fix(GHA): specify version

.github/workflows/call-update-data-r.yml

@@ -6,11 +6,12 @@ on:
   push:
     paths:
       - 'data-raw/**'
+
   workflow_dispatch:
 
 jobs:
   call-workflow:
-    uses: NOAA-FIMS/ecosystemom/.github/workflows/update-data-r.yml
+    uses: NOAA-FIMS/ecosystemom/.github/workflows/update-data-r.yml@main
     secrets:
       PAT: ${{ secrets.PAT }}
     with:

.github/workflows/update-data-r.yml

@@ -59,12 +59,12 @@ jobs:
 
       - name: Run R code to update files in /data
         run: |
-          devtools::install()
+          devtools::install(quick = TRUE)
           r_scripts <- list.files("data-raw", pattern = "\\.R$", full.names = TRUE)
           if (length(r_scripts) > 0) {
             for (script in r_scripts) {
-              # Capture exit code so failures actually stop the GHA runner
-              status <- system2(paste("Rscript ", shQuote(script)))
+              message("Executing script: ", script)
+              status <- system2("Rscript", args = script)
               if (status != 0) stop(paste("Script failed:", script))
             }
           } else {

data-raw/ewe_ecosim_base_nwatlantic.R

@@ -15,7 +15,7 @@ raw_file_path <- fs::path(
 # Extract the functional groups from the model's basic estimates file.
 # The `get_functional_groups` function reads
 # the specified CSV file to get a list of all functional groups in the model.
-functional_groups <- get_functional_groups(
+functional_groups <- ecosystemom::get_functional_groups(
   file_path = fs::path(
     raw_file_path, "basic_estimates.csv"
   )
@@ -25,7 +25,7 @@ functional_groups <- get_functional_groups(
 # The `load_model` function reads all the necessary
 # files from the specified directory to construct the full model object.
 # It requires the list of functional groups that was extracted in the previous step.
-ewe_ecosim_base_nwatlantic <- load_model(
+ewe_ecosim_base_nwatlantic <- ecosystemom::load_model(
   directory = raw_file_path,
   type = "ewe_ecosim",
   functional_groups = functional_groups

data-raw/ewe_ecosim_with_environmental_data_nwatlantic.R

@@ -15,7 +15,7 @@ raw_file_path <- fs::path(
 # Extract the functional groups from the model's basic estimates file.
 # The `get_functional_groups` function reads
 # the specified CSV file to get a list of all functional groups in the model.
-functional_groups <- get_functional_groups(
+functional_groups <- ecosystemom::get_functional_groups(
   file_path = fs::path(
     raw_file_path, "basic_estimates.csv"
   )
@@ -25,7 +25,7 @@ functional_groups <- get_functional_groups(
 # The `load_model` function reads all the necessary
 # files from the specified directory to construct the full model object.
 # It requires the list of functional groups that was extracted in the previous step.
-ewe_ecosim_with_environmental_data_nwatlantic <- load_model(
+ewe_ecosim_with_environmental_data_nwatlantic <- ecosystemom::load_model(
   directory = raw_file_path,
   type = "ewe_ecosim",
   functional_groups = functional_groups