trying a DESCRIPTION file and testing infrastructure

.Rbuildignore

@@ -0,0 +1,31 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+.*\.tar\.gz$
+.*\.toc$
+.*\.zip$
+^\.lintr$
+
+
+CONTRIBUTING\.md
+cran-comments\.md
+^docs$
+^LICENSE$
+vignettes/.*_cache$
+vignettes/.*\.log$
+
+^\.httr-oauth$
+^revdep$
+^\.github$
+^codecov\.yml$
+^CRAN-RELEASE$
+^data/*
+^.git
+^.gitignore
+
+^.gitmodules
+
+Biomass_borealDataPrep.*
+.*zip
+citation.*
+figures

.github/workflows/render-module-rmd.yaml

@@ -3,6 +3,7 @@ on:
     branches:
       - main
       - master
+      - development
   push:
     branches:
       - main

Biomass_borealDataPrep.R

@@ -18,7 +18,7 @@ defineModule(sim, list(
   loadOrder = list(after = c("Biomass_speciesData"),
                    before = c("Biomass_core")),
   reqdPkgs = list("assertthat", "crayon", "data.table", "dplyr", "fasterize",  "ggplot2",
-                  "merTools", "plyr", "rasterVis", "sf", "terra",
+                  "merTools", "plyr", "rasterVis", "sf", "terra", "Require",
                   "reproducible (>= 2.1.0)",
                   "SpaDES.core (>= 2.1.0)", "SpaDES.tools (>= 2.0.0)",
                   "PredictiveEcology/LandR (>= 1.1.1)",
@@ -1344,6 +1344,13 @@ plottingFn <- function(sim) {
   )
 }
 
+#' Save files
+#'
+#' Generic function using `saveFiles`
+#'
+#' @return For side effect, saved files as per sim
+#'
+#' @param sim A simList
 Save <- function(sim) {
   sim <- saveFiles(sim)
   return(invisible(sim))

DESCRIPTION

@@ -0,0 +1,48 @@
+Package: Biomass.borealDataPrep
+Type: Package
+Title: Biomass_borealDataPrep
+Version: 1.5.7.9002
+Description: paste A data preparation module for parameterizing `Biomass_core` from open data sources, within the Boreal forest of Canada.
+Date: 2024-06-13
+Authors@R: 
+  c(person("Yong", "Luo", email = "[email protected]", role = c("aut")),                
+    person(c("Eliot", "J", "B"), "McIntire", email = "[email protected]", 
+        role = c("aut", "cre")), person(c("Ceres"), "Barros",                            
+        email = "[email protected]", role = c("aut")), person(c("Alex",                
+        "M."), "Chubaty", email = "[email protected]", role = c("aut")))              
+Imports:
+    assertthat,
+    crayon,
+    data.table,
+    dplyr,
+    fasterize,
+    ggplot2,
+    LandR (>= 1.1.1),
+    merTools,
+    pemisc,
+    plyr,
+    rasterVis,
+    reproducible (>= 2.1.0),
+    sf,
+    SpaDES.core (>= 2.1.0),
+    SpaDES.project (>= 0.0.8.9026),
+    SpaDES.tools (>= 2.0.0),
+    terra
+Suggests:
+    knitr,
+    RCurl,
+    rmarkdown,
+    roxygen2,
+    testthat,
+    withr,
+    XML
+Remotes:
+    PredictiveEcology/LandR,
+    PredictiveEcology/pemisc@development,
+    PredictiveEcology/SpaDES.project@development
+Encoding: UTF-8
+License: GPL-3
+VignetteBuilder: knitr, rmarkdown
+ByteCompile: yes
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1

NAMESPACE

@@ -1,5 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
+export(spinUpPartial)
+import(SpaDES.core)
+import(SpaDES.project)
+import(SpaDES.tools)
+import(assertthat)
+import(dplyr)
+import(fasterize)
+import(ggplot2)
+import(pemisc)
+import(plyr)
+import(rasterVis)
+import(reproducible)
+import(sf)
+import(terra)
 importFrom(LandR,asInteger)
 importFrom(LandR,subsetDT)
 importFrom(crayon,cyan)

R/imports.R

@@ -0,0 +1,42 @@
+#' @import assertthat
+NULL
+
+#' @import dplyr
+NULL
+
+#' @import fasterize
+NULL
+
+
+#' @import ggplot2
+NULL
+
+#' @import plyr
+NULL
+
+#' @import rasterVis
+NULL
+
+#' @import sf
+NULL
+
+
+#' @import terra
+NULL
+
+#' @import reproducible
+NULL
+
+#' @import SpaDES.core
+NULL
+
+
+#' @import SpaDES.tools
+NULL
+
+#' @import SpaDES.project
+NULL
+
+#' @import pemisc
+NULL
+

R/updateYoungBiomasses.R

@@ -1,3 +1,5 @@
+#' Update young biomasses
+#'
 #' @param young data.table not unlinke `cohortData`
 #' @param modelBiomass named list with items "mod", "pred", "rsq", "scaledVarsModelB".
 #' @param ... For anything, used for Cache. Not used internally here.
@@ -190,7 +192,7 @@ spinUpPartial <- function(pixelCohortData, speciesEcoregion, maxAge,
   } else {
     modules <- "Biomass_core"
   }
-  
+
   outputs <- data.frame(expand.grid(objectName = "cohortData",
                                     saveTime = unique(seq(times$start, times$end, by = 1)),
                                     eventPriority = 1, fun = "qs::qsave",

tests/test-all.R

@@ -0,0 +1,2 @@
+library(testthat)
+test_check("Biomass.borealDataPrep")