diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index dec2daf..308a0d5 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index f60d047..da54e13 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: lint
 
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 184ae64..f57508e 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:
diff --git a/.github/workflows/test-container-dl-calc.yaml b/.github/workflows/test-container-dl-calc.yaml
new file mode 100644
index 0000000..4ce7e76
--- /dev/null
+++ b/.github/workflows/test-container-dl-calc.yaml
@@ -0,0 +1,73 @@
+name: Test Coverage for Download and Calculate via Apptainer
+
+on:
+  push:
+    branches: [main, master, dev]
+  pull_request:
+    branches: [main, master, dev]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Create run_dl_calc_tests.R dynamically
+        run: |
+          mkdir -p tests/testthat  # Ensure the directory exists
+          echo 'testthat::test_file("tests/testthat/test_download.R")' > tests/testthat/run_dl_calc_tests.R
+          echo 'testthat::test_file("tests/testthat/test_calculate.R")' >> tests/testthat/run_dl_calc_tests.R
+
+      - name: Install Apptainer dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y \
+          libseccomp-dev \
+          squashfs-tools \
+          cryptsetup \
+          wget
+
+      - name: Install Apptainer
+        run: |
+          wget https://github.com/apptainer/apptainer/releases/download/v1.1.0/apptainer-1.1.0.tar.gz
+          tar -xvf apptainer-1.1.0.tar.gz
+          cd apptainer-1.1.0
+          ./mconfig && make -C builddir && sudo make -C builddir install
+
+      - name: Restore .sif file from cache
+        id: cache-sif
+        uses: actions/cache@v3
+        with:
+          path: beethoven_dl_calc.sif
+          key: sif-cache-${{ runner.os }}-${{ hashFiles('container/beethoven_dl_calc.def') }}
+          restore-keys: |
+            sif-cache-${{ runner.os }}-
+
+      - name: Build the Apptainer container (if cache miss)
+        if: steps.cache-sif.outputs.cache-hit != 'true'
+        run: |
+          apptainer build --fakeroot beethoven_dl_calc.sif container/beethoven_dl_calc.def
+
+      - name: Cache the .sif file
+        if: steps.cache-sif.outputs.cache-hit != 'true'
+        uses: actions/cache@v3
+        with:
+          path: beethoven_dl_calc.sif
+          key: sif-cache-${{ runner.os }}-${{ hashFiles('container/beethoven_dl_calc.def') }}
+
+      - name: Check if .sif file exists
+        run: |
+          if [ ! -f beethoven_dl_calc.sif ]; then
+            echo "Error: .sif file not found!"
+            exit 1
+          fi
+
+      - name: Run R tests
+        run: |
+          apptainer exec \
+            --bind $PWD/inst:/pipeline \
+            --bind $PWD/input:/input \
+            --bind $PWD:/mnt \
+            beethoven_dl_calc.sif \
+            Rscript /mnt/tests/testthat/run_dl_calc_tests.R
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 220709d..51f2bbb 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -3,9 +3,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: test-coverage-local
 
diff --git a/.gitignore b/.gitignore
index a961705..593e14a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -106,4 +106,8 @@ slurm_error.log
 /doc/
 
 # interactive targets
-targets_start.Rout
\ No newline at end of file
+targets_start.Rout
+
+.netrc
+.urs_cookies
+beethoven_branching_notes.txt
\ No newline at end of file
diff --git a/NAMESPACE b/NAMESPACE
index 5733c21..d82ed22 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,6 +9,7 @@ export(calc_geos_strict)
 export(calc_gmted_direct)
 export(calc_narr2)
 export(calculate)
+export(convert_cv_index_rset)
 export(feature_raw_download)
 export(fit_base_learner)
 export(fit_base_tune)
diff --git a/R/base_learner.R b/R/base_learner.R
index 7f5de0a..a4f0fa1 100644
--- a/R/base_learner.R
+++ b/R/base_learner.R
@@ -506,6 +506,7 @@ assign_learner_cv <-
 #' training-test data.frames and a column of labels.
 #' @author Insang Song
 #' @importFrom rsample make_splits manual_rset
+#' @export
 convert_cv_index_rset <-
   function(
     cvindex,
diff --git a/_targets.R b/_targets.R
index e90e030..1cc6de4 100755
--- a/_targets.R
+++ b/_targets.R
@@ -1,123 +1,80 @@
 library(targets)
 library(tarchetypes)
-library(future)
-library(future.batchtools)
 library(dplyr)
-library(
-  beethoven,
-  lib.loc = "/ddn/gs1/home/manwareme/R/x86_64-pc-linux-gnu-library/4.3"
-)
-library(tidymodels)
-library(bonsai)
-# library(
-#   torch,
-#   lib.loc = "/ddn/gs1/biotools/R/lib64/R/library"
-# )
+library(crew)
+library(future)
+library(beethoven)
+library(amadeus)
 
