epizootic now runs on foreach

I was having problems with future and furrr in this package, so the parallelization engine has switched to doParallel/foreach instead.
viralemergence · Mar 21, 2024 · 0874905 · 0874905
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commit 0874905
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -40,7 +40,7 @@ jobs:
      # setup-r-dependencies is removed !
      # instead, we're handling dependencies with renv
       - name: Cache packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.RENV_PATHS_ROOT }}
           key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,11 +20,11 @@ Imports:
     tibble (>= 3.2.1),
     R6 (>= 2.5.1),
     cli (>= 3.6.1),
-    furrr (>= 0.3.1),
-    future (>= 1.33.0),
     raster (>= 3.6),
     qs (>= 0.25.7),
-    poems (>= 1.1.0)
+    poems (>= 1.1.0),
+    doParallel (>= 1.0.16),
+    foreach (>= 1.5.1)
 Suggests: 
     testthat (>= 3.0.0),
     geosphere (>= 1.5),

diff --git a/NAMESPACE b/NAMESPACE
@@ -18,11 +18,10 @@ import(poems)
 import(purrr)
 import(tibble)
 importFrom(R6,R6Class)
-importFrom(furrr,furrr_options)
-importFrom(furrr,future_map)
-importFrom(future,multisession)
-importFrom(future,plan)
-importFrom(future,sequential)
+importFrom(doParallel,registerDoParallel)
+importFrom(doParallel,stopImplicitCluster)
+importFrom(foreach,"%dopar%")
+importFrom(foreach,foreach)
 importFrom(poems,SimulationModel)
 importFrom(qs,qsave)
 importFrom(raster,nlayers)

diff --git a/R/SimulationHandler.R b/R/SimulationHandler.R
@@ -8,11 +8,10 @@
 #' for parallelization, handles errors differently, and has a different default
 #' data format (\code{.qs}).
 #'
-#' @importFrom future plan
-#' @importFrom future sequential
-#' @importFrom future multisession
-#' @importFrom furrr furrr_options
-#' @importFrom furrr future_map
+#' @importFrom foreach foreach
+#' @importFrom foreach %dopar%
+#' @importFrom doParallel registerDoParallel
+#' @importFrom doParallel stopImplicitCluster
 #' @importFrom qs qsave
 #' @importFrom R6 R6Class
 #' @export SimulationHandler
@@ -265,34 +264,30 @@ SimulationHandler <- R6Class("SimulationHandler",
       }
       model <- NULL # release from memory
 
-      # Parallelize and simulate
-      if (self$parallel_cores == 1) {
-        plan(sequential)
-      } else {
-        plan(multisession, workers = self$parallel_cores)
-      }
-
-      simulation_log <- future_map(1:nrow(self$sample_data), \(j) {
+      doParallel::registerDoParallel(cores = self$parallel_cores)
+      simulation_log <- foreach(i = 1:nrow(self$sample_data),
+                                .packages = c("raster"),
+                                .errorhandling = c("pass")) %dopar% {
 
         # Clone the model
         model <- self$nested_model$clone()
 
         # Set the model sample attributes
-        self$set_model_sample(model, j)
+        self$set_model_sample(model, i)
         if (length(model$error_messages)) {
           return(list(successful = FALSE, message = self$get_message_sample("Error(s) setting model %s sample attributes", i), errors = model$error_messages))
         }
 
         # Create and run the simulator
-        simulator <- self$model_simulator$new_clone(simulation_model = model, sample_id = j)
+        simulator <- self$model_simulator$new_clone(simulation_model = model, sample_id = i)
         simulator_run_status <- simulator$run()
 
         # Substitute sample details into the simulator run status message
-        simulator_run_status$message <- self$get_message_sample(simulator_run_status$message, j)
+        simulator_run_status$message <- self$get_message_sample(simulator_run_status$message, i)
 
         # Save results
         if (!is.null(simulator$results)) {
-          results_file <- file.path(self$results_dir, paste0(self$get_results_filename(j), self$results_ext))
+          results_file <- file.path(self$results_dir, paste0(self$get_results_filename(i), self$results_ext))
           suppressWarnings(try(
             if (self$results_ext == ".qs") {
               qsave(simulator$results, results_file)
@@ -309,7 +304,8 @@ SimulationHandler <- R6Class("SimulationHandler",
         }
 
         return(simulator_run_status)
-      }, .options = furrr_options(seed = TRUE, conditions = character()))
+      }
+      doParallel::stopImplicitCluster()
 
       # Summarize and write log to a file
       simulation_log <- self$log_simulation(simulation_log)

diff --git a/renv.lock b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.2",
+    "Version": "4.3.3",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -172,17 +172,6 @@
       ],
       "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
     },
-    "digest": {
-      "Package": "digest",
-      "Version": "0.6.34",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a"
-    },
     "doParallel": {
       "Package": "doParallel",
       "Version": "1.0.17",
@@ -256,37 +245,6 @@
       ],
       "Hash": "618609b42c9406731ead03adf5379850"
     },
-    "furrr": {
-      "Package": "furrr",
-      "Version": "0.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "future",
-        "globals",
-        "lifecycle",
-        "purrr",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "da7a4c32196cb2262a41dd5a25d486ff"
-    },
-    "future": {
-      "Package": "future",
-      "Version": "1.33.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "digest",
-        "globals",
-        "listenv",
-        "parallel",
-        "parallelly",
-        "utils"
-      ],
-      "Hash": "e57e292737f7a4efa9d8a91c5908222c"
-    },
     "gdistance": {
       "Package": "gdistance",
       "Version": "1.6.4",
@@ -327,17 +285,6 @@
       ],
       "Hash": "45aa4def70a402e7d20efde490c13ecb"
     },
-    "globals": {
-      "Package": "globals",
-      "Version": "0.16.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "codetools"
-      ],
-      "Hash": "baa9585ab4ce47a9f4618e671778cc6f"
-    },
     "glue": {
       "Package": "glue",
       "Version": "1.7.0",
@@ -421,16 +368,6 @@
       ],
       "Hash": "b8552d117e1b808b09a832f589b79035"
     },
-    "listenv": {
-      "Package": "listenv",
-      "Version": "0.9.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "e2fca3e12e4db979dccc6e519b10a7ee"
-    },
     "locfit": {
       "Package": "locfit",
       "Version": "1.5-9.8",
@@ -490,18 +427,6 @@
       ],
       "Hash": "df58958f293b166e4ab885ebcad90e02"
     },
-    "parallelly": {
-      "Package": "parallelly",
-      "Version": "1.36.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "parallel",
-        "tools",
-        "utils"
-      ],
-      "Hash": "bca377e1c87ec89ebed77bba00635b2e"
-    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",