From 83bff2401975057d8ec05d1f263b01f3c88668fe Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Thu, 11 Sep 2025 10:38:38 -0400
Subject: [PATCH 01/19] feat: config environment

---
 R/config.R | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 R/config.R

diff --git a/R/config.R b/R/config.R
new file mode 100644
index 0000000..1654194
--- /dev/null
+++ b/R/config.R
@@ -0,0 +1 @@
+config <- new.env()
\ No newline at end of file

From 54717b3020687156278815f56a5cc1809e6a2cd3 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Thu, 11 Sep 2025 10:39:21 -0400
Subject: [PATCH 02/19] feat: config-dependent variables moved to config env

---
 R/globals.R | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/R/globals.R b/R/globals.R
index d911a16..0ac84da 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -1,18 +1,17 @@
 # Define extent of exported data (ai_app_extent)
-ai_app_crs <- sf::st_crs("EPSG:3857")
+config$ai_app_crs <- sf::st_crs("EPSG:3857")
 
 # Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
-ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
+config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
                    1118889.97485796, 15538711.0963092)
 
 # Configure S3 bucket, its url and the path within it used for flow output
-s3_bucket_name <- "avianinfluenza"
-s3_flow_path <- "flow/"
-s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
-
+config$s3_bucket_name <- "avianinfluenza"
+config$s3_flow_path <- "flow/"
+config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
 
 # Define local cache for temporary output images
 # Will then be copied to AWS
-local_cache <- tempdir()
+config$local_cache <- tempdir()
 if(!file.exists(local_cache))
    dir.create(local_cache)

From d7aa22a6b13153dcb70c610a1ee317580fbe6194 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Thu, 11 Sep 2025 10:40:01 -0400
Subject: [PATCH 03/19] feat: move state variables created by set_s3_config and
 retrieved by get_s3_config to config environment

---
 R/flow.R | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index 2b81f7b..fddd4ac 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -2,26 +2,27 @@
 #'
 #' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.
 set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
-  assign(".s3_config", list(
+  config$option <- list(
     access_key = access_key,
     secret_key = secret_key,
     region = region,
     bucket = bucket
-  ), envir = .GlobalEnv)
+  )
 }
 
 #' Get S3 configuration from explicit config, environment variables, or IAM role
 get_s3_config <- function() {
-  config <- if (exists(".s3_config", envir = .GlobalEnv)) get(".s3_config", envir = .GlobalEnv) else list()
-  access_key <- config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
-  secret_key <- config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
-  region     <- config$region     %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
-  bucket     <- config$bucket     %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
+  config_option_list <- config$option %||% list()
+  access_key <- config_option_list$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
+  secret_key <- config_option_list$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
+  region <- config_option_list$region %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
+  bucket <- config_option_list$bucket %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
   list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)
 }
 
 #' Null coalescing operator for config values
 `%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
+
 #' @import BirdFlowR
 
 if(FALSE) {

From 0ab83e746073d50ad113751455a1b736da2c0d6d Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:07:07 -0400
Subject: [PATCH 04/19] fix: delete old config file

---
 R/config.R | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 R/config.R

diff --git a/R/config.R b/R/config.R
deleted file mode 100644
index 1654194..0000000
--- a/R/config.R
+++ /dev/null
@@ -1 +0,0 @@
-config <- new.env()
\ No newline at end of file

From 23a95c33ded07596d48dfcc635e87968b45f6b4f Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:08:31 -0400
Subject: [PATCH 05/19] feat: new s3_config file with s3_config environment
 definition and get, set, helper functions

---
 R/flow.R      | 25 -------------------------
 R/s3_config.R | 26 ++++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 25 deletions(-)
 create mode 100644 R/s3_config.R

diff --git a/R/flow.R b/R/flow.R
index cde7be1..3231c02 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -1,28 +1,3 @@
-#' Set S3 configuration explicitly
-#'
-#' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.
-set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
-  config$option <- list(
-    access_key = access_key,
-    secret_key = secret_key,
-    region = region,
-    bucket = bucket
-  )
-}
-
-#' Get S3 configuration from explicit config, environment variables, or IAM role
-get_s3_config <- function() {
-  config_option_list <- config$option %||% list()
-  access_key <- config_option_list$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
-  secret_key <- config_option_list$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
-  region <- config_option_list$region %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
-  bucket <- config_option_list$bucket %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
-  list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)
-}
-
-#' Null coalescing operator for config values
-`%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
-
 if(FALSE) {
    # Manually set function arguments for dev and debugging
    # Running code here allows running function body code outside of the
diff --git a/R/s3_config.R b/R/s3_config.R
new file mode 100644
index 0000000..9aa32ee
--- /dev/null
+++ b/R/s3_config.R
@@ -0,0 +1,26 @@
+s3_config <- new.env()
+
+#' Set S3 configuration explicitly
+#'
+#' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.
+set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
+  assign(".s3_config", list(
+    access_key = access_key,
+    secret_key = secret_key,
+    region = region,
+    bucket = bucket
+  ), envir = .GlobalEnv)
+}
+
+#' Get S3 configuration from explicit config, environment variables, or IAM role
+get_s3_config <- function() {
+  config <- if (exists(".s3_config", envir = .GlobalEnv)) get(".s3_config", envir = .GlobalEnv) else list()
+  access_key <- config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
+  secret_key <- config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
+  region     <- config$region     %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
+  bucket     <- config$bucket     %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
+  list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)
+}
+
+#' Null coalescing operator for config values
+`%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
\ No newline at end of file

