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Merge branch 'develop' into model-run-workflow
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meetagrawal09 authored Sep 25, 2024
2 parents 2a3d512 + 5f7bdfe commit 3fa4084
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6 changes: 3 additions & 3 deletions Makefile.depends
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Expand Up @@ -18,13 +18,13 @@ $(call depends,models/fates): | .install/base/logger .install/base/remote .insta
$(call depends,models/gday): | .install/base/logger .install/base/remote .install/base/utils
$(call depends,models/jules): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
$(call depends,models/ldndc): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
$(call depends,models/linkages): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
$(call depends,models/linkages): | .install/base/db .install/base/logger .install/base/remote .install/base/utils .install/modules/data.land
$(call depends,models/lpjguess): | .install/base/logger .install/base/remote .install/base/utils
$(call depends,models/maat): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils .install/modules/data.atmosphere
$(call depends,models/maespa): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
$(call depends,models/preles): | .install/base/logger .install/base/utils .install/modules/data.atmosphere
$(call depends,models/sibcasa): | .install/base/logger .install/base/utils
$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere
$(call depends,models/sibcasa): | .install/base/logger
$(call depends,models/sipnet): | .install/base/logger .install/base/remote .install/base/utils .install/modules/data.atmosphere .install/modules/data.land
$(call depends,models/stics): | .install/base/logger .install/base/remote .install/base/settings .install/base/utils
$(call depends,models/template): | .install/base/db .install/base/logger .install/base/utils
$(call depends,modules/allometry): | .install/base/db
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3 changes: 1 addition & 2 deletions base/db/tests/Rcheck_reference.log
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Expand Up @@ -62,8 +62,7 @@ The Date field is over a month old.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
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4 changes: 0 additions & 4 deletions base/qaqc/tests/Rcheck_reference.log
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Expand Up @@ -21,10 +21,6 @@
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Authors@R field gives no person with name and roles.
Authors@R field gives no person with maintainer role, valid email
address and non-empty name.
License stub is invalid DCF.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘README.Rmd’
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3 changes: 1 addition & 2 deletions base/remote/tests/Rcheck_reference.log
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,7 @@
* checking whether package ‘PEcAn.remote’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
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3 changes: 1 addition & 2 deletions base/settings/tests/Rcheck_reference.log
Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,7 @@ The Date field is over a month old.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘examples’
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3 changes: 1 addition & 2 deletions base/visualization/tests/Rcheck_reference.log
Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,7 @@ The Date field is over a month old.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
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3 changes: 0 additions & 3 deletions base/workflow/DESCRIPTION
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Expand Up @@ -17,9 +17,6 @@ Authors@R: c(person("Mike", "Dietze", role = c("aut"),
person("Shawn", "Serbin", role = c("aut"),
email = "[email protected]"),
person("University of Illinois, NCSA", role = c("cph")))
Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
Maintainer: David LeBauer <[email protected]>
Description: The Predictive Ecosystem Carbon Analyzer
(PEcAn) is a scientific workflow management tool that
is designed to simplify the management of model
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10 changes: 1 addition & 9 deletions base/workflow/tests/Rcheck_reference.log
Original file line number Diff line number Diff line change
Expand Up @@ -62,15 +62,7 @@ The Date field is over a month old.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
Author: ‘David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin’
Authors@R: ‘Mike Dietze [aut], David LeBauer [aut, cre], Xiaohui Feng [aut], Dan Wang [aut], Carl Davidson [aut], Rob Kooper [aut], Shawn Serbin [aut], University of Illinois, NCSA [cph]’

Maintainer field differs from that derived from Authors@R
Maintainer: ‘David LeBauer <[email protected]>’
Authors@R: ‘David LeBauer <[email protected]>’
License stub is invalid DCF.
