\n");
-            return Err(extendr_err!("Failed to read model file:\n{msg}"));
-        }
+        Err(e) => return Err(extendr_err!("Failed to read model file:\n{e}")),
     };
+
     let mut robj_model = model_to_robj(&mut model, &mod_path)?;
     add_run_status_attr(&mut robj_model, &mod_path)?;
 

src/rust/nonmem/src/utils.rs

@@ -193,7 +193,8 @@ fn assemble_top_level(model: Model, source: PathBuf) -> Result<ModelLocation> {
 
 fn parse_model_from_disk(path: &Path) -> Result<Model> {
     let content = fs::read_to_string(path).map_to_extendr_err("Failed to read model file")?;
-    Model::parse(&content).map_err(|_| extendr_err!("Failed to parse model: {}", path.display()))
+    Model::parse(path, &content)
+        .map_err(|_| extendr_err!("Failed to parse model: {}", path.display()))
 }
 
 /// Resolve the final `.ext` file path for a model, honoring `$EST FILE=`.
@@ -348,8 +349,8 @@ pub fn try_parse_model(path: &str) -> Option<Model> {
     let model_path = find_output_file(search_path, "mod")
         .or_else(|_| find_output_file(path, "ctl"))
         .ok()?;
-    let content = fs::read_to_string(model_path).ok()?;
-    Model::parse(&content).ok()
+    let content = fs::read_to_string(&model_path).ok()?;
+    Model::parse(model_path, &content).ok()
 }
 
 /// Gets the comment type from pharos.toml configuration