From 0c076f57a1eeabd0dda6a2d485a64c04414ece60 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:10:26 -0400
Subject: [PATCH 06/19] fix: rename config$<var> to s3_config$<var>

---
 R/globals.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/globals.R b/R/globals.R
index 0ac84da..8dbaf94 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -1,17 +1,17 @@
 # Define extent of exported data (ai_app_extent)
-config$ai_app_crs <- sf::st_crs("EPSG:3857")
+s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
 
 # Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
-config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
+s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
                    1118889.97485796, 15538711.0963092)
 
-# Configure S3 bucket, its url and the path within it used for flow output
-config$s3_bucket_name <- "avianinfluenza"
-config$s3_flow_path <- "flow/"
-config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
+# s3_configure S3 bucket, its url and the path within it used for flow output
+s3_config$s3_bucket_name <- "avianinfluenza"
+s3_config$s3_flow_path <- "flow/"
+s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
 
 # Define local cache for temporary output images
 # Will then be copied to AWS
-config$local_cache <- tempdir()
+s3_config$local_cache <- tempdir()
 if(!file.exists(local_cache))
-   dir.create(local_cache)
+   dir.create(s3_config$local_cache)

From af15577fa9230047d18efe6d2bbfc87eca0d4748 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:14:01 -0400
Subject: [PATCH 07/19] feat: s3_config env in get and set config functions

---
 R/s3_config.R | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/R/s3_config.R b/R/s3_config.R
index 9aa32ee..9386d5d 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -4,23 +4,20 @@ s3_config <- new.env()
 #'
 #' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.
 set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
-  assign(".s3_config", list(
-    access_key = access_key,
-    secret_key = secret_key,
-    region = region,
-    bucket = bucket
-  ), envir = .GlobalEnv)
+  s3_config$access_key <- access_key
+  s3_config$secret_key <- secret_key
+  s3_config$region <- region
+  s3_config$bucket <- bucket
 }
 
 #' Get S3 configuration from explicit config, environment variables, or IAM role
 get_s3_config <- function() {
-  config <- if (exists(".s3_config", envir = .GlobalEnv)) get(".s3_config", envir = .GlobalEnv) else list()
-  access_key <- config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
-  secret_key <- config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
-  region     <- config$region     %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
-  bucket     <- config$bucket     %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
+  access_key <- s3_config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
+  secret_key <- s3_config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
+  region <- s3_config$region %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
+  bucket <- s3_config$bucket %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
   list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)
 }
 
 #' Null coalescing operator for config values
-`%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
\ No newline at end of file
+`%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b

From 56a00481746b168b06efbe91885109e5d5e182f8 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:16:01 -0400
Subject: [PATCH 08/19] feat: move global config vars to s3_config.R

---
 R/globals.R   | 17 -----------------
 R/s3_config.R | 17 +++++++++++++++++
 2 files changed, 17 insertions(+), 17 deletions(-)
 delete mode 100644 R/globals.R

diff --git a/R/globals.R b/R/globals.R
deleted file mode 100644
index 8dbaf94..0000000
--- a/R/globals.R
+++ /dev/null
@@ -1,17 +0,0 @@
-# Define extent of exported data (ai_app_extent)
-s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
-
-# Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
-s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
-                   1118889.97485796, 15538711.0963092)
-
-# s3_configure S3 bucket, its url and the path within it used for flow output
-s3_config$s3_bucket_name <- "avianinfluenza"
-s3_config$s3_flow_path <- "flow/"
-s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
-
-# Define local cache for temporary output images
-# Will then be copied to AWS
-s3_config$local_cache <- tempdir()
-if(!file.exists(local_cache))
-   dir.create(s3_config$local_cache)
diff --git a/R/s3_config.R b/R/s3_config.R
index 9386d5d..6496bb5 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -1,5 +1,22 @@
 s3_config <- new.env()
 
+# Define extent of exported data (ai_app_extent)
+s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
+
+# Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
+s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
+                   1118889.97485796, 15538711.0963092)
+
+# s3_configure S3 bucket, its url and the path within it used for flow output
+s3_config$s3_bucket_name <- "avianinfluenza"
+s3_config$s3_flow_path <- "flow/"
+s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
+
+# Define local cache for temporary output images, will then be copied to AWS
+s3_config$local_cache <- tempdir()
+if(!file.exists(s3_config$local_cache))
+   dir.create(s3_config$local_cache)
+
 #' Set S3 configuration explicitly
 #'
 #' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.

