Merge pull request #3300 from Sweetdevil144/gsoc-develop

Remove dependency on `data.atmosphere` from `data.land`

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

docker/depends/pecan_package_dependencies.csv

@@ -261,7 +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

modules/data.land/DESCRIPTION

@@ -41,7 +41,6 @@ Imports:
     neonstore,
     swfscMisc,
     PEcAn.benchmark,
-    PEcAn.data.atmosphere,
     PEcAn.DB,
     PEcAn.logger,
     PEcAn.remote,

modules/data.land/NEWS.md

@@ -8,6 +8,7 @@
 ## Removed
 
 * `find.land()` has been removed. It is not used anywhere we know if, has apparently not been working for some time, and relied on the `maptools` package which is scheduled for retirement.
+* Removed dependency on `PEcAn.data.atmosphere`, notably by retrieving site latitude and longitude directly from `PEcAn.DB::query.site` instead of custom lookups (#3300, Abhinav Pandey).
 
 # PEcAn.data.land 1.7.1
 

modules/data.land/R/ic_process.R

@@ -50,7 +50,7 @@ ic_process <- function(settings, input, dir, overwrite = FALSE){
   on.exit(PEcAn.DB::db.close(con), add = TRUE)
 
   #grab site lat and lon info
-  latlon <- PEcAn.data.atmosphere::db.site.lat.lon(site$id, con = con)
+  latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")] 
   # setup site database number, lat, lon and name and copy for format.vars if new input
   new.site <- data.frame(id = as.numeric(site$id),
                          lat = latlon$lat,

modules/data.land/R/soil_process.R

@@ -29,7 +29,7 @@ soil_process <- function(settings, input, dbfiles, overwrite = FALSE,run.local=T
   con <- PEcAn.DB::db.open(dbparms$bety)
   on.exit(PEcAn.DB::db.close(con), add = TRUE)
   # get site info
-  latlon <- PEcAn.data.atmosphere::db.site.lat.lon(site$id, con = con)
+  latlon <- PEcAn.DB::query.site(site$id, con = con)[c("lat", "lon")]
   new.site <- data.frame(id = as.numeric(site$id),
                          lat = latlon$lat,
                          lon = latlon$lon)

modules/data.land/R/write_ic.R

@@ -55,7 +55,7 @@ write_ic <- function(in.path, in.name, start_date, end_date,
   # read in registration xml for pool specific information
   register.xml <- system.file(paste0("register.", model$type, ".xml"), package = paste0("PEcAn.", model$type))
   if(file.exists(register.xml)){
-    register     <- PEcAn.data.atmosphere::read.register(register.xml, con = NULL)
+    register     <- XML::xmlToList(XML::xmlParse(register.xml))
 
   }else{
     PEcAn.logger::logger.warn("No model register file found")

modules/data.land/tests/Rcheck_reference.log

@@ -13,7 +13,7 @@
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... NOTE
-Imports includes 35 non-default packages.
+Imports includes 34 non-default packages.
 Importing from so many packages makes the package vulnerable to any of
 them becoming unavailable.  Move as many as possible to Suggests and
 use conditionally.