From 0b7abee146b8d35aaffcf242d02d05b83337a8b5 Mon Sep 17 00:00:00 2001
From: Noam Ross <ross@ecohealthalliance.org>
Date: Fri, 11 Aug 2023 12:19:29 -0400
Subject: [PATCH] project workflow improvements

 - Use capsule for easier renv management
 - Create a separate sandbox targets project
 - Load multiple .env files
    - Use .env_user for setting USE_CAPSULE and TAR_PROJECT)
 - .gitignore stuff appropriately to retain outputs and keep meta files
 - Add all_targets() convenience function
---
 .Rprofile          | 23 +++++++++++++++--------
 .gitignore         | 12 +++++++-----
 R/utils.R          | 29 +++++++++++++++++++++++++++++
 _targets.R         | 18 +++++++-----------
 _targets_sandbox.R | 13 +++++++++++++
 targets.yaml       |  6 ++++++
 6 files changed, 77 insertions(+), 24 deletions(-)
 create mode 100644 R/utils.R
 create mode 100644 _targets_sandbox.R
 create mode 100644 targets.yaml

diff --git a/.Rprofile b/.Rprofile
index 68d6a25..f13c8ce 100644
--- a/.Rprofile
+++ b/.Rprofile
@@ -1,17 +1,24 @@
-if (file.exists(".env")) {
-  try(readRenviron(".env"))
-} else {
-  message("No .env file")
+for (env_file in list.files(all.files = TRUE, pattern = "^\\.env.*")) {
+  try(readRenviron(env_file), silent = TRUE)
 }
 
+
 # Put the project library *outside* the project
 #Sys.setenv(RENV_PATHS_LIBRARY_ROOT = file.path(normalizePath("~/.renv-project-libraries", mustWork = FALSE)))
 
-if (file.exists("renv/activate.R")) {
-  source("renv/activate.R")
+if(Sys.getenv("USE_CAPSULE") %in% c("1", "TRUE", "true")) {
+  if (interactive() && file.exists("renv.lock")) {
+    message("renv library not loaded (found env var USE_CAPSULE=", Sys.getenv("USE_CAPSULE"), "). Use `capsule` functions (see https://github.com/MilesMcBain/capsule)")
+    if(require(capsule, quietly = TRUE)) {
+    capsule::whinge()
+    } else {
+      message('Install {capsule} with install.packages("capsule", repos = c(mm = "https://milesmcbain.r-universe.dev", getOption("repos")))')
+    }
+  }
 } else {
-  message("No renv/activate.R")
-} 
+  source("renv/activate.R")
+}
+
 
 # Use the local user's .Rprofile when interactive.
 # Good for keeping local preferences, but not always reproducible.
diff --git a/.gitignore b/.gitignore
index 34d29e5..59a636f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,12 +3,14 @@
 .RData
 .Ruserdata
 .DS_Store
-_targets/objects
-_targets.yaml
+.env_user
+_targets/
+_targets/*
+!_targets/meta/meta
+_targets_sandbox/
+_targets_sandbox/*
+!_targets_sandbox/meta/meta
 nohup.out
-outputs/
-!outputs/.gitkeep
-!outputs/example_report.html
 data/archive
 data/**/*.csv.gz
 data/**/*.grib
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 0000000..929c908
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,29 @@
+#' Collect all targets and lists of targets in the environment
+all_targets <- function(env = parent.env(environment()), type = "tar_target") {
+  rfn <- function(obj) inherits(obj, type) || (is.list(obj) && all(vapply(obj, rfn, logical(1))))
+  objs <- ls(env)
+  out <- list()
+  for(o in objs) {
+    obj <- get(o, envir = env)
+    if (rfn(obj)) {
+      out[[length(out) + 1]] <- obj
+    }
+  }
+  return(out)
+}
+
+# TODO: convenience functions for reading targets from S3
+# Need to figure out the best way for these to work with both regular and 
+# file-type targets, which should emerge from working with them in the sandbox
+# tar_read_s3 <- function(target_name, bucket = Sys.getenv("AWS_BUCKET_ID"),
+#                         prefix = "_targets") {
+#   ## if target_name does not exist, convert the symbol to character
+#   if (!exists(target_name)) {
+#     target_name <- as.character(substitute(target_name))
+#   }
+#     
+# }
+#   
+# tar_load_s3 <- function(target_name, ...) {
+#   
+# }
\ No newline at end of file
diff --git a/_targets.R b/_targets.R
index 2df25bb..1aca922 100644
--- a/_targets.R
+++ b/_targets.R
@@ -1,3 +1,9 @@
+# Re-record current dependencies for CAPSULE users
+if(Sys.getenv("USE_CAPSULE") %in% c("1", "TRUE", "true"))
+  capsule::capshot(c("packages.R",
+                     list.files(pattern = "_targets.*\\.(r|R)$", full.names = TRUE),
+                     list.files("R", pattern = "\\.(R|r)$", full.names = TRUE)))
+
 # Load packages (in packages.R) and load project-specific functions in R folder
 suppressPackageStartupMessages(source("packages.R"))
 for (f in list.files(here::here("R"), full.names = TRUE)) source (f)
@@ -234,14 +240,4 @@ test_targets <- tar_plan(
 )
 
 # List targets -----------------------------------------------------------------
-
-list(
-  static_targets,
-  dynamic_targets,
-  data_targets,
-  model_targets,
-  deploy_targets,
-  plot_targets,
-  report_targets,
-  test_targets
-)
+all_targets()
diff --git a/_targets_sandbox.R b/_targets_sandbox.R
new file mode 100644
index 0000000..febcc7b
--- /dev/null
+++ b/_targets_sandbox.R
@@ -0,0 +1,13 @@
+# Re-record current dependencies for CAPSULE users
+if(Sys.getenv("USE_CAPSULE") %in% c("1", "TRUE", "true"))
+  capsule::capshot(c("packages.R",
+                     list.files(pattern = "_targets.*\\.(r|R)$", full.names = TRUE),
+                     list.files("R", pattern = "\\.(R|r)$", full.names = TRUE)))
+
+# Load packages (in packages.R) and load project-specific functions in R folder
+suppressPackageStartupMessages(source("packages.R"))
+for (f in list.files(here::here("R"), full.names = TRUE)) source (f)
+
+
+
+all_targets()
\ No newline at end of file
diff --git a/targets.yaml b/targets.yaml
new file mode 100644
index 0000000..7d47d67
--- /dev/null
+++ b/targets.yaml
@@ -0,0 +1,6 @@
+main:
+  store: _targets
+  script: _targets.R
+sandbox:
+  store: _targets_sandbox
+  script: _targets_sandbox.R