-Sys.setenv("LD_LIBRARY_PATH" = paste("/ddn/gs1/biotools/R/lib64/R/customlib", Sys.getenv("LD_LIBRARY_PATH"), sep = ":"))
 
-# replacing yaml file.
+# targets store location corresponds to _targets/ in the root of the project
 tar_config_set(
-  store = "/ddn/gs1/home/manwareme/beethoven/beethoven_targets"
+  store = "/opt/_targets"
+)
+
+# crew contollers
+# For now, one is set, but we can explore the use of multiple controllers
+# Can also explore making the workers input for bash script or Rscript
+geo_controller <- crew_controller_local(
+  name = "geo_controller",
+  workers = 16L,
+  launch_max = 8L,
+  seconds_idle = 120
 )
 
-# maximum future exportable object size is set 50GB
-# TODO: the maximum size error did not appear until recently
-#       and suddenly appeared. Need to investigate the cause.
-#       Should be removed after the investigation.
-# options(future.globals.maxSize = 50 * 2^30)
-options(future.globals.maxSize = 60 * 1024^3)  # 60 GiB
 
 
-generate_list_download <- FALSE
+# Setting up the NASA Earthdata token inside the container
+# This needs to be tested
+if (!nzchar(Sys.getenv("NASA_EARTHDATA_TOKEN"))){
+  tar_source("/mnt/NASA_token_setup.R")
+  file.exists(".netrc")
+  file.exists(".urs_cookies")
+  file.exists(".dodsrc")
+}
+
 
 arglist_download <-
   set_args_download(
     char_period = c("2018-01-01", "2022-12-31"),
-    char_input_dir = "input",
-    nasa_earth_data_token = NULL,#Sys.getenv("NASA_EARTHDATA_TOKEN"),
-    mod06_filelist = "inst/targets/mod06_links_2018_2022.csv",
-    export = generate_list_download,
-    path_export = "inst/targets/download_spec.qs"
+    char_input_dir = "/input",
+    nasa_earth_data_token = Sys.getenv("NASA_EARTHDATA_TOKEN"),
+    mod06_filelist = "/pipeline/targets/mod06_links_2018_2022.csv",
+    export = TRUE,
+    path_export = "/pipeline/targets/download_spec.qs"
   )
 
-generate_list_calc <- FALSE
 
-arglist_common <-
-  set_args_calc(
-    char_siteid = "site_id",
-    char_timeid = "time",
-    char_period = c("2018-01-01", "2022-12-31"),
-    num_extent = c(-126, -62, 22, 52),
-    char_user_email = paste0(Sys.getenv("USER"), "@nih.gov"),
-    export = generate_list_calc,
-    path_export = "inst/targets/calc_spec.qs",
-    char_input_dir = "/ddn/gs1/group/set/Projects/NRT-AP-Model/input"
-  )
 
-tar_source("inst/targets/targets_initialize.R")
-tar_source("inst/targets/targets_download.R")
-tar_source("inst/targets/targets_calculate_fit.R")
-tar_source("inst/targets/targets_calculate_predict.R")
-tar_source("inst/targets/targets_baselearner.R")
-tar_source("inst/targets/targets_metalearner.R")
-tar_source("inst/targets/targets_predict.R")
 
 
-# bypass option
-Sys.setenv("BTV_DOWNLOAD_PASS" = "TRUE")
 
-#
-# bind custom built GDAL
-# Users should export the right path to the GDAL library
-# by export LD_LIBRARY_PATH=.... command.
+### NOTE: It is important to source the scipts after the global variables are defined from the set_args functions
+ #tar_source("/pipeline/targets/targets_aqs.R")
+ tar_source("/pipeline/targets/targets_download.R")
 