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
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1 change: 1 addition & 0 deletions docker/depends/pecan_deps_from_github.txt
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ araiho/linkages_package
chuhousen/amerifluxr
ebimodeling/[email protected]
MikkoPeltoniemi/Rpreles
RemkoDuursma/Maeswrap
ropensci/geonames
ropensci/nneo
SticsRPacks/SticsOnR
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21 changes: 15 additions & 6 deletions docker/depends/pecan_package_dependencies.csv
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
"dplyr","*","models/biocro","Imports",FALSE
"dplyr","*","models/ed","Imports",FALSE
"dplyr","*","models/ldndc","Imports",FALSE
"dplyr","*","models/sipnet","Imports",FALSE
"dplyr","*","models/stics","Imports",FALSE
"dplyr","*","modules/assim.sequential","Imports",FALSE
"dplyr","*","modules/benchmark","Imports",FALSE
Expand Down Expand Up @@ -123,6 +124,9 @@
"jsonlite","*","modules/data.remote","Suggests",FALSE
"keras3",">= 1.0.0","modules/assim.sequential","Suggests",FALSE
"knitr","*","base/visualization","Suggests",FALSE
"knitr","*","models/biocro","Suggests",FALSE
"knitr","*","models/ed","Suggests",FALSE
"knitr","*","models/maat","Suggests",FALSE
"knitr","*","modules/data.atmosphere","Suggests",FALSE
"knitr","*","modules/priors","Suggests",FALSE
"knitr",">= 1.42","base/db","Suggests",FALSE
Expand Down Expand Up @@ -262,16 +266,17 @@
"PEcAn.data.atmosphere","*","models/ed","Imports",TRUE
"PEcAn.data.atmosphere","*","models/jules","Imports",TRUE
"PEcAn.data.atmosphere","*","models/ldndc","Imports",TRUE
"PEcAn.data.atmosphere","*","models/linkages","Imports",TRUE
"PEcAn.data.atmosphere","*","models/maat","Imports",TRUE
"PEcAn.data.atmosphere","*","models/maespa","Imports",TRUE
"PEcAn.data.atmosphere","*","models/preles","Imports",TRUE
"PEcAn.data.atmosphere","*","models/sipnet","Depends",TRUE
"PEcAn.data.atmosphere","*","models/sipnet","Imports",TRUE
"PEcAn.data.land","*","base/all","Depends",TRUE
"PEcAn.data.land","*","base/workflow","Imports",TRUE
"PEcAn.data.land","*","models/biocro","Imports",TRUE
"PEcAn.data.land","*","models/ed","Imports",TRUE
"PEcAn.data.land","*","models/ldndc","Imports",TRUE
"PEcAn.data.land","*","models/linkages","Imports",TRUE
"PEcAn.data.land","*","models/sipnet","Imports",TRUE
"PEcAn.data.land","*","modules/assim.sequential","Suggests",TRUE
"PEcAn.data.land","*","modules/benchmark","Suggests",TRUE
"PEcAn.data.remote","*","base/all","Depends",TRUE
Expand All @@ -281,6 +286,7 @@
"PEcAn.DB","*","base/settings","Imports",TRUE
"PEcAn.DB","*","base/workflow","Imports",TRUE
"PEcAn.DB","*","models/biocro","Suggests",TRUE
"PEcAn.DB","*","models/linkages","Imports",TRUE
"PEcAn.DB","*","models/template","Imports",TRUE
"PEcAn.DB","*","modules/allometry","Imports",TRUE
"PEcAn.DB","*","modules/assim.batch","Imports",TRUE
Expand Down Expand Up @@ -395,11 +401,10 @@
"PEcAn.utils","*","models/fates","Imports",TRUE
"PEcAn.utils","*","models/gday","Depends",TRUE
"PEcAn.utils","*","models/jules","Imports",TRUE
"PEcAn.utils","*","models/linkages","Depends",TRUE
"PEcAn.utils","*","models/linkages","Imports",TRUE
"PEcAn.utils","*","models/lpjguess","Imports",TRUE
"PEcAn.utils","*","models/maat","Imports",TRUE
"PEcAn.utils","*","models/maespa","Imports",TRUE
"PEcAn.utils","*","models/preles","Depends",TRUE
"PEcAn.utils","*","models/preles","Imports",TRUE
"PEcAn.utils","*","models/sipnet","Imports",TRUE
"PEcAn.utils","*","modules/assim.batch","Imports",TRUE
Expand All @@ -416,7 +421,6 @@
"PEcAn.utils",">= 1.4.8","models/cable","Imports",TRUE
"PEcAn.utils",">= 1.4.8","models/dvmdostem","Imports",TRUE
