resolved conflict

Merge branch 'develop' of https://github.com/JoshuaPloshay/pecan into develop

# Conflicts:
#	modules/assim.sequential/R/downscale_function.R

CHANGELOG.md

@@ -47,6 +47,8 @@ see if you need to change any of these:
 - Added the new feature of the block-based SDA workflow, which supports the parallel computation.
 - Added new SDA workflow for the 342 North America anchor sites.
 - Added new feature of preparing initial conditions for MODIS LAI, AGB, ISCN SOC, and soil moisture across NA anchor sites.
+- Added GEDI AGB preparation workflow.
+- Added new feature of downloading datasets from the NASA DAAC ORNL database.
 
 ### Fixed
 

CONTRIBUTING.md

@@ -10,7 +10,7 @@ New functionality is typically directed toward modules to provide a slimmer PEcA
 Generally, new model should be added to the models folder and new modules should be added to the modules folder.
 Exceptions include code that is reused in many models or modules and wrapper functions that call specific implementations in models; these can be placed in the core packages.
 
-If you are unsure of whether your contribution should be implemented as a model, module or part of PEcAn Core, you may visit [Chat Room](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLWEzOTM1ZjhmYWUxNzYwYzkxMWVlODAyZWQwYjliYzA0MDA0MjE4YmMyOTFhMjYyMjYzN2FjODE4N2Y4YWFhZmQ) or ask on the pecan-develop mailing list for advice.
+If you are unsure of whether your contribution should be implemented as a model, module or part of PEcAn Core, you may join our [Slack Channel](https://join.slack.com/t/pecanproject/shared_invite/enQtMzkyODUyMjQyNTgzLWEzOTM1ZjhmYWUxNzYwYzkxMWVlODAyZWQwYjliYzA0MDA0MjE4YmMyOTFhMjYyMjYzN2FjODE4N2Y4YWFhZmQ).
 
 ## Creating Issues
 

Makefile

@@ -46,7 +46,7 @@ ALL_PKGS_D := $(BASE_D) $(MODULES_D) $(MODELS_D)
 
 SETROPTIONS := "options(Ncpus = ${NCPUS})"
 
-EXPECTED_ROXYGEN_VERSION := 7.2.3
+EXPECTED_ROXYGEN_VERSION := 7.3.1
 INSTALLED_ROXYGEN_VERSION := $(shell Rscript \
 	-e "if (requireNamespace('roxygen2', quietly = TRUE)) {" \
 	-e   "cat(as.character(packageVersion('roxygen2')))" \
@@ -152,11 +152,11 @@ clean:
 .install/roxygen2: | .install .install/devtools
 	+ ./scripts/time.sh "roxygen2 ${1}" Rscript -e ${SETROPTIONS} \
 		-e "if (!requireNamespace('roxygen2', quietly = TRUE)" \
-		-e "    || packageVersion('roxygen2') != '7.2.3') {" \
+		-e "    || packageVersion('roxygen2') != '"${EXPECTED_ROXYGEN_VERSION}"') {" \
 		-e "  cran <- c(getOption('repos'), 'cloud.r-project.org')" \
-		-e "  remotes::install_version('roxygen2', '7.2.3', repos = cran, upgrade = FALSE)" \
+		-e "  remotes::install_version('roxygen2', '"${EXPECTED_ROXYGEN_VERSION}"', repos = cran, upgrade = FALSE)" \
 		-e "}"
-	$(eval INSTALLED_ROXYGEN_VERSION := 7.2.3)
+	$(eval INSTALLED_ROXYGEN_VERSION := ${EXPECTED_ROXYGEN_VERSION})
 	echo `date` > $@
 
 .install/testthat: | .install

Makefile.depends

@@ -32,7 +32,7 @@ $(call depends,modules/assim.batch): | .install/base/db .install/base/logger .in
 $(call depends,modules/assim.sequential): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/base/workflow .install/modules/benchmark .install/modules/data.land .install/modules/data.remote .install/modules/uncertainty
 $(call depends,modules/benchmark): | .install/base/db .install/base/logger .install/base/settings .install/base/utils .install/modules/data.land
 $(call depends,modules/data.atmosphere): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils
-$(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark .install/modules/data.atmosphere
+$(call depends,modules/data.land): | .install/base/db .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/base/visualization .install/modules/benchmark
 $(call depends,modules/data.remote): | .install/base/db .install/base/logger .install/base/remote .install/base/utils
 $(call depends,modules/meta.analysis): | .install/base/db .install/base/logger .install/base/settings .install/base/utils
 $(call depends,modules/priors): | .install/base/logger .install/base/visualization .install/modules/meta.analysis