-# arglist_common is generated above
-plan(
-  list(
-    tweak(
-      future.batchtools::batchtools_slurm,
-      template = "inst/targets/template_slurm.tmpl",
-      resources =
-        list(
-          memory = 8,
-          log.file = "slurm_run.log",
-          ncpus = 1, partition = "geo", ntasks = 1,
-          email = arglist_common$char_user_email,
-          error.file = "slurm_error.log"
-        )
-    ),
-    multicore
-  )
-)
+# Toy test files - note we will not have functions defined like this directly in
+# the _targets.R file
+my_fun_a <- function(n) {
+  rnorm(n)
+}
+
+my_fun_b <- function(x) {
+  x^2
+}
 
-# # invalidate any nodes older than 180 days: force running the pipeline
-# tar_invalidate(any_of(tar_older(Sys.time() - as.difftime(180, units = "days"))))
 
 
-# # nullify download target if bypass option is set
-if (Sys.getenv("BTV_DOWNLOAD_PASS") == "TRUE") {
-  target_download <- NULL
-}
 
-# targets options
-# For GPU support, users should be aware of setting environment
-# variables and GPU versions of the packages.
-# TODO: check if the controller and resources setting are required
 tar_option_set(
-  packages = c(
-    "beethoven", "amadeus", "chopin", "targets", "tarchetypes",
-    "data.table", "sf", "terra", "exactextractr",
-    #"crew", "crew.cluster", 
-    "tigris", "dplyr",
-    "future.batchtools", "qs", "collapse", "bonsai",
-    "tidymodels", "tune", "rsample", "torch", "brulee",
-    "glmnet", "xgboost",
-    "future", "future.apply", "future.callr", "callr",
-    "stars", "rlang", "parallelly"
-  ),
-  library = c("/ddn/gs1/group/set/isong-archive/r-libs"),
-  repository = "local",
+  packages =
+    c( "amadeus", "targets", "tarchetypes",
+      "data.table", "sf", "terra", "exactextractr",
+       "dplyr", "qs", "callr",  "stars", "rlang"),
+  controller = crew_controller_group(geo_controller),
+  resources = tar_resources(
+    crew = tar_resources_crew(controller = "geo_controller")
+  ),  
   error = "abridge",
   memory = "transient",
   format = "qs",
@@ -127,15 +84,65 @@ tar_option_set(
   seed = 202401L
 )
 
-# should run tar_make_future()
+  list(
+    tar_target(name = A, command = my_fun_a(100)),
+    tar_target(name = B, command = my_fun_b(A), pattern = A),
+    tar_target(name = save_input, command = saveRDS(B, "/input/input.rds")),
+    tar_target( # Test download data with amadeus
+      download_test,
+      amadeus::download_narr(
+      variables = c("weasd", "omega"),
+      year = c(2023, 2023),
+      directory_to_save = "/input/narr_monolevel",
+      acknowledgement = TRUE,
+      download = TRUE, 
+      remove_command = TRUE
+    )
+  ),
+   target_download
+  )
+
+
+# Style below that uses sources scripts for targets by pipeline step
+# Note that variables created in _targets.R are in the same local
+# environment as the sourced scripts
+
+# list(
+#   target_init,
+#   target_download
+  # target_calculate_fit,
+  # target_baselearner#,
+  # target_metalearner,
+  # target_calculate_predict,
+  # target_predict,
+  # # documents and summary statistics
+  # targets::tar_target(
+  #   summary_urban_rural,
+  #   summary_prediction(
+  #     grid_filled,
+  #     level = "point",
+  #     contrast = "urbanrural"))
+  # ,
+  # targets::tar_target(
+  #   summary_state,
+  #   summary_prediction(
+  #     grid_filled,
+  #     level = "point",
+  #     contrast = "state"
+  #   )
+  # )
+# )
+
+# targets::tar_visnetwork(targets_only = TRUE)
+# END OF FILE
 
