Merge branch 'develop' into fix/docker-pull-arm64

.github/workflows/book.yml

@@ -18,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     container: 
-      image: pecan/depends:R4.1
+      image: pecan/depends:develop-R4.1
 
     steps:
     # checkout source code

.github/workflows/check.yml

@@ -32,7 +32,7 @@ jobs:
       _R_CHECK_SYSTEM_CLOCK_: 0
 
     container: 
-      image: pecan/depends:R${{ inputs.R-version }}
+      image: pecan/depends:develop-R${{ inputs.R-version }}
 
     steps:
     # checkout source code

.github/workflows/ci-weekly.yml

@@ -14,6 +14,7 @@ jobs:
       matrix:
         R:
           - "4.3"
+          - "4.4"
           - "devel"
     uses: ./.github/workflows/test.yml
     with:
@@ -26,6 +27,7 @@ jobs:
       matrix:
         R:
           - "4.3"
+          - "4.4"
           - "devel"
     uses: ./.github/workflows/check.yml
     with:
@@ -39,6 +41,7 @@ jobs:
       matrix:
         R:
           - "4.3"
+          - "4.4"
           - "devel"
     uses: ./.github/workflows/sipnet.yml
     with:

.github/workflows/docker-build-image.yml

@@ -83,11 +83,13 @@ jobs:
           # generate Docker tags based on the following events/attributes
           tags: |
             type=schedule
-            type=ref,event=branch
+            type=ref,event=branch,enable=${{ inputs.r-version == '4.1' }}
+            type=ref,event=branch,suffix=-R${{ inputs.r-version }}
             type=ref,event=pr
-            type=semver,pattern={{version}}
-            type=semver,pattern={{major}}.{{minor}}
-            type=semver,pattern={{major}}
+            type=semver,pattern={{version}},enable=${{ inputs.r-version == '4.1' }}
+            type=semver,pattern={{major}}.{{minor}},enable=${{ inputs.r-version == '4.1' }}
+            type=semver,pattern={{major}},enable=${{ inputs.r-version == '4.1' }}
+            type=semver,pattern={{version}},suffix=-R${{ inputs.r-version }}
 
       # setup docker build
       - name: Set up QEMU

.github/workflows/docker.yml

@@ -22,7 +22,13 @@ on:
           - 4.3
           - 4.4
           - devel
-
+  schedule:
+    # 1:30 AM UTC, different R version each day
+    - cron: '30 1 * * 1' # Rdevel
+    - cron: '30 1 * * 2' # R4.4
+    - cron: '30 1 * * 3' # R4.3
+    - cron: '30 1 * * 4' # R4.2
+    - cron: '30 1 * * 5' # R4.1
 
 jobs:
   # ----------------------------------------------------------------------
@@ -35,9 +41,28 @@ jobs:
   rversion:
     runs-on: ubuntu-latest
     steps:
-       - run: echo "null"
+      - id: mon
+        if: github.event.schedule == '30 1 * * 1'
+        run: echo "R_VERSION=devel" >> "$GITHUB_OUTPUT"
+      - id: tue
+        if: github.event.schedule == '30 1 * * 2'
+        run: echo "R_VERSION=4.4" >> "$GITHUB_OUTPUT"
+      - id: wed
+        if: github.event.schedule == '30 1 * * 3'
+        run: echo "R_VERSION=4.3" >> "$GITHUB_OUTPUT"
+      - id: thu
+        if: github.event.schedule == '30 1 * * 4'
+        run: echo "R_VERSION=4.2" >> "$GITHUB_OUTPUT"
+      - id: fri
+        if: github.event.schedule == '30 1 * * 5'
+        run: echo "R_VERSION=4.1" >> "$GITHUB_OUTPUT"
+      - id: default
+        if: github.event_name != 'schedule'
+        run: echo "R_VERSION=${{ github.event.inputs.r_version || '4.1' }}" >> "$GITHUB_OUTPUT"
     outputs:
-      R_VERSION: ${{ github.event.inputs.r_version || '4.1' }}
+      # Note: "steps.*" seems to mean "all step ids", not "all steps"
+      # If seeing weird results here, check that all steps above have an id set.
+      R_VERSION: ${{ join(steps.*.outputs.R_VERSION, '') }}
 
   # ----------------------------------------------------------------------
   # depends image has all the dependencies installed

.github/workflows/download-met-data.yml

@@ -26,7 +26,7 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     container: 
-      image: pecan/depends:R4.1
+      image: pecan/depends:develop-R4.1
 
     steps:
     # checkout source code

.github/workflows/sipnet.yml

@@ -26,7 +26,7 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     container: 
-      image: pecan/depends:R${{ inputs.R-version }}
+      image: pecan/depends:develop-R${{ inputs.R-version }}
 
     steps:
     # checkout source code

.github/workflows/test.yml

@@ -27,7 +27,7 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     container: 
-      image: pecan/depends:R${{ inputs.R-version }}
+      image: pecan/depends:develop-R${{ inputs.R-version }}
 
     steps:
     # checkout source code

models/linkages/R/model2netcdf.LINKAGES.R

@@ -15,9 +15,11 @@
 model2netcdf.LINKAGES <- function(outdir, sitelat, sitelon, start_date = NULL,
                                   end_date = NULL, pft_names = NULL) {
   # , PFTs) { logger.severe('NOT IMPLEMENTED')
-
+
+  ## Create a new enviroment 
+  linkages_env <- new.env()
   ### Read in model output in linkages format
-  load(file.path(outdir, "linkages.out.Rdata"))
+  load(file.path(outdir, "linkages.out.Rdata"),envir = linkages_env)
   # linkages.output.dims <- dim(linkages.output)
 