base/all/DESCRIPTION

@@ -79,4 +79,4 @@ Copyright: Authors
 LazyData: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

base/db/DESCRIPTION

@@ -81,4 +81,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

base/logger/DESCRIPTION

@@ -30,5 +30,5 @@ Suggests:
     withr
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

base/qaqc/DESCRIPTION

@@ -38,4 +38,4 @@ LazyData: FALSE
 Encoding: UTF-8
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

base/remote/DESCRIPTION

@@ -35,4 +35,4 @@ License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

base/settings/DESCRIPTION

@@ -29,5 +29,5 @@ Suggests:
     testthat (>= 2.0.0),
     withr
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

base/utils/DESCRIPTION

@@ -58,5 +58,5 @@ License: BSD_3_clause + file LICENSE
 Copyright: Authors
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

base/utils/R/help.R

@@ -31,7 +31,6 @@
 ##'
 ##' Current development is focused on developing PEcAn into a real-time data assimilation and forecasting system. This system will provide a detailed analysis of the past and present ecosystem functioning that seamlessly transitions into forecasts.
 ##'
-##' @docType package
 ##' @name PEcAn
 ##' @aliases PECAn pecan package-pecan
-NULL
+"_PACKAGE"

base/visualization/DESCRIPTION

@@ -50,5 +50,5 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

base/workflow/DESCRIPTION

@@ -48,4 +48,4 @@ Suggests:
     withr
 Copyright: Authors
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

base/workflow/R/do_conversions.R

@@ -73,6 +73,13 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
       ## which is done locally in rundir and then rsync'ed to remote
       ## rather than having a model-format soils file that is processed remotely
     }
+
+    # Phenology data extraction
+    if(input.tag == "leaf_phenology" && is.null(input$path)){
+      #settings$run$inputs[[i]]$path <- PEcAn.data.remote::extract_phenology_MODIS(site_info,start_date,end_date,outdir,run_parallel = TRUE,ncores = NULL)
+      needsave <- TRUE
+    }
+
     # met conversion
 
     if (input.tag == "met") {

book_source/02_demos_tutorials_workflows/05_developer_workflows/03_coding_practices/04-roxygen.Rmd

