Merge pull request #62 from cmu-delphi/ds/doc2

refactor(run.R)+doc(README): only read env vars

Author: dshemetov

README.md

@@ -10,21 +10,25 @@ The repo is also structured as an R package, which means that it is easy to shar
 # Install renv and R dependencies.
 make install
 
-# Run the pipeline wrapper run.R.
-make run
-```
-
-## Development
-
-### Sample `.Renviron` Settings
-
-```sh
+# Set your .Renviron settings.
 EPIDATR_USE_CACHE=true
 DEBUG_MODE=true
 USE_SHINY=false
 TAR_PROJECT=covid_hosp_explore
+EXTERNAL_SCORES_PATH=
+
+# Run the pipeline wrapper run.R.
+make run
 ```
 
+-   `EPIDATR_USE_CACHE` controls whether `epidatr` functions use the cache.
+-   `DEBUG_MODE` controls whether `targets::tar_make` is run with the `callr_function=NULL`, which allows for debugging.
+-   `USE_SHINY` controls whether we start a Shiny server after producing the targets.
+-   `TAR_PROJECT` controls which `targets` project is run by `run.R`.
+-   `EXTERNAL_SCORES_PATH` controls where external scores are loaded from. If not set, external scores are not used.
+
+## Development
+
 ### Directory Layout
 
 -   `run.R` and `Makefile`: the main entrypoint for all pipelines

run.R

@@ -26,65 +26,15 @@
 #   saveRDS(scorecards, "exploration-scorecards-2023-10-04.RDS")
 
 print("Reading environment variables (TAR_PROJECT, EXTERNAL_SCORES_PATH, DEBUG_MODE, USE_SHINY)...")
-tar_project <- Sys.getenv("TAR_PROJECT", "")
+tar_project <- Sys.getenv("TAR_PROJECT", "covid_hosp_explore")
 external_scores_path <- Sys.getenv("EXTERNAL_SCORES_PATH", "")
-debug_mode <- Sys.getenv("DEBUG_MODE", "")
-use_shiny <- Sys.getenv("USE_SHINY", "")
+debug_mode <- as.logical(Sys.getenv("DEBUG_MODE", TRUE))
+use_shiny <- as.logical(Sys.getenv("USE_SHINY", FALSE))
 
-readline_wrapper <- function(msg) {
-  if (interactive()) {
-    txt <- readline(msg)
-  } else {
-    cat(msg)
-    txt <- readLines("stdin", n = 1)
-  }
-  return(txt)
-}
-if (tar_project == "") {
-  project_selection <- readline_wrapper("Which project would you like to run?
-1: covid_hosp_explore
-2: flu_hosp_explore
-3: covid_hosp_prod
-4: flu_hosp_prod
-Input: ")
-  tar_project <- switch(as.character(project_selection),
-    "1" = "covid_hosp_explore",
-    "2" = "flu_hosp_explore",
-    "3" = "covid_hosp_prod",
-    "4" = "flu_hosp_prod",
-    # else
-    stop("selection `", project_selection, "` is invalid")
-  )
-} else {
-  cat("Using project: ", tar_project, "\n")
-}
-Sys.setenv(TAR_PROJECT = tar_project)
-
-
-if (external_scores_path == "") {
-  external_scores_path <- readline_wrapper("Path to RDS file containing external forecast scores, if desired:")
-} else {
-  cat("Using external scores from ", external_scores_path, "\n")
-}
-Sys.setenv(EXTERNAL_SCORES_PATH = external_scores_path)
-
-if (debug_mode == "") {
-  debug_mode <- readline_wrapper("Would you like to run debug mode? (y/[N]): ")
-} else {
-  cat("Debug mode: ", debug_mode, "\n")
-  if (as.logical(debug_mode)) {
-    debug_mode <- "y"
-  }
-}
-
-if (use_shiny == "") {
-  use_shiny <- readline_wrapper("Would you like to run the shiny app? (y/[N]): ")
-} else {
-  cat("Use shiny: ", use_shiny, "\n")
-  if (as.logical(use_shiny)) {
-    use_shiny <- "y"
-  }
-}
+cat("Using project: ", tar_project, "\n")
+if (external_scores_path != "") cat("Using external scores from ", external_scores_path, "\n")
+if (debug_mode) cat("Debug mode is on.")
+if (use_shiny) cat("Running shiny server after results.")
 
 
 suppressPackageStartupMessages({
@@ -97,15 +47,15 @@ store_dir <- tar_path_store()
 if (!dir.exists(store_dir)) dir.create(store_dir)
 
 tar_manifest()
-if (debug_mode == "y") {
+if (debug_mode) {
   tar_make(callr_function = NULL)
 } else {
   tar_make()
 }
 # tar_make_clustermq(workers = 2) # nolint
 # tar_make_future(workers = 2) # nolint
 
-if (use_shiny == "y") {
+if (use_shiny) {
   # Prevent functions defined in /R dir from being loaded unnecessarily
   options(shiny.autoload.r = FALSE)