From 0aa02fa6178be34484a8a577f49cb0abc35153e2 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:16:55 -0400
Subject: [PATCH 09/19] chore: remove helper comments and documentation

---
 R/s3_config.R              |  8 +-------
 man/get_s3_config.Rd       | 11 -----------
 man/grapes-or-or-grapes.Rd | 11 -----------
 man/set_s3_config.Rd       | 16 ----------------
 4 files changed, 1 insertion(+), 45 deletions(-)
 delete mode 100644 man/get_s3_config.Rd
 delete mode 100644 man/grapes-or-or-grapes.Rd
 delete mode 100644 man/set_s3_config.Rd

diff --git a/R/s3_config.R b/R/s3_config.R
index 6496bb5..4a14a03 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -4,8 +4,7 @@ s3_config <- new.env()
 s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
 
 # Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
-s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368,
-                   1118889.97485796, 15538711.0963092)
+s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
 
 # s3_configure S3 bucket, its url and the path within it used for flow output
 s3_config$s3_bucket_name <- "avianinfluenza"
@@ -17,9 +16,6 @@ s3_config$local_cache <- tempdir()
 if(!file.exists(s3_config$local_cache))
    dir.create(s3_config$local_cache)
 
-#' Set S3 configuration explicitly
-#'
-#' Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.
 set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
   s3_config$access_key <- access_key
   s3_config$secret_key <- secret_key
@@ -27,7 +23,6 @@ set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, b
   s3_config$bucket <- bucket
 }
 
-#' Get S3 configuration from explicit config, environment variables, or IAM role
 get_s3_config <- function() {
   access_key <- s3_config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
   secret_key <- s3_config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
@@ -36,5 +31,4 @@ get_s3_config <- function() {
   list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)
 }
 
-#' Null coalescing operator for config values
 `%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
diff --git a/man/get_s3_config.Rd b/man/get_s3_config.Rd
deleted file mode 100644
index 71b2e21..0000000
--- a/man/get_s3_config.Rd
+++ /dev/null
@@ -1,11 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/flow.R
-\name{get_s3_config}
-\alias{get_s3_config}
-\title{Get S3 configuration from explicit config, environment variables, or IAM role}
-\usage{
-get_s3_config()
-}
-\description{
-Get S3 configuration from explicit config, environment variables, or IAM role
-}
diff --git a/man/grapes-or-or-grapes.Rd b/man/grapes-or-or-grapes.Rd
deleted file mode 100644
index 6c41ad5..0000000
--- a/man/grapes-or-or-grapes.Rd
+++ /dev/null
@@ -1,11 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/flow.R
-\name{\%||\%}
-\alias{\%||\%}
-\title{Null coalescing operator for config values}
-\usage{
-a \%||\% b
-}
-\description{
-Null coalescing operator for config values
-}
diff --git a/man/set_s3_config.Rd b/man/set_s3_config.Rd
deleted file mode 100644
index c97a5e1..0000000
--- a/man/set_s3_config.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/flow.R
-\name{set_s3_config}
-\alias{set_s3_config}
-\title{Set S3 configuration explicitly}
-\usage{
-set_s3_config(
-  access_key = NULL,
-  secret_key = NULL,
-  region = NULL,
-  bucket = NULL
-)
-}
-\description{
-Allows user to set S3 credentials and bucket at runtime. If not set, environment variables or IAM role will be used.
-}

From 07338a98c8c3e4f3ecde886ddc76a692fa2b77c2 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 19 Sep 2025 16:29:06 -0400
Subject: [PATCH 10/19] feat: s3_config$ prefix for flow variables

