Merge branch 'develop'

.Rprofile

@@ -114,4 +114,10 @@ if (interactive()) {
     store = file.path(.get_prj_shared_path(), "_targets"),
     config = "reports/_targets.yaml"
   )
+
+  .run <- function() {
+    source(here::here("dev/run.R")) # check and make pipeline.
+  }
+  ui_info("Exexute {ui_code('.run()')} to make the pipeline.")
+
 }

01-FIRST_RUN.R

@@ -6,6 +6,13 @@
 ## run the following code (after having renamed your project's folder
 ## at your convenience)
 {
+  if (!requireNamespace("renv", quietly = TRUE)) {
+    stop(
+      "Before to run this all, please `install.packages('renv')`."
+    )
+  }
+  renv::restore(prompt = FALSE)
+  rstudioapi::restartSession()
   prj_name <- basename(here::here())
   fs::file_move(
     here::here("laims.analysis.Rproj"),  # old project's name
@@ -45,10 +52,11 @@ usethis::edit_r_environ("project")
 
 ## [Optional] Finaly, update all your packages in the project's library.
 renv::upgrade()
+rstudioapi::restartSession()
 renv::update()
 renv::status()
 renv::snapshot()
-
+rstudioapi::restartSession()
 
 ## At your convenience, replace your readme file
 usethis::use_readme_rmd()

R/utils.R

@@ -1,6 +1,6 @@
 
 # Here below put your small tiny supporting functions -------------
-
+`%||%` <- function(x, y) if (is.null(x)) y else x
 
 view_in_excel <- function(.data) {
   if (interactive()) {
@@ -22,7 +22,7 @@ extract_fct_names <- function(path) {
 
 
 
-get_input_data_path <- function(x) {
+get_input_data_path <- function(x = "") {
   file.path(
     Sys.getenv("PRJ_SHARED_PATH"),
     Sys.getenv("INPUT_DATA_FOLDER"),
@@ -31,7 +31,7 @@ get_input_data_path <- function(x) {
     normalizePath()
 }
 
-get_output_data_path <- function(x) {
+get_output_data_path <- function(x = "") {
   file.path(
     Sys.getenv("PRJ_SHARED_PATH"),
     Sys.getenv("OUTPUT_DATA_FOLDER"),
@@ -42,13 +42,31 @@ get_output_data_path <- function(x) {
 
 
 share_objects <- function(obj_list) {
-  file_name <- paste0(names(obj_list), ".rds")
+  now <- lubridate::now() |>
+    stringr::str_remove_all("\\W+") |>
+    stringr::str_sub(1, 12)
+
+  file_name_now <- stringr::str_c(
+    names(obj_list), "-", now, ".rds"
+  )
 
-  obj_paths <- file.path(get_output_data_path(file_name)) |>
+  file_name_latest <- stringr::str_c(
+    names(obj_list), "-", "latest", ".rds"
+  )
+
+  obj_paths_now <- get_output_data_path(file_name_now) |>
+    normalizePath(mustWork = FALSE) |>
+    purrr::set_names(names(obj_list))
+
+  obj_paths_latest <- get_output_data_path(file_name_latest) |>
     normalizePath(mustWork = FALSE) |>
     purrr::set_names(names(obj_list))
 
   # Those must be RDS
-  purrr::walk2(obj_list, obj_paths, readr::write_rds)
-  obj_paths
+  obj_list |>
+    purrr::walk2(obj_paths_now, readr::write_rds)
+  obj_list |>
+    purrr::walk2(obj_paths_latest, readr::write_rds)
+
+  obj_paths_latest
 }

_targets.R

@@ -1,41 +1,48 @@
 library(targets)
 library(tarchetypes)
-# This is an example _targets.R file. Every
-# {targets} pipeline needs one.
-# Use tar_script() to create _targets.R and tar_edit()
-# to open it again for editing.
-# Then, run tar_make() to run the pipeline
-# and tar_read(result) to view the results.
+library(crew)  # parallel computing
+controller <- crew::crew_controller_local(
+  name = "anvur_controller",
+  workers = 1
+)
+
+# Set target-specific options such as packages.
+tar_option_set(
+  # error handling
+  error = "continue", # "null" create target with non-errored branches
+  workspace_on_error = TRUE,
+  # fast data formats
+  format = "qs",
+  # parallel computing
+  storage = "worker",
+  retrieval = "worker",
+  controller = controller
+)
 