-list(
-  target_init,
-  target_download,
-  target_calculate_fit,
-  target_baselearner,
-  target_metalearner,
-  target_calculate_predict#,
+# list(
+#   target_init,
+#   target_download,
+#   target_calculate_fit,
+#   target_baselearner,
+#   target_metalearner,
+#   target_calculate_predict#,
   # target_predict,
   # # documents and summary statistics
   # targets::tar_target(
diff --git a/init_targets_storage.sh b/archive/init_targets_storage.sh
similarity index 100%
rename from init_targets_storage.sh
rename to archive/init_targets_storage.sh
diff --git a/run_interactive.sh b/archive/run_interactive.sh
similarity index 100%
rename from run_interactive.sh
rename to archive/run_interactive.sh
diff --git a/run_slurm.sh b/archive/run_slurm.sh
similarity index 100%
rename from run_slurm.sh
rename to archive/run_slurm.sh
diff --git a/setup_hook.sh b/archive/setup_hook.sh
similarity index 100%
rename from setup_hook.sh
rename to archive/setup_hook.sh
diff --git a/container/beethoven_dl_calc.def b/container/beethoven_dl_calc.def
new file mode 100644
index 0000000..5b5227d
--- /dev/null
+++ b/container/beethoven_dl_calc.def
@@ -0,0 +1,42 @@
+BootStrap: docker
+From: rocker/geospatial:latest
+
+%post
+    # Update package list
+    apt-get update
+
+    # Install locales and generate the necessary locale
+    apt-get install -y locales
+    locale-gen en_US.UTF-8
+
+    # Install fonts for Unicode support
+    apt-get install -y fonts-dejavu fonts-liberation fonts-noto fonts-unifont
+
+    # Set locale for the environment
+    echo "LANG=en_US.UTF-8" >> /etc/default/locale
+    echo "LC_ALL=en_US.UTF-8" >> /etc/default/locale
+    export LANG=en_US.UTF-8
+    export LC_ALL=en_US.UTF-8
+
+
+    mkdir /pipeline
+    mkdir /input
+    mkdir /opt/_targets
+
+    Rscript -e "install.packages(c('pak','targets','tarchetypes','crew','crew.cluster','testthat'))"
+    Rscript -e "pak::pkg_install('NIEHS/amadeus')"
+    Rscript -e "remotes::install_github('NIEHS/beethoven')"
+
+
+
+   
+%environment
+    # Set locale for the container environment
+    export LANG=en_US.UTF-8
+    export LC_ALL=en_US.UTF-8
+    export TERM=xterm-256color
+
+%runscript
+
+%labels
+  basic geospatial with targets and crew plus unicode text so the target progress prints nicely
\ No newline at end of file
diff --git a/container/build_dl_calc.sh b/container/build_dl_calc.sh
new file mode 100644
index 0000000..b66b1a0
--- /dev/null
+++ b/container/build_dl_calc.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# usage: build_apptainer_image.sh [full file path]
+# where full file path ends with .sif, with full directory path to save the image
+# after the image is built, group write/execution privileges are given
+
+# Recommended to run this script interactively via `sh build_dl_calc.sh`
+apptainer build --fakeroot beethoven_dl_calc.sif beethoven_dl_calc.def
\ No newline at end of file
diff --git a/container/run_container_dl_calc.sh b/container/run_container_dl_calc.sh
new file mode 100644
index 0000000..5d0909b
--- /dev/null
+++ b/container/run_container_dl_calc.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=download_calc
+#SBATCH --partition=geo
+#SBATCH --mem=128G
+#SBATCH --cpus-per-task=4
+#SBATCH --ntasks=16
+#SBATCH --output=../slurm_messages/slurm-%j.out
+#SBATCH --error=../slurm_messages/slurm-%j.err
+#SBATCH --mail-user=kyle.messier@nih.gov
+#SBATCH --mail-type=ALL
+
+
+# Run the container
+# .sif file sites in "root/container", thus we need to go up one level with bind mounts 
+apptainer exec \
+  --bind $PWD/inst:/pipeline \
+  --bind $PWD/input:/input \
+  --bind $PWD/_targets:/opt/_targets \
+  --bind $PWD:/mnt \
+  beethoven_dl_calc.sif \
+  Rscript /mnt/run.R
+
+
diff --git a/container/run_dl_calc_local_tests.sh b/container/run_dl_calc_local_tests.sh
new file mode 100644
index 0000000..72c81a2
--- /dev/null
+++ b/container/run_dl_calc_local_tests.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=dl_calc_tests
+#SBATCH --partition=geo
+#SBATCH --mem=128G
+#SBATCH --cpus-per-task=4
+#SBATCH --ntasks=16
+#SBATCH --output=../slurm_messages/slurm-%j.out
+#SBATCH --error=../slurm_messages/slurm-%j.err
+#SBATCH --mail-user=kyle.messier@nih.gov
+#SBATCH --mail-type=ALL
+
+
+
+
+apptainer exec \
+  --bind $PWD/../inst:/pipeline \
+  --bind $PWD/../input:/input \
+  --bind $PWD/../_targets:/opt/_targets \
+  --bind $PWD/..:/mnt \
+  beethoven_dl_calc.sif \
+  Rscript /mnt/tests/testthat/test_download.R
+
+
diff --git a/tests/testthat/test-calculate.R b/tests/testthat/test-calculate.R
index 91e6e62..4b6e49e 100644
--- a/tests/testthat/test-calculate.R
+++ b/tests/testthat/test-calculate.R
@@ -5,6 +5,7 @@
 ################################################################################
 ##### par_narr
 testthat::test_that("par_narr (weasd + omega)", {
+  testthat::skip_on_ci()
   withr::local_package("rlang")
 