---
 R/flow.R | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index 3231c02..35ac373 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -132,11 +132,11 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
   pred_weeks <- BirdFlowR::lookup_timestep_sequence(bf, start = week, n = n, direction = direction)
   png_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".png")
   symbology_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".json")
-  png_bucket_paths <- paste0(s3_flow_path, cache_prefix, png_files)
-  symbology_bucket_paths <- paste0(s3_flow_path, cache_prefix, symbology_files)
-  png_urls <- paste0(s3_flow_url, cache_prefix, png_files)
-  symbology_urls <- paste0(s3_flow_url, cache_prefix, symbology_files)
-  tiff_bucket_path <- paste0(s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")
+  png_bucket_paths <- paste0(s3_config$s3_flow_path, cache_prefix, png_files)
+  symbology_bucket_paths <- paste0(s3_config$s3_flow_path, cache_prefix, symbology_files)
+  png_urls <- paste0(s3_config$s3_flow_url, cache_prefix, png_files)
+  symbology_urls <- paste0(s3_config$s3_flow_url, cache_prefix, symbology_files)
+  tiff_bucket_path <- paste0(s3_config$s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")
 
   # --- CACHE CHECK BLOCK ---
   cache_hit <- TRUE
@@ -179,7 +179,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
         start = list(week = week, taxa = taxa, loc = loc),
         status = "cached",
         result = result,
-        geotiff = if (save_local) tiff_local_path else paste0(s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
+        geotiff = if (save_local) tiff_local_path else paste0(s3_config$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
       )
     )
   }
@@ -240,25 +240,25 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
 
   log_progress("Projecting and cropping raster for web output.")
   log_progress(paste0("combined class: ", class(combined)))
-  log_progress(paste0("ai_app_crs$input: ", ai_app_crs$input))
-  log_progress(paste0("ai_app_extent: ", ai_app_extent))
+  log_progress(paste0("s3_config$ai_app_crs$input: ", s3_config$ai_app_crs$input))
+  log_progress(paste0("s3_config$ai_app_extent: ", s3_config$ai_app_extent))
   if (is.null(combined) || !inherits(combined, "SpatRaster")) {
     log_progress("ERROR: combined raster is NULL or not a SpatRaster. Aborting.")
     return(format_error("combined raster is NULL or not a SpatRaster"))
   }
-  if (is.null(ai_app_crs$input)) {
-    log_progress("ERROR: ai_app_crs$input is NULL. Aborting.")
-    return(format_error("ai_app_crs$input is NULL"))
+  if (is.null(s3_config$ai_app_crs$input)) {
+    log_progress("ERROR: s3_config$ai_app_crs$input is NULL. Aborting.")
+    return(format_error("s3_config$ai_app_crs$input is NULL"))
   }
-  if (is.null(ai_app_extent)) {
-    log_progress("ERROR: ai_app_extent is NULL. Aborting.")
-    return(format_error("ai_app_extent is NULL"))
+  if (is.null(s3_config$ai_app_extent)) {
+    log_progress("ERROR: s3_config$ai_app_extent is NULL. Aborting.")
+    return(format_error("s3_config$ai_app_extent is NULL"))
   }
 
   log_progress("Projecting")
-  web_raster <- combined |> terra::project(ai_app_crs$input)
+  web_raster <- combined |> terra::project(s3_config$ai_app_crs$input)
   log_progress("Cropping")
-  web_raster <- terra::crop(web_raster, ai_app_extent)
+  web_raster <- terra::crop(web_raster, s3_config$ai_app_extent)
   log_progress("Done cropping")
   png_paths <- file.path(out_path, png_files)
   symbology_paths <- file.path(out_path, symbology_files)
@@ -346,7 +346,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
       start = list(week = week, taxa = taxa, loc = loc),
       status = "success",
       result = result,
-      geotiff = if (save_local) tiff_path else paste0(s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
+      geotiff = if (save_local) tiff_path else paste0(s3_config$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
     )
   )
 }

From 6aec47a8105888eda5df25365289619d4caa95b6 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 16:28:11 -0400
Subject: [PATCH 11/19] feat: move all s3_config params to set_s3_config

---
 R/s3_config.R | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/R/s3_config.R b/R/s3_config.R
index 4a14a03..6886a59 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -1,26 +1,34 @@
 s3_config <- new.env()
 
 # Define extent of exported data (ai_app_extent)
-s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
+# s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
 
 # Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
-s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
+# s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
 
 # s3_configure S3 bucket, its url and the path within it used for flow output
-s3_config$s3_bucket_name <- "avianinfluenza"
-s3_config$s3_flow_path <- "flow/"
-s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
+# s3_config$s3_bucket_name <- "avianinfluenza"
+# s3_config$s3_flow_path <- "flow/"
+# s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
 