"PEcAn.utils",">= 1.4.8","models/ldndc","Imports",TRUE
"PEcAn.utils",">= 1.4.8","models/sibcasa","Imports",TRUE
"PEcAn.utils",">= 1.4.8","models/stics","Imports",TRUE
"PEcAn.utils",">= 1.4.8","models/template","Imports",TRUE
"PEcAn.visualization","*","modules/assim.sequential","Suggests",TRUE
Expand Down Expand Up @@ -488,6 +492,9 @@
"rlang",">= 0.2.0","modules/data.atmosphere","Imports",FALSE
"rlist","*","modules/assim.sequential","Suggests",FALSE
"rmarkdown","*","base/visualization","Suggests",FALSE
"rmarkdown","*","models/biocro","Suggests",FALSE
"rmarkdown","*","models/ed","Suggests",FALSE
"rmarkdown","*","models/maat","Suggests",FALSE
"rmarkdown","*","modules/priors","Suggests",FALSE
"rmarkdown","*","modules/rtm","Suggests",FALSE
"rmarkdown",">= 2.19","base/db","Suggests",FALSE
Expand Down Expand Up @@ -556,6 +563,7 @@
"sp","*","modules/data.land","Imports",FALSE
"sp","*","modules/data.remote","Imports",FALSE
"stats","*","base/qaqc","Imports",FALSE
"stats","*","models/sipnet","Imports",FALSE
"stats","*","modules/allometry","Imports",FALSE
"stats","*","modules/assim.batch","Imports",FALSE
"stats","*","modules/assim.sequential","Suggests",FALSE
Expand Down Expand Up @@ -613,9 +621,9 @@
"testthat",">= 2.0.0","base/utils","Suggests",FALSE
"testthat",">= 2.0.0","models/biocro","Suggests",FALSE
"testthat",">= 2.0.0","modules/benchmark","Suggests",FALSE
"testthat",">= 2.0.0","modules/data.atmosphere","Suggests",FALSE
"testthat",">= 3.0.0","models/sibcasa","Suggests",FALSE
"testthat",">= 3.0.4","base/qaqc","Suggests",FALSE
"testthat",">= 3.1.7","modules/data.atmosphere","Suggests",FALSE
"tibble","*","base/db","Imports",FALSE
"tibble","*","models/ed","Imports",FALSE
"tibble","*","models/fates","Imports",FALSE
Expand Down Expand Up @@ -645,6 +653,7 @@
"utils","*","base/all","Imports",FALSE
"utils","*","base/logger","Imports",FALSE
"utils","*","models/ed","Imports",FALSE
"utils","*","models/linkages","Imports",FALSE
"utils","*","modules/allometry","Imports",FALSE
"utils","*","modules/assim.batch","Imports",FALSE
"utils","*","modules/assim.sequential","Suggests",FALSE
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2 changes: 2 additions & 0 deletions models/biocro/.Rbuildignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
Dockerfile
model_info.json
5 changes: 3 additions & 2 deletions models/biocro/DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -27,15 +27,16 @@ Imports:
rlang
Suggests:
BioCro,
knitr,
testthat (>= 2.0.0),
mockery (>= 0.3.0),
PEcAn.DB,
rmarkdown,
RPostgreSQL
Remotes:
github::ebimodeling/[email protected]
License: BSD_3_clause + file LICENSE
Copyright: Energy Biosciences Institute, Authors
LazyLoad: yes
LazyData: FALSE
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.3.2
2 changes: 1 addition & 1 deletion models/biocro/R/get_biocro_defaults.R
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ from_bc <- function(dfname){
#' *_initial_values, *_parameters, *_modules
#'
#' @param genus Name of the genus (or really any string BioCro uses as a *_parameters prefix)
#' @return a list in the format expected by \code{BioCro::\link[BioCro:Gro]{Gro}},
#' @return a list in the format expected by `BioCro::Gro()`,
#' containing four lists named `type`, `initial_values`, `parameters`, and `modules`,
#' or NULL if genus not found
#' @export
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52 changes: 26 additions & 26 deletions models/biocro/R/met2model.BIOCRO.R
Original file line number Diff line number Diff line change
Expand Up @@ -107,37 +107,37 @@ met2model.BIOCRO <- function(in.path, in.prefix, outfolder, overwrite = FALSE,
##' @name cf2biocro
##' @title Convert CF-formatted met data to BioCro met