@@ -70,3 +70,24 @@ PEcAn's automated testing (Travis) will check if any documentation is out of dat
 These files were changed by the build process:
 {...}
 ```
+
+
+
+#### Updating to a new Roxygen version
+
+For consistency across packages and machines, all PEcAn developers need to compile documentation with the same version of Roxygen. Roxygen itself will check for this and refuse to rebuild a package that was last touched by a newer version of Roxygen, but the warning it gives is very quiet and easy to miss. We take a louder approach by hardcoding the expected Roxygen version into PEcAn's Makefile and throwing a build failure if the installed Roxygen is not an exact match.
+
+When it is time for everyone to update to a newer Roxygen, follow the same procedure we used when updating from 7.2.3 to 7.3.1, replacing version strings as appropriate:
+
+* Before starting, work with the team to merge/close as many existing PRs as feasible -- this process touches a lot of files and is likely to create merge conflicts in other PRs.
+* Edit the Makefile to change `EXPECTED_ROXYGEN_VERSION := 7.2.3` to `EXPECTED_ROXYGEN_VERSION := 7.3.1`.
+* Run `make clean && make document` to be sure Roxygen has been run on all packages.
+* Check the console output for warnings from Roxygen, and fix them as needed. New versions often get pickier about formatting issues that used to be considered minor.
+* Run `./scripts/generate_dependencies.R` to update the version of Roxygen recorded as a Docker dependency.
+* Grep the PEcAn folder for the string `7.3.1` to make sure no references were missed.
+  - e.g. this time I found  a remaining `RoxygenNote: 7.2.3` in models/cable/DESCRIPTION -- Make currently skips cable, so I redocumented it manually.
+* Review all changes.
+  - The changes should mostly just consist of updated `RoxygenNote:` lines in all the DESCRIPTION files.
+  - In all cases but extra-double-specially if any NAMESPACE files change, make sure you understand what happened rather than blindly committing the changes. Usually the new version is an improvement, but this is the time to check.
+* Once all looks good, commit and push.
+* Make a loud announcement, e.g. on Slack, to tell all developers to update roxygen2 on their machines as soon as the PR is merged.

book_source/03_topical_pages/04_R_workflow.Rmd

@@ -121,6 +121,12 @@ The main script that handles Met Processing, is [`met.process`](https://github.c
 
 ### Converting from PEcAn standard to model-specific format {#workflow-met-model}
 
+## Input phenological Data {#workflow-input-phenology}
+
+To enable the use of MODIS phenology data (MODIS Land Cover Dynamics (MCD12Q2)) to update the phenological parameters (leaf-on date) and (leaf-off date) at each restart timepoint: 
+ 1. Generate the phenological parameter CSV file by running `PEcAn.data.remote::extract_phenology_MODIS`.
+ 2. Provide the generated phenological parameter CSV file to `settings$run$inputs$leaf_phenology$path`.
+
 ## Traits {#workflow-traits}
 
 (TODO: Under construction)
@@ -130,6 +136,7 @@ The main script that handles Met Processing, is [`met.process`](https://github.c
 (TODO: Under construction)
 
 ## Model Configuration {#workflow-modelconfig}
+To enable the state data assimilation with sub-annual data, default `conflict` in `model2netcdf` should be `TRUE`. 
 
 (TODO: Under construction)
 

docker/depends/pecan_deps_from_github.txt

@@ -7,3 +7,4 @@ ropensci/geonames
 ropensci/nneo
 SticsRPacks/SticsOnR
 SticsRPacks/SticsRFiles
+VangiElia/GEDI4R

docker/depends/pecan_package_dependencies.csv

@@ -75,9 +75,11 @@
 "future","*","modules/data.atmosphere","Suggests",FALSE
 "future","*","modules/data.land","Imports",FALSE
 "future","*","modules/data.remote","Imports",FALSE
+"GEDI4R","*","modules/data.remote","Suggests",FALSE
 "geonames","> 0.998","modules/data.atmosphere","Imports",FALSE
 "getPass","*","base/remote","Suggests",FALSE
 "getPass","*","modules/data.land","Suggests",FALSE
+"getPass","*","modules/data.remote","Suggests",FALSE
 "ggmcmc","*","modules/meta.analysis","Suggests",FALSE
 "ggplot2","*","base/utils","Suggests",FALSE
 "ggplot2","*","base/visualization","Imports",FALSE
@@ -103,6 +105,7 @@
 "grDevices","*","modules/allometry","Imports",FALSE
 "grDevices","*","modules/assim.batch","Imports",FALSE
 "grDevices","*","modules/benchmark","Imports",FALSE
+"grDevices","*","modules/data.remote","Suggests",FALSE
 "grid","*","base/visualization","Suggests",FALSE
 "gridExtra","*","modules/assim.sequential","Suggests",FALSE
 "gridExtra","*","modules/benchmark","Imports",FALSE
@@ -112,10 +115,12 @@
 "httr","*","base/remote","Imports",FALSE
 "httr","*","modules/data.atmosphere","Imports",FALSE
 "httr","*","modules/data.land","Imports",FALSE
+"httr","*","modules/data.remote","Suggests",FALSE
 "IDPmisc","*","modules/assim.batch","Imports",FALSE
 "jsonlite","*","base/remote","Imports",FALSE
 "jsonlite","*","models/stics","Imports",FALSE
 "jsonlite","*","modules/data.atmosphere","Imports",FALSE
+"jsonlite","*","modules/data.remote","Suggests",FALSE
 "knitr",">= 1.42","base/db","Suggests",FALSE
 "knitr",">= 1.42","base/qaqc","Suggests",FALSE
 "knitr",">= 1.42","modules/allometry","Suggests",FALSE
@@ -256,7 +261,6 @@
 "PEcAn.data.atmosphere","*","models/maespa","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/preles","Imports",TRUE
 "PEcAn.data.atmosphere","*","models/sipnet","Depends",TRUE
-"PEcAn.data.atmosphere","*","modules/data.land","Imports",TRUE
 "PEcAn.data.land","*","base/all","Depends",TRUE
 "PEcAn.data.land","*","base/workflow","Imports",TRUE
 "PEcAn.data.land","*","models/biocro","Imports",TRUE
@@ -471,6 +475,7 @@
 "rlang","*","modules/assim.sequential","Imports",FALSE
 "rlang","*","modules/benchmark","Imports",FALSE
 "rlang","*","modules/data.land","Imports",FALSE
+"rlang","*","modules/data.remote","Imports",FALSE
 "rlang","*","modules/uncertainty","Imports",FALSE
 "rlang",">= 0.2.0","modules/data.atmosphere","Imports",FALSE
 "rlist","*","modules/assim.sequential","Suggests",FALSE
@@ -480,48 +485,48 @@
 "rmarkdown",">= 2.19","modules/assim.batch","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/meta.analysis","Suggests",FALSE
 "rmarkdown",">= 2.19","modules/photosynthesis","Suggests",FALSE