 # Define local cache for temporary output images, will then be copied to AWS
-s3_config$local_cache <- tempdir()
-if(!file.exists(s3_config$local_cache))
-   dir.create(s3_config$local_cache)
+# s3_config$local_cache <- tempdir()
+# if(!file.exists(s3_config$local_cache))
+#    dir.create(s3_config$local_cache)
 
 set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
   s3_config$access_key <- access_key
   s3_config$secret_key <- secret_key
   s3_config$region <- region
   s3_config$bucket <- bucket
+  s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
+  s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
+  s3_config$s3_bucket_name <- "avianinfluenza"
+  s3_config$s3_flow_path <- "flow/"
+  s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
+  s3_config$local_cache <- tempdir()
+  if(!file.exists(s3_config$local_cache))
+    dir.create(s3_config$local_cache)
 }
 
 get_s3_config <- function() {

From dfde6cbbb0d7f6a853d10ab10edef5e8e5ee7dfb Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 16:29:12 -0400
Subject: [PATCH 12/19] style: potential TODO item

---
 R/s3_config.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/s3_config.R b/R/s3_config.R
index 6886a59..001452e 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -31,6 +31,7 @@ set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, b
     dir.create(s3_config$local_cache)
 }
 
+# TODO: add all s3_config params here?
 get_s3_config <- function() {
   access_key <- s3_config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
   secret_key <- s3_config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)

From 27ec4458edcdd4dd50ed1a6d42030454c75fe211 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 16:33:34 -0400
Subject: [PATCH 13/19] feat: set s3_config before tests

---
 tests/testthat/setup.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index d6b67ae..f4be360 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -1 +1,2 @@
-load_models()
\ No newline at end of file
+load_models()
+set_s3_config()

From a674d2b0f500c5e7f682a0ddf5c75ef739124d5c Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 16:42:11 -0400
Subject: [PATCH 14/19] feat: log flag to turn logging on/off

---
 R/flow.R      | 4 +++-
 R/s3_config.R | 5 ++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index 35ac373..42045fe 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -85,7 +85,9 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
   }
 
   log_progress <- function(msg) {
-    cat(sprintf("[%s] %s\n", Sys.time(), msg), file = "./flow_debug.log", append = TRUE)
+    if(s3_config$log) {
+      cat(sprintf("[%s] %s\n", Sys.time(), msg), file = "./flow_debug.log", append = TRUE)
+    }
   }
 
   log_progress(paste0("Starting flow function with arguments: loc=", loc, ", week=", week, ", taxa=", taxa, ", n=", n, ", direction=", direction, ", save_local=", save_local))
diff --git a/R/s3_config.R b/R/s3_config.R
index 001452e..184dbb6 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -16,11 +16,12 @@ s3_config <- new.env()
 # if(!file.exists(s3_config$local_cache))
 #    dir.create(s3_config$local_cache)
 
-set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL) {
+set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE) {
   s3_config$access_key <- access_key
   s3_config$secret_key <- secret_key
   s3_config$region <- region
   s3_config$bucket <- bucket
+
   s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
   s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
   s3_config$s3_bucket_name <- "avianinfluenza"
@@ -29,6 +30,8 @@ set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, b
   s3_config$local_cache <- tempdir()
   if(!file.exists(s3_config$local_cache))
     dir.create(s3_config$local_cache)
+  
+  s3_config$log <- log
 }
 
 # TODO: add all s3_config params here?

From acaa61e0f4be2f910f3d442a66043a36435a0176 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 16:45:45 -0400
Subject: [PATCH 15/19] feat: log_file_path parameter for flow to store logs

---
 R/flow.R      | 2 +-
 R/s3_config.R | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index 42045fe..0bcfb9b 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -86,7 +86,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
 
   log_progress <- function(msg) {
     if(s3_config$log) {
-      cat(sprintf("[%s] %s\n", Sys.time(), msg), file = "./flow_debug.log", append = TRUE)
+      cat(sprintf("[%s] %s\n", Sys.time(), msg), file = s3_config$log_file_path, append = TRUE)
     }
   }
 
diff --git a/R/s3_config.R b/R/s3_config.R
index 184dbb6..f396f00 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -16,7 +16,7 @@ s3_config <- new.env()
 # if(!file.exists(s3_config$local_cache))
 #    dir.create(s3_config$local_cache)
 
-set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE) {
+set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE, log_file_path = "./flow_debug.log") {
   s3_config$access_key <- access_key
   s3_config$secret_key <- secret_key
   s3_config$region <- region
@@ -32,6 +32,7 @@ set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, b
     dir.create(s3_config$local_cache)
   
   s3_config$log <- log
+  s3_config$log_file_path <- log_file_path
 }
 
 # TODO: add all s3_config params here?

From 2878bcf977c0bc04478544364967826f1fae02c6 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 16:57:46 -0400
Subject: [PATCH 16/19] feat: local_temp_path variable for writing files
 locally