##' @param met data.table object with met for a single site; output from \code{\link{load.cfmet}}
##' \itemize{
##' \item {year} {int}
##' \item {month} {int}
##' \item {day} {int: day of month (1-31)}
##' \item {doy} {int: day of year (1-366)}
##' \item {hour} {int (0-23)}
##' \item {date} {YYYY-MM-DD HH:MM:SS POSIXct}
##' \item {wind_speed} {num m/s}
##' \item {northward_wind}
##' \item {eastward_wind}
##' \item {ppfd} {optional; if missing, requires surface_downwelling_shortwave_flux_in_air}
##' \item {surface_downwelling_shortwave_flux_in_air}
##' \item {air_pressure (Pa)} {optional; if missing, requires relative_humidity}
##' \item {specific_humidity} {optional; if missing, requires relative_humidity}
##' \item {relative_humidity} {optional; if missing, requires air_pressure and specific_humidity}
##' \item {precipitation_flux}
##' \item {air_temperature}
##' \describe{
##' \item{year}{int}
##' \item{month}{int}
##' \item{day}{int: day of month (1-31)}
##' \item{doy}{int: day of year (1-366)}
##' \item{hour}{int (0-23)}
##' \item{date}{YYYY-MM-DD HH:MM:SS POSIXct}
##' \item{wind_speed}{num m/s}
##' \item{northward_wind}{}
##' \item{eastward_wind}{}
##' \item{ppfd}{optional; if missing, requires surface_downwelling_shortwave_flux_in_air}
##' \item{surface_downwelling_shortwave_flux_in_air}{}
##' \item{air_pressure (Pa)}{optional; if missing, requires relative_humidity}
##' \item{specific_humidity}{optional; if missing, requires relative_humidity}
##' \item{relative_humidity}{optional; if missing, requires air_pressure and specific_humidity}
##' \item{precipitation_flux}{}
##' \item{air_temperature}{}
##' }
##' @param longitude in degrees east, used for calculating solar noon
##' @param zulu2solarnoon logical; if TRUE, convert time from GMT to local solar time.
##' @return data.table / data.frame with fields
##' \itemize{
##' \item {doy} {day of year}
##' \item {hr} {hour}
##' \item {solar} {solar radiation (PPFD)}
##' \item {temp} {temperature, degrees celsius}
##' \item {rh} {relative humidity, as fraction (0-1)}
##' \item {windspeed} {m/s}
##' \item {precip} {cm/h}
##' \describe{
##' \item{doy}{day of year}
##' \item{hr}{hour}
##' \item{solar}{solar radiation (PPFD)}
##' \item{temp}{temperature, degrees celsius}
##' \item{rh}{relative humidity, as fraction (0-1)}
##' \item{windspeed}{m/s}
##' \item{precip}{cm/h}
##' }
##' @export cf2biocro
##' @export
##' @importFrom data.table :=
##' @author David LeBauer
cf2biocro <- function(met, longitude = NULL, zulu2solarnoon = FALSE) {
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50 changes: 25 additions & 25 deletions models/biocro/man/cf2biocro.Rd

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2 changes: 1 addition & 1 deletion models/biocro/man/get_biocro_defaults.Rd

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13 changes: 2 additions & 11 deletions models/biocro/tests/Rcheck_reference.log
Original file line number Diff line number Diff line change
Expand Up @@ -73,17 +73,8 @@ The Date field is over a month old.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
Author: ‘David LeBauer, Deepak Jaiswal, Christopher Black’
Authors@R: ‘David LeBauer [aut, cre], Chris Black [aut], Deepak Jaiswal [aut], University of Illinois, NCSA [cph]’

Maintainer field differs from that derived from Authors@R
Maintainer: ‘David LeBauer <[email protected]>’
Authors@R: ‘David LeBauer <[email protected]>’

* checking top-level files ... NOTE
Non-standard files/directories found at top level:
‘Dockerfile’ ‘model_info.json’
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
Expand Down
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