Merge pull request #3 from dynverse/devel

Devel

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dyncli
 Type: Package
 Title: CLI helper package for creating TI containers
-Version: 0.0.2
+Version: 0.0.2.9000
 Authors@R: c(
     person(
       "Robrecht", 
@@ -51,9 +51,9 @@ Imports:
   tidyr,
   yaml
 Remotes:  
-    dynverse/dynparam@master,
-    dynverse/dynutils@master,
-    dynverse/dynwrap@master
+    dynverse/dynparam@devel,
+    dynverse/dynutils@devel,
+    dynverse/dynwrap@devel
 VignetteBuilder: knitr
 Suggests: 
     knitr,

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(create_ti_method_definition)
 export(main)
 export(write_output)
 import(assertthat)

R/main.R

@@ -6,9 +6,11 @@
 #' @param args The arguments to be read by dyncli
 #' @param definition_location The location of the definition file of the method
 #'
+#'
+#'
 #' @importFrom optparse OptionParser add_option make_option parse_args
-#' @importFrom dynwrap create_ti_method_definition
 #' @importFrom yaml read_yaml
+#' @importFrom dynwrap create_ti_method_definition
 #'
 #' @export
 main <- function(
@@ -70,14 +72,23 @@ main <- function(
     # add final parameters
     add_option("--verbosity", type = "integer", default = 1, help = "The verbosity level: 0 => none, 1 => critical (default), 2 => info, 3 => debug.") %>%
     add_option("--seed", type = "integer", help = "A seed to be set to ensure reproducibility.") %>%
-    add_option("--debug", type = "logical", default = FALSE)
+    add_option("--debug", action = "store_true")
 
 
   debug("Parsing arguments\n")
 
   parsed_args <- parse_args(parser, args = args)
   debug("Arguments:\n", paste(deparse(parsed_args), collapse = "\n"), "\n")
 
+  # if debug, return command to debug
+  if (isTRUE(parsed_args$debug)) {
+    args <- args[args != "--debug"]
+    args_debug <- paste0(deparse(args, width.cutoff = 500), collapse = "\n")
+    command <- paste0("task <- dyncli::main(", args_debug, ")", collapse = "")
+    cat("Use this command inside R to load the data: \n", crayon::bold(command), "\n")
+    quit(save = "no")
+  }
+
   ##########################################
   ##              PARSE TASK              ##
   ##########################################
@@ -200,10 +211,6 @@ main <- function(
 
   info("Finished processing data\n")
 
-  if (isTRUE(task$debug)) {
-    browser()
-  }
-
   task
 }
 

R/method_create_ti_method_definition.R

@@ -1,61 +0,0 @@
-#' Create a TI method from a local method definition file
-#'
-#' The local method definition file describes a method that is runnable on the local system.
-#'
-#' @param script Location of the script that will be executed. Has to contain a #!
-#' @inheritParams dynwrap:::.method_process_definition
-#'
-#' @keywords create_ti_method
-#'
-#' @importFrom yaml read_yaml
-#'
-#' @export
-create_ti_method_definition <- function(
-  definition,
-  script,
-  return_function = TRUE
-) {
-  definition_path <- definition
-  definition <- dynwrap:::.method_load_definition(definition)
-
-  definition$run <- list(
-    backend = "script",
-    script = script,
-    definition = definition_path
-  )
-
-  dynwrap:::.method_process_definition(definition = definition, return_function = return_function)
-}
-
-
-.method_execution_execute_script <- function(method, preproc_meta) {
-  # copy over script and rds
-  file.copy(normalizePath(method$run$script), preproc_meta$dir_dynwrap)
-  script_location <- basename(method$run$script)
-  file.copy(normalizePath(method$run$definition), paste0(preproc_meta$dir_dynwrap, "/definition.yml"))
-
-  # print information if desired
-  if (preproc_meta$verbose) {
-    cat("Input saved to ", preproc_meta$dir_dynwrap, "\n", sep = "")
-  }
-
-  # run script
-  command <- paste0("./", script_location)
-  args <- c("--dataset", "input.h5", "--output", "output.h5")
-
-  if (preproc_meta$debug) {
-    stop(paste0(c(command, args), collapse = " "))
-  }
-
-  process <- processx::run(
-    command = command,
-    args = args,
-    wd = preproc_meta$dir_dynwrap,
-    echo = preproc_meta$verbose,
-    echo_cmd = as.logical(preproc_meta$verbose) || preproc_meta$debug,
-    spinner = TRUE
-  )
-
-  # return output
-  dynutils::read_h5(file.path(preproc_meta$dir_dynwrap, "output.h5"))
-}

tests/testthat/test-create_ti_method_definition.R

@@ -50,8 +50,16 @@ dyncli::write_output(trajectory, dataset$output)
 
   readr::write_file(run_r_string, "run.R")
 
+  system("chmod +x run.R")
+
   method <- create_ti_method_definition("definition.yml", "run.R")
 
+  dataset <- dynwrap::example_dataset
+
+  trajectory <- dynwrap::infer_trajectory(dataset, method())
+
+  expect_true(dynwrap::is_wrapper_with_trajectory(trajectory))
+
   file.remove("definition.yml")
   file.remove("run.R")
 })

vignettes/create_ti_method_script.Rmd

@@ -13,6 +13,7 @@ vignette: >
 
 ```{r setup}
 library(dynwrap)
+library(dyncli)
 ```
 
 An alternative to wrapping a script inside R, is to wrap it using an external script. Because this does not provide any dependency management, this is not really useful for method end-users, but rather as a way to easily develop a TI method and to ultimately step up towards [containerised wrapping](../create_ti_method_container).
@@ -142,7 +143,7 @@ method <- create_ti_method_definition(
   "run.R"
 )
 dataset <- dynwrap::example_dataset
-trajectory <- infer_trajectory(dataset, method(), verbose = TRUE)
+trajectory <- infer_trajectory(dataset, method(), verbose = TRUE, debug = TRUE)
 ```