---
 R/flow.R      | 13 +++++++------
 R/s3_config.R |  3 ++-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index 0bcfb9b..a4bc820 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -139,6 +139,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
   png_urls <- paste0(s3_config$s3_flow_url, cache_prefix, png_files)
   symbology_urls <- paste0(s3_config$s3_flow_url, cache_prefix, symbology_files)
   tiff_bucket_path <- paste0(s3_config$s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")
+  local_temp_path <- s3_config$local_temp_path
 
   # --- CACHE CHECK BLOCK ---
   cache_hit <- TRUE
@@ -154,9 +155,9 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
     tiff_exists <- aws.s3::object_exists(object = tiff_bucket_path, bucket = s3_cfg$bucket)
     if (!tiff_exists) cache_hit <- FALSE
   } else {
-    # Local cache: check if all files exist in localtmp
-    dir.create("localtmp", showWarnings = FALSE)
-    local_cache_prefix <- file.path("localtmp", gsub("/", "_", cache_prefix))
+    # Local cache: check if all files exist in local_temp_path
+    dir.create(local_temp_path, showWarnings = FALSE)
+    local_cache_prefix <- file.path(local_temp_path, gsub("/", "_", cache_prefix))
     png_local_paths <- file.path(local_cache_prefix, png_files)
     json_local_paths <- file.path(local_cache_prefix, symbology_files)
     tiff_local_path <- file.path(local_cache_prefix, paste0(flow_type, "_", taxa, ".tif"))
@@ -175,7 +176,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
       )
       log_progress(paste0("Cached result for week ", pred_weeks[i], ": url=", result[[i]]$url, ", legend=", result[[i]]$legend))
     }
-    log_progress(if (save_local) "Returned cached result from localtmp" else "Returned cached result from S3")
+    log_progress(if (save_local) "Returned cached result from local_temp_path" else "Returned cached result from S3")
     return(
       list(
         start = list(week = week, taxa = taxa, loc = loc),
@@ -189,8 +190,8 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
 
   # Continue with prediction
   if (save_local || !s3_enabled) {
-    dir.create("localtmp", showWarnings = FALSE)
-    out_path <- file.path("localtmp", gsub("/", "_", cache_prefix))
+    dir.create(local_temp_path, showWarnings = FALSE)
+    out_path <- file.path(local_temp_path, gsub("/", "_", cache_prefix))
     dir.create(out_path, recursive = TRUE, showWarnings = FALSE)
   } else {
     out_path <- tempfile(pattern = "flow_", tmpdir = "/dev/shm")
diff --git a/R/s3_config.R b/R/s3_config.R
index f396f00..c6c788a 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -16,7 +16,7 @@ s3_config <- new.env()
 # if(!file.exists(s3_config$local_cache))
 #    dir.create(s3_config$local_cache)
 
-set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE, log_file_path = "./flow_debug.log") {
+set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE, log_file_path = "./flow_debug.log", local_temp_path = "localtmp") {
   s3_config$access_key <- access_key
   s3_config$secret_key <- secret_key
   s3_config$region <- region
@@ -33,6 +33,7 @@ set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, b
   
   s3_config$log <- log
   s3_config$log_file_path <- log_file_path
+  s3_config$local_temp_path <- local_temp_path
 }
 
 # TODO: add all s3_config params here?

From a49d11c850199e4f55e3b14f5713f914b4345914 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Wed, 24 Sep 2025 17:23:30 -0400
Subject: [PATCH 17/19] docs: add sf to imports

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 896f281..900ea82 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -13,7 +13,8 @@ Imports:
     plumber,
     jsonlite,
     aws.s3,
-    terra
+    terra,
+    sf
 Suggests: 
     testthat (>= 3.0.0),
     callthat,

From 36e16381e6d14cc88106d5899722a0ba8897bb76 Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 26 Sep 2025 16:34:00 -0400
Subject: [PATCH 18/19] feat: add all s3_config variables to get_s3_config and
 generalize null coalescing function

---
 R/s3_config.R | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/R/s3_config.R b/R/s3_config.R
index c6c788a..16ad164 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -36,13 +36,29 @@ set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, b
   s3_config$local_temp_path <- local_temp_path
 }
 
