Claude/r package fz wrapper 0137pb lvie79 ppp1 nejz nyah

.Rbuildignore

@@ -10,3 +10,5 @@
 ^\.claude$
 ^cran-comments\.md$
 ^tests/testthat/\.fz$
+^doc$
+^Meta$

.gitignore

@@ -56,3 +56,5 @@ __pycache__/
 .Python
 venv/
 env/
+/doc/
+/Meta/

DESCRIPTION

@@ -12,6 +12,7 @@ Description: Provides R bindings to the 'funz-fz' Python package using
     algorithm-driven analyses by substituting variable placeholders in text
     input files and collecting outputs into data frames. Calculators can run
     locally (shell), over SSH, or on 'SLURM' clusters.
+    See <https://github.com/Funz/fz> for the underlying framework.
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 Language: en-US

R/config.R

@@ -7,9 +7,9 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   get_interpreter()  # e.g. "python"
+#'   get_interpreter()
 #' }
 #' }
 get_interpreter <- function() {
@@ -27,10 +27,10 @@ get_interpreter <- function() {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   set_interpreter("R")      # evaluate formulas with R
-#'   set_interpreter("python") # evaluate formulas with Python (default)
+#'   set_interpreter("R")
+#'   set_interpreter("python")
 #' }
 #' }
 set_interpreter <- function(interpreter) {
@@ -46,9 +46,9 @@ set_interpreter <- function(interpreter) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   as.character(get_log_level())  # e.g. "WARNING"
+#'   as.character(get_log_level())
 #' }
 #' }
 get_log_level <- function() {
@@ -66,11 +66,11 @@ get_log_level <- function() {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   set_log_level("DEBUG")    # maximum verbosity
-#'   set_log_level("WARNING")  # default
-#'   set_log_level("ERROR")    # errors only
+#'   set_log_level("DEBUG")
+#'   set_log_level("WARNING")
+#'   set_log_level("ERROR")
 #' }
 #' }
 set_log_level <- function(level) {
@@ -88,7 +88,7 @@ set_log_level <- function(level) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   cfg <- get_config()
 #'   cfg$max_workers
@@ -108,7 +108,7 @@ get_config <- function() {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   print_config()
 #' }
@@ -127,11 +127,11 @@ print_config <- function() {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   Sys.setenv(FZ_MAX_WORKERS = "8")
 #'   reload_config()
-#'   get_config()$max_workers  # now 8
+#'   get_config()$max_workers
 #' }
 #' }
 reload_config <- function() {