-"roxygen2","== 7.2.3","base/all","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/db","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/logger","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/qaqc","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/remote","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/settings","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/utils","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/visualization","Roxygen",FALSE
-"roxygen2","== 7.2.3","base/workflow","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/basgra","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/biocro","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/cable","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/clm45","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/dalec","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/dvmdostem","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/ed","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/fates","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/gday","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/jules","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/ldndc","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/linkages","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/lpjguess","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/maat","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/maespa","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/preles","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/sibcasa","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/sipnet","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/stics","Roxygen",FALSE
-"roxygen2","== 7.2.3","models/template","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/allometry","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/assim.batch","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/assim.sequential","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/benchmark","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/data.atmosphere","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/data.land","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/data.remote","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/emulator","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/meta.analysis","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/photosynthesis","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/priors","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/rtm","Roxygen",FALSE
-"roxygen2","== 7.2.3","modules/uncertainty","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/all","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/db","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/logger","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/qaqc","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/remote","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/settings","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/utils","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/visualization","Roxygen",FALSE
+"roxygen2","== 7.3.1","base/workflow","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/basgra","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/biocro","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/cable","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/clm45","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/dalec","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/dvmdostem","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/ed","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/fates","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/gday","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/jules","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/ldndc","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/linkages","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/lpjguess","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/maat","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/maespa","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/preles","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/sibcasa","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/sipnet","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/stics","Roxygen",FALSE
+"roxygen2","== 7.3.1","models/template","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/allometry","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/assim.batch","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/assim.sequential","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/benchmark","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/data.atmosphere","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/data.land","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/data.remote","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/emulator","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/meta.analysis","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/photosynthesis","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/priors","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/rtm","Roxygen",FALSE
+"roxygen2","== 7.3.1","modules/uncertainty","Roxygen",FALSE
 "RPostgres","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","base/db","Suggests",FALSE
 "RPostgreSQL","*","models/biocro","Suggests",FALSE
@@ -531,6 +536,7 @@
 "sf","*","modules/assim.sequential","Suggests",FALSE
 "sf","*","modules/data.atmosphere","Imports",FALSE
 "sf","*","modules/data.land","Imports",FALSE
+"sf","*","modules/data.remote","Suggests",FALSE
 "SimilarityMeasures","*","modules/benchmark","Imports",FALSE
 "sirt","*","modules/data.land","Imports",FALSE
 "sp","*","base/visualization","Suggests",FALSE
@@ -631,6 +637,7 @@
 "utils","*","modules/assim.batch","Imports",FALSE
 "utils","*","modules/assim.sequential","Suggests",FALSE
 "utils","*","modules/benchmark","Imports",FALSE
+"utils","*","modules/data.remote","Suggests",FALSE
 "utils","*","modules/photosynthesis","Imports",FALSE
 "vdiffr",">= 1.0.2","base/qaqc","Suggests",FALSE
 "withr","*","base/db","Suggests",FALSE

models/basgra/DESCRIPTION

@@ -24,4 +24,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

models/biocro/DESCRIPTION

@@ -39,4 +39,4 @@ Copyright: Energy Biosciences Institute, Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

models/cable/DESCRIPTION

@@ -22,4 +22,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

models/clm45/DESCRIPTION

@@ -26,4 +26,4 @@ Copyright: Authors
 LazyLoad: yes
 LazyData: FALSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1