-# TODO: add all s3_config params here?
 get_s3_config <- function() {
-  access_key <- s3_config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA)
-  secret_key <- s3_config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA)
-  region <- s3_config$region %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA)
-  bucket <- s3_config$bucket %||% Sys.getenv("S3_BUCKET_NAME", unset = NA)
-  list(access_key = access_key, secret_key = secret_key, region = region, bucket = bucket)
+  list(
+    access_key = s3_config$access_key %||% Sys.getenv("AWS_ACCESS_KEY_ID", unset = NA),
+    secret_key = s3_config$secret_key %||% Sys.getenv("AWS_SECRET_ACCESS_KEY", unset = NA),
+    region = s3_config$region %||% Sys.getenv("AWS_DEFAULT_REGION", unset = NA),
+    bucket = s3_config$bucket %||% Sys.getenv("S3_BUCKET_NAME", unset = NA),
+    ai_app_crs = s3_config$ai_app_crs %||% NA,
+    ai_app_extent = s3_config$ai_app_extent %||% NA,
+    s3_bucket_name = s3_config$s3_bucket_name %||% NA,
+    s3_flow_path = s3_config$s3_flow_path %||% NA,
+    s3_flow_url = s3_config$s3_flow_url %||% NA,
+    local_cache = s3_config$local_cache %||% NA,
+    log = s3_config$log %||% NA,
+    log_file_path = s3_config$log_file_path %||% NA,
+    local_temp_path = s3_config$local_temp_path %||% NA
+  )
 }
 
-`%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
+# `%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
+
+`%||%` <- function(a, b) {
+  if (is.null(a)) return(b)
+  if (is.atomic(a) && length(a) == 1 && is.na(a)) return(b)
+  if (is.character(a) && length(a) == 1 && !nzchar(a)) return(b)
+  a
+}

From aa9d72226a1db21f1e68ce663a80d1c6987013da Mon Sep 17 00:00:00 2001
From: Atharva Shahane <atharvashahane28@gmail.com>
Date: Fri, 26 Sep 2025 16:37:29 -0400
Subject: [PATCH 19/19] feat: use get_s3_config in flow

---
 R/flow.R      | 45 ++++++++++++++++++++-------------------------
 R/s3_config.R | 18 ------------------
 2 files changed, 20 insertions(+), 43 deletions(-)

diff --git a/R/flow.R b/R/flow.R
index a4bc820..c7d7351 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -67,11 +67,6 @@ save_local_path <- "config/save_local.flag"
 #'    `type`
 #' @export
 flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE) {
-  # TODO:
-  # utils::data("species", package = "BirdFlowAPI", envir = environment())
-
-  # load_models()
-
   s3_cfg <- get_s3_config()
   s3_enabled <- !is.na(s3_cfg$bucket) && nzchar(s3_cfg$bucket)
 
@@ -85,8 +80,8 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
   }
 
   log_progress <- function(msg) {
-    if(s3_config$log) {
-      cat(sprintf("[%s] %s\n", Sys.time(), msg), file = s3_config$log_file_path, append = TRUE)
+    if(s3_cfg$log) {
+      cat(sprintf("[%s] %s\n", Sys.time(), msg), file = s3_cfg$log_file_path, append = TRUE)
     }
   }
 
@@ -134,12 +129,12 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
   pred_weeks <- BirdFlowR::lookup_timestep_sequence(bf, start = week, n = n, direction = direction)
   png_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".png")
   symbology_files <- paste0(flow_type, "_", taxa, "_", pred_weeks, ".json")
-  png_bucket_paths <- paste0(s3_config$s3_flow_path, cache_prefix, png_files)
-  symbology_bucket_paths <- paste0(s3_config$s3_flow_path, cache_prefix, symbology_files)
-  png_urls <- paste0(s3_config$s3_flow_url, cache_prefix, png_files)
-  symbology_urls <- paste0(s3_config$s3_flow_url, cache_prefix, symbology_files)
-  tiff_bucket_path <- paste0(s3_config$s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")
-  local_temp_path <- s3_config$local_temp_path
+  png_bucket_paths <- paste0(s3_cfg$s3_flow_path, cache_prefix, png_files)
+  symbology_bucket_paths <- paste0(s3_cfg$s3_flow_path, cache_prefix, symbology_files)
+  png_urls <- paste0(s3_cfg$s3_flow_url, cache_prefix, png_files)
+  symbology_urls <- paste0(s3_cfg$s3_flow_url, cache_prefix, symbology_files)
+  tiff_bucket_path <- paste0(s3_cfg$s3_flow_path, cache_prefix, flow_type, "_", taxa, ".tif")
+  local_temp_path <- s3_cfg$local_temp_path
 