   ### Determine number of years and output timestep
@@ -47,21 +49,21 @@ model2netcdf.LINKAGES <- function(outdir, sitelat, sitelon, start_date = NULL,
     ## Setup outputs for netCDF file in appropriate units
     output <- list()
     ## standard variables: Carbon Pools
-    output[[1]]  <- ag.biomass[y, ]  # Above Ground Biomass in kgC/m2
-    output[[2]]  <- ag.biomass[y, ]  # Total Live Biomass in kgC/m2 (no distinction from AGB in linkages)
-    output[[3]]  <- total.soil.carbon[y, ]  # TotSoilCarb in kgC/m2
-    output[[4]]  <- c(ag.biomass[y, ], total.soil.carbon[y, ], leaf.litter[y, ], area[y, ])  # Carb Pools in kgC/m2
+    output[[1]]  <- linkages_env$ag.biomass[y, ]  # Above Ground Biomass in kgC/m2
+    output[[2]]  <- linkages_env$ag.biomass[y, ]  # Total Live Biomass in kgC/m2 (no distinction from AGB in linkages)
+    output[[3]]  <- linkages_env$total.soil.carbon[y, ]  # TotSoilCarb in kgC/m2
+    output[[4]]  <- c(linkages_env$ag.biomass[y, ], linkages_env$total.soil.carbon[y, ], linkages_env$leaf.litter[y, ], linkages_env$area[y, ])  # Carb Pools in kgC/m2
     output[[5]]  <- c("AGB", "Soil Organic Matter", "Leaf Litter", "LAI")  # poolname
-    output[[6]]  <- ag.npp[y, ]  # GWBI = NPP in linkages
-    output[[7]]  <- hetero.resp[y, ]  # HeteroResp in kgC/m^2/s
-    output[[8]]  <- ag.npp[y, ]  # NPP = GWBI in linkages
-    output[[9]]  <- nee[y, ]  # NEE #possibly questionable
-    output[[10]] <- et[y, ]  # Evap in kg/m^2/s
-    output[[11]] <- agb.pft[, y, ]
-    output[[12]] <- f.comp[, y]
-    output[[13]] <- area[y, ]  #LAI
-    output[[14]] <- water[y, ]  #soil moisture
-    output[[15]] <- abvgroundwood.biomass[y,] #AbvGroundWood just wood no leaves
+    output[[6]]  <- linkages_env$ag.npp[y, ]  # GWBI = NPP in linkages
+    output[[7]]  <- linkages_env$hetero.resp[y, ]  # HeteroResp in kgC/m^2/s
+    output[[8]]  <- linkages_env$ag.npp[y, ]  # NPP = GWBI in linkages
+    output[[9]]  <- linkages_env$nee[y, ]  # NEE #possibly questionable
+    output[[10]] <- linkages_env$et[y, ]  # Evap in kg/m^2/s
+    output[[11]] <- linkages_env$agb.pft[, y, ]
+    output[[12]] <- linkages_env$f.comp[, y]
+    output[[13]] <- linkages_env$area[y, ]  #LAI
+    output[[14]] <- linkages_env$water[y, ]  #soil moisture
+    output[[15]] <- linkages_env$abvgroundwood.biomass[y,] #AbvGroundWood just wood no leaves
     output[[16]] <- seq_along(pft_names) 
 
     # ******************** Declare netCDF variables ********************#
@@ -75,7 +77,7 @@ model2netcdf.LINKAGES <- function(outdir, sitelat, sitelon, start_date = NULL,
     dim.cpools <- ncdf4::ncdim_def("cpools", "", vals = 1:4, longname = "Carbon Pools")
     dim.cpools1 <- ncdf4::ncdim_def("cpools", "", vals = 1:4, longname = "Carbon Pools", create_dimvar = FALSE)
     #dim.pfts <- ncdim_def("pfts", "", vals = 1:nrow(agb.pft), longname = "PFTs", create_dimvar = FALSE)
-    dim.pfts <- ncdf4::ncdim_def(name = "pft", units = "unitless", vals = 1:length(agb.pft[, 1, 1]), longname = "Plant Functional Type", unlim = TRUE)
+    dim.pfts <- ncdf4::ncdim_def(name = "pft", units = "unitless", vals = 1:length(linkages_env$agb.pft[, 1, 1]), longname = "Plant Functional Type", unlim = TRUE)
 
 
     for (i in seq_along(output)) {

models/linkages/R/write_restart.LINKAGES.R

@@ -134,16 +134,21 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time,
   }
   print(paste0("runid = ", runid))
 