 # Define custom functions and other global objects.
 # This is where you write source(\"R/functions.R\")
 # if you keep your functions in external scripts.
 list.files(here::here("R"), pattern = "\\.R$", full.names = TRUE) |>
   lapply(source) |> invisible()
 
-# Set target-specific options such as packages.
-tar_option_set(
-  error = "continue",
-  workspace_on_error = TRUE
-)
 
 # End this file with a list of target objects.
 list(
 
   # Import your file from custom (shared) location, and preprocess them
-  tar_target(
+  tar_files_input(
     db_raw_path,
-    file.path(get_input_data_path("db_raw.csv")),
-    format = "file"
+    # get_input_data_path("db_raw.csv"), # single
+    get_input_data_path() |>
+      list.files(pattern = "\\.csv$", full.names = TRUE) # multiple
   ),
 
-  # Use {qs} in {targets} to save space and time in save/load objects
-  tar_target(db_raw, import_data(db_raw_path), format = "qs"),
-  tar_target(db, preprocess(db_raw), format = "qs"),
+  tar_target(db_raw, import_data(db_raw_path)),
+  tar_target(db, preprocess(db_raw)),
 
 
   # Call your custom functions as needed.
-  tar_target(relevantResult, relevant_computation(db), format = "qs"),
+  tar_target(relevantResult, relevant_computation(db)),
 
   # compile yor report
   tar_render(report, here::here("reports/report.Rmd")),

dev/00-template_setup.R

@@ -4,10 +4,10 @@ stop("00-setup.R is not intended to be re-run/sourced.", call. = FALSE)
 # Development packages ---------------------------------------------
 
 dev_pkgs <- c(
-  "checkmate", "covr", "devtools", "distill", "fs", "here", "htmltools",
-  "knitr", "lintr", "purrr", "qs", "rstudioapi", "spelling",
-  "stringr", "targets", "tarchetypes", "testthat", "usethis",
-  "withr"
+  "checkmate", "covr", "crew", "devtools", "distill", "fs", "here",
+  "htmltools", "knitr", "lintr", "purrr", "qs", "rstudioapi",
+  "spelling", "stringr", "targets", "tarchetypes", "testthat",
+  "usethis", "withr"
 )
 renv::install(dev_pkgs)
 

dev/run.R

@@ -1,36 +1,27 @@
 # To view your current pipeline status, and possibly run/update it,
 # you can simply source/execute this script (maybe using the
 # `dev/03-run_cycle.R` script)
-{
-  function(proceed = TRUE, save_all = TRUE) {
-    if (interactive()) {
-      if (
-        requireNamespace("rstudioapi") &&
-        rstudioapi::isAvailable() &&
-        save_all
-      ) {
-        rstudioapi::documentSaveAll()
-      }
-
-      targets::tar_visnetwork() |>
-        print()
+(\() if (interactive()) {
+  if (
+    requireNamespace("rstudioapi") &&
+    rstudioapi::isAvailable()
+  ) {
+    usethis::ui_done("All scripts saved.")
+    rstudioapi::documentSaveAll()
+  }
 
-      proceed <- usethis::ui_yeah(paste0(
-        "Do you want to make your pipeline? ",
-        "({usethis::ui_code('tar_make')})"
-      ))
-    }
+  usethis::ui_todo("Check your pipeline.")
+  targets::tar_visnetwork() |>
+    print()
 
-    if (proceed) {
-      withr::with_envvar(
-        list(RSTUDIO_VERSION = "2021.09.0"), {
-          # devtools::test(stop_on_failure = TRUE)
-          targets::tar_make()
-        }
-      )
-      targets::tar_visnetwork(targets_only = TRUE) |>
-        print()
-    }
+  usethis::ui_todo("Make your pipeline.")
+  if (usethis::ui_yeah("Do you want to make your pipeline?")) {
+    targets::tar_make()
+    usethis::ui_todo("Review the updated status.")
+    targets::tar_visnetwork(targets_only = TRUE, outdated = FALSE) |>
+      print()
   }
-}()
+})()
+
+