   # --- CACHE CHECK BLOCK ---
   cache_hit <- TRUE
@@ -182,7 +177,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
         start = list(week = week, taxa = taxa, loc = loc),
         status = "cached",
         result = result,
-        geotiff = if (save_local) tiff_local_path else paste0(s3_config$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
+        geotiff = if (save_local) tiff_local_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
       )
     )
   }
@@ -243,25 +238,25 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
 
   log_progress("Projecting and cropping raster for web output.")
   log_progress(paste0("combined class: ", class(combined)))
-  log_progress(paste0("s3_config$ai_app_crs$input: ", s3_config$ai_app_crs$input))
-  log_progress(paste0("s3_config$ai_app_extent: ", s3_config$ai_app_extent))
+  log_progress(paste0("s3_cfg$ai_app_crs$input: ", s3_cfg$ai_app_crs$input))
+  log_progress(paste0("s3_cfg$ai_app_extent: ", s3_cfg$ai_app_extent))
   if (is.null(combined) || !inherits(combined, "SpatRaster")) {
     log_progress("ERROR: combined raster is NULL or not a SpatRaster. Aborting.")
     return(format_error("combined raster is NULL or not a SpatRaster"))
   }
-  if (is.null(s3_config$ai_app_crs$input)) {
-    log_progress("ERROR: s3_config$ai_app_crs$input is NULL. Aborting.")
-    return(format_error("s3_config$ai_app_crs$input is NULL"))
+  if (is.null(s3_cfg$ai_app_crs$input)) {
+    log_progress("ERROR: s3_cfg$ai_app_crs$input is NULL. Aborting.")
+    return(format_error("s3_cfg$ai_app_crs$input is NULL"))
   }
-  if (is.null(s3_config$ai_app_extent)) {
-    log_progress("ERROR: s3_config$ai_app_extent is NULL. Aborting.")
-    return(format_error("s3_config$ai_app_extent is NULL"))
+  if (is.null(s3_cfg$ai_app_extent)) {
+    log_progress("ERROR: s3_cfg$ai_app_extent is NULL. Aborting.")
+    return(format_error("s3_cfg$ai_app_extent is NULL"))
   }
 
   log_progress("Projecting")
-  web_raster <- combined |> terra::project(s3_config$ai_app_crs$input)
+  web_raster <- combined |> terra::project(s3_cfg$ai_app_crs$input)
   log_progress("Cropping")
-  web_raster <- terra::crop(web_raster, s3_config$ai_app_extent)
+  web_raster <- terra::crop(web_raster, s3_cfg$ai_app_extent)
   log_progress("Done cropping")
   png_paths <- file.path(out_path, png_files)
   symbology_paths <- file.path(out_path, symbology_files)
@@ -349,7 +344,7 @@ flow <- function(loc, week, taxa, n, direction = "forward", save_local = FALSE)
       start = list(week = week, taxa = taxa, loc = loc),
       status = "success",
       result = result,
-      geotiff = if (save_local) tiff_path else paste0(s3_config$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
+      geotiff = if (save_local) tiff_path else paste0(s3_cfg$s3_flow_url, cache_prefix, flow_type, "_", taxa, ".tif")
     )
   )
 }
diff --git a/R/s3_config.R b/R/s3_config.R
index 16ad164..4c88da8 100644
--- a/R/s3_config.R
+++ b/R/s3_config.R
@@ -1,21 +1,5 @@
 s3_config <- new.env()
 
-# Define extent of exported data (ai_app_extent)
-# s3_config$ai_app_crs <- sf::st_crs("EPSG:3857")
-
-# Note now storing extent as a simple vector (xmin, xmax, ymin, ymax) in EPSG:3857
-# s3_config$ai_app_extent <- c(-18924313.4348565, -5565974.53966368, 1118889.97485796, 15538711.0963092)
-
-# s3_configure S3 bucket, its url and the path within it used for flow output
-# s3_config$s3_bucket_name <- "avianinfluenza"
-# s3_config$s3_flow_path <- "flow/"
-# s3_config$s3_flow_url <- "https://avianinfluenza.s3.us-east-2.amazonaws.com/flow/"
-
-# Define local cache for temporary output images, will then be copied to AWS
-# s3_config$local_cache <- tempdir()
-# if(!file.exists(s3_config$local_cache))
-#    dir.create(s3_config$local_cache)
-
 set_s3_config <- function(access_key = NULL, secret_key = NULL, region = NULL, bucket = NULL, log = TRUE, log_file_path = "./flow_debug.log", local_temp_path = "localtmp") {
   s3_config$access_key <- access_key
   s3_config$secret_key <- secret_key
@@ -54,8 +38,6 @@ get_s3_config <- function() {
   )
 }
 
-# `%||%` <- function(a, b) if (!is.null(a) && !is.na(a) && nzchar(a)) a else b
-
 `%||%` <- function(a, b) {
   if (is.null(a)) return(b)
   if (is.atomic(a) && length(a) == 1 && is.na(a)) return(b)