R/core-functions.R

@@ -9,20 +9,15 @@
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   # Write a template with two variables and their defaults
 #'   tf <- tempfile(fileext = ".txt")
 #'   writeLines(c("pressure = ${P~1.013}", "volume = ${V~22.4}"), tf)
 #'
 #'   model <- list(varprefix = "$", delim = "{}", formulaprefix = "@",
 #'                 commentline = "#")
 #'
 #'   vars <- fzi(tf, model)
-#'   # vars$P == 1.013, vars$V == 22.4
-#'
-#'   # Using an installed model alias instead of an inline dict:
-#'   # vars <- fzi(tf, "PerfectGas")
 #' }
 #' }
 fzi <- function(input_path, model) {
@@ -46,7 +41,7 @@ fzi <- function(input_path, model) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   tf <- tempfile(fileext = ".txt")
 #'   writeLines(c("P = ${P~1.013}", "V = ${V~22.4}"), tf)
@@ -55,10 +50,7 @@ fzi <- function(input_path, model) {
 #'                 commentline = "#")
 #'   out <- tempfile()
 #'
-#'   # Single case: one compiled directory P=2,V=11.2
 #'   fzc(tf, list(P = 2.0, V = 11.2), model, out)
-#'
-#'   # Grid: 2 x 2 = 4 compiled directories
 #'   fzc(tf, list(P = c(1.0, 2.0), V = c(11.2, 22.4)), model, out)
 #' }
 #' }
@@ -81,21 +73,18 @@ fzc <- function(input_path, input_variables, model, output_dir = "output") {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   # After running a simulation that wrote "result = 42" to output.txt:
-#'   out_dir <- "my_results/P=2,V=11.2"
+#'   out_dir <- file.path(tempdir(), "P=2,V=11.2")
+#'   dir.create(out_dir, recursive = TRUE)
+#'   writeLines("result = 42", file.path(out_dir, "output.txt"))
 #'
 #'   model <- list(
 #'     varprefix = "$", delim = "{}", formulaprefix = "@", commentline = "#",
 #'     output = list(result = "grep 'result' output.txt | cut -d= -f2")
 #'   )
 #'
 #'   values <- fzo(out_dir, model)
-#'   # values$result == "42"
-#'
-#'   # Glob to read all cases at once:
-#'   # values <- fzo("my_results/*", model)
 #' }
 #' }
 fzo <- function(output_path, model) {
@@ -128,9 +117,8 @@ fzo <- function(output_path, model) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   # Template: shell script that writes sum of x and y
 #'   tf <- tempfile(fileext = ".sh")
 #'   writeLines(c(
 #'     "#!/bin/sh",
@@ -142,13 +130,8 @@ fzo <- function(output_path, model) {
 #'     output = list(result = "grep result output.txt | cut -d= -f2")
 #'   )
 #'
-#'   # Two values of x, one value of y -> 2 cases
 #'   results <- fzr(tf, list(x = c(1L, 2L), y = 3L), model,
 #'                  calculators = "sh://bash input.sh")
-#'   # results is a data frame with columns x, y, result
-#'
-#'   # Using an installed model alias:
-#'   # results <- fzr("input.txt", list(P = c(1, 2, 3)), "PerfectGas")
 #' }
 #' }
 fzr <- function(input_path, input_variables, model,
@@ -180,17 +163,13 @@ fzr <- function(input_path, input_variables, model,
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
-#'   # List everything
 #'   info <- fzl()
-#'   names(info$models)       # e.g. c("PerfectGas", "Moret")
-#'   names(info$calculators)  # e.g. c("sh://")
+#'   names(info$models)
+#'   names(info$calculators)
 #'
-#'   # Check only models whose name starts with "Perfect"
 #'   info <- fzl(models = "Perfect*")
-#'
-#'   # Probe calculators to verify they are reachable
 #'   info <- fzl(check = TRUE)
 #' }
 #' }
@@ -225,7 +204,7 @@ fzl <- function(models = "*", calculators = "*", check = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   tf <- tempfile(fileext = ".txt")
 #'   writeLines(c("x = ${x~0}", "y = ${y~0}"), tf)
@@ -235,7 +214,6 @@ fzl <- function(models = "*", calculators = "*", check = FALSE) {
 #'     output = list(z = "grep z output.txt | cut -d= -f2")
 #'   )
 #'
-#'   # Run 30 Monte Carlo samples over x in [0,1] and y in [-5,5]
 #'   result <- fzd(
 #'     tf,
 #'     list(x = "[0;1]", y = "[-5;5]"),

R/install.R

@@ -36,7 +36,7 @@ fz_install <- function(method = "auto", conda = "auto", pip = TRUE, ...) {
 #' @importFrom reticulate py_module_available
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   message("fz is available!")
 #' } else {
@@ -65,7 +65,7 @@ fz_available <- function() {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   install_model("Funz/Model-PerfectGas")
 #' }
@@ -90,7 +90,7 @@ install_model <- function(source, global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   install_algorithm("Funz/Algorithm-MonteCarlo")
 #' }
@@ -111,7 +111,7 @@ install_algorithm <- function(source, global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   uninstall_model("PerfectGas")
 #' }
@@ -132,7 +132,7 @@ uninstall_model <- function(model_name, global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   uninstall_algorithm("MonteCarlo")
 #' }
@@ -152,10 +152,10 @@ uninstall_algorithm <- function(algorithm_name, global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   models <- list_installed_models()
-#'   names(models)  # e.g. c("PerfectGas")
+#'   names(models)
 #' }
 #' }
 list_installed_models <- function(global = FALSE) {
@@ -173,7 +173,7 @@ list_installed_models <- function(global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   algos <- list_installed_algorithms()
 #'   names(algos)
@@ -193,7 +193,7 @@ list_installed_algorithms <- function(global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   names(list_models())
 #' }
@@ -212,7 +212,7 @@ list_models <- function(global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   install("Funz/Model-PerfectGas")
 #' }
@@ -232,7 +232,7 @@ install <- function(source, global = FALSE) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' if (fz_available()) {
 #'   uninstall("PerfectGas")
 #' }

README.md

@@ -139,4 +139,4 @@ Contributions are welcome. Please open a Pull Request or file an issue at
 
 ## License
 
-MIT — see [LICENSE](LICENSE).
+BSD 3-Clause — see [LICENSE](LICENSE.md).