+  # Create a new enviroment
+  linkages_env <- new.env()
   # load output
-  load(outfile)
+  load(outfile, envir = linkages_env)
 
-  ntrees <- ntrees.kill[, ncol(ntrees.kill), 1]  # number of trees
+  ntrees <- linkages_env$ntrees.kill[, ncol(linkages_env$ntrees.kill), 1]  # number of trees
 
   if(sum(ntrees)==0) {
     #reloads spin up if theres nothing in the output file
     print('No survivors. Reusing spinup.')
-    load(file.path(outdir, runid,list.files(file.path(outdir, runid))[grep(list.files(file.path(outdir, runid)),pattern='linkages')][1]))
-    ntrees <- ntrees.kill[, ncol(ntrees.kill), 1]  # number of trees
+    # new enviroment for spin up data 
+    linkages_env_spinup <- new.env()
+    spinup_file <- file.path(outdir, runid,list.files(file.path(outdir, runid))[grep(list.files(file.path(outdir, runid)),pattern='linkages')][1])
+    load(spinup_file, envir = linkages_env_spinup)
+    ntrees <- linkages_env_spinup$ntrees.kill[, ncol(linkages_env_spinup$ntrees.kill), 1]  # number of trees
 
   }
 
@@ -152,11 +157,11 @@ write_restart.LINKAGES <- function(outdir, runid, start.time, stop.time,
   tyl    <- tyl
   C.mat  <- C.mat
 
-  nogro  <- as.vector(nogro.save[, ncol(nogro.save), 1])  ## no growth indicator
+  nogro  <- as.vector(linkages_env$nogro.save[, ncol(linkages_env$nogro.save), 1])  ## no growth indicator
   ksprt  <- matrix(0, 1, nspec)  ## kill sprout indicator ## LOOK INTO THIS
-  iage   <- as.vector(iage.save[, ncol(iage.save), 1])  # individual age
+  iage   <- as.vector(linkages_env$iage.save[, ncol(linkages_env$iage.save), 1])  # individual age
 
-  dbh    <- as.vector(dbh.save[, ncol(dbh.save), 1])
+  dbh    <- as.vector(linkages_env$dbh.save[, ncol(linkages_env$dbh.save), 1])
 
   n.index <- c(rep(1, ntrees[1]))
   for (i in 2:length(settings$pfts)) {

models/linkages/tests/Rcheck_reference.log

@@ -50,37 +50,7 @@ Suggests or Enhances not in mainstream repositories:
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘ag.biomass’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘total.soil.carbon’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘leaf.litter’
-model2netcdf.LINKAGES: no visible binding for global variable ‘area’
-model2netcdf.LINKAGES: no visible binding for global variable ‘ag.npp’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘hetero.resp’
-model2netcdf.LINKAGES: no visible binding for global variable ‘nee’
-model2netcdf.LINKAGES: no visible binding for global variable ‘et’
-model2netcdf.LINKAGES: no visible binding for global variable ‘agb.pft’
-model2netcdf.LINKAGES: no visible binding for global variable ‘f.comp’
-model2netcdf.LINKAGES: no visible binding for global variable ‘water’
-model2netcdf.LINKAGES: no visible binding for global variable
-  ‘abvgroundwood.biomass’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘ntrees.kill’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘nogro.save’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘iage.save’
-write_restart.LINKAGES: no visible binding for global variable
-  ‘dbh.save’
-Undefined global functions or variables:
-  abvgroundwood.biomass ag.biomass ag.npp agb.pft area
-  db.close db.open db.query dbh.save et f.comp
-  hetero.resp iage.save leaf.litter nee nogro.save
-  ntrees.kill total.soil.carbon water
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK

modules/benchmark/DESCRIPTION

@@ -4,19 +4,23 @@ Title: PEcAn Functions Used for Benchmarking
 Version: 1.7.3.9000
 Authors@R: c(person("Mike", "Dietze", role = c("aut", "cre"),
                      email = "dietze@bu.edu"),
+             person("Betsy", "Cowdery", role = c("aut"),
+                     email = "emcowdery@gmail.com"),
              person("David", "LeBauer", role = c("aut"),
-                     email = "dlebauer@email.arizona.edu"),
+                     email = "dlebauer@gmail.com"),
              person("Rob", "Kooper", role = c("aut"),
                      email = "kooper@illinois.edu"),
              person("Toni", "Viskari", role = c("aut")),
              person("University of Illinois, NCSA", role = c("cph")))
-Author: Michael Dietze, David LeBauer, Rob Kooper, Toni Viskari
+Author: Michael Dietze, Betsy Cowdery, David LeBauer, Rob Kooper, Toni Viskari
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PEcAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
+    efficacy of scientific investigation. The PEcAn.benchmark package provides 
+    utilities for comparing models and data, including a suite of statistical 
+    metrics and plots.
 Imports:
     dplyr,
     ggplot2,