   # sample location
diff --git a/tests/testthat/test-injection.R b/tests/testthat/test-injection.R
index aa4403e..dfa6e68 100644
--- a/tests/testthat/test-injection.R
+++ b/tests/testthat/test-injection.R
@@ -123,7 +123,7 @@ testthat::test_that("set_target_years", {
 
 ################################################################################
 ##### inject_calc
-testthat::test_that("inject_calc (hms + hms)", {
+testthat::test_that("inject_calc (hms + nei)", {
   
   withr::local_package("rlang")
 
@@ -188,6 +188,7 @@ testthat::test_that("inject_calc (hms + hms)", {
     crs = "EPSG:4326"
   )
 
+  testthat::skip_on_ci()
   # expect no errors (nei)
   testthat::expect_no_error(
     nei_injected <- inject_calculate(
diff --git a/tests/testthat/test-meta.R b/tests/testthat/test-meta.R
index 056ad75..4c96426 100644
--- a/tests/testthat/test-meta.R
+++ b/tests/testthat/test-meta.R
@@ -257,7 +257,7 @@ testthat::test_that("predict_meta_learner", {
   )
 
   # expect no error for meta fit
-  testthat::expect_no_error(
+  testthat::expect_warning(
     meta4 <- fit_meta_learner(
       data = dt_meta,
       p_col_sel = 0.5,
diff --git a/tests/testthat/test_calculate.R b/tests/testthat/test_calculate.R
new file mode 100644
index 0000000..94a4871
--- /dev/null
+++ b/tests/testthat/test_calculate.R
@@ -0,0 +1,13 @@
+################################################################################
+##### unit and integration tests for covariate calculations
+##### Currently arbitrary placeholders
+##### 
+
+################################################################################
+##### 
+testthat::test_that("calculate targets work", {
+
+ a <- 1
+ testthat::expect_equal(a, 1)
+
+})
diff --git a/tests/testthat/test_download.R b/tests/testthat/test_download.R
new file mode 100644
index 0000000..fc706b8
--- /dev/null
+++ b/tests/testthat/test_download.R
@@ -0,0 +1,16 @@
+################################################################################
+##### unit and integration tests for data download
+##### Currently arbitrary placeholders
+##### 
+
+################################################################################
+##### loadargs
+testthat::test_that("download targets work", {
+
+ a <- 1
+ testthat::expect_equal(a, 1)
+
+ b <- 2
+ testthat::expect_equal(b, 2) 
+
+})
diff --git a/tools/targets-old/targets_configuration.csv b/tools/targets-old/targets_configuration.csv
index c3a3fe0..00b1dd7 100644
--- a/tools/targets-old/targets_configuration.csv
+++ b/tools/targets-old/targets_configuration.csv
@@ -1,71 +1,3 @@
-"index","last_updated","command","name_targets_short","value","class","name_targets_long","rclass","role_suffix","stage","source","spacetime","remarks"
-0,"2024/3/15","paste0","root_custom","../../../../group/set/Projects/NRT-AP-Model/","path","character_feature_userroot","character","feature_userroot","","","",""
-1,"2024/3/15","getwd","root_absolute","missing","path","character_feature_absoluteroot","character","feature_absoluteroot","","","",""
-2,"2024/3/15","paste0","root_relative",".","path","character_feature_relativeroot","character","feature_relativeroot","","","",""
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