Merge pull request #3078 from PecanProject/ncvar_put-debug

Better debugging for `model2netcdf.ED2`

CHANGELOG.md

@@ -33,6 +33,7 @@ see if you need to change any of these:
 - Initial LDNDC model coupling
 - `PEcAn.settings::read.settings()` now strips comments so HTML style comments (e.g. `<!-- a comment -->`) are now allowed in pecan.xml files
 - `PEcAn.logger::setLevel()` now invisibly returns the previously set logger level
+-  Warning messages for `model2netcdf.ed2()` coming from `ncdf4::ncvar_put()` now are prepended with the variable name for easier debugging (#3078)
 - Added optional `process_partial` argument to `model2netcdf.ED2()` to allow it to process existing output from failed runs.
 
 We are slowly change the license from NCSA opensource to BSD-3 to help with publishing PEcAn to CRAN.
@@ -64,9 +65,9 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
   the cdo_setup argument in the template job file. In detail, people will need
   to specify cdosetup = "module load cdo/2.0.6" in the host section. More details
   are in the Create_Multi_settings.R script. (#3052)
+- Fixed a bug in `model2netcdf.ed2()` where .nc file connections were being closed multiple times, printing warnings (#3078)
 - Fixed a bug causing the model2netcdf.ED2() step in jobs.sh to be incorrectly written (#3075)
 
-
 ### Changed
 
 - Using R4.0 and R4.1 tags to build PEcAn. Default is now 4.1

models/ed/NEWS.md

@@ -1,8 +1,11 @@
 # PEcAn.ED2 (development version)
 
+* Warning messages for `model2netcdf.ed2()` coming from `ncdf4::ncvar_put()` now are prepended with the variable name for easier debugging (#3078)
+* Fixed a bug in `model2netcdf.ed2()` where .nc file connections were being closed multiple times, printing warnings (#3078)
 * Fixed a bug affecting the generation of job.sh for runs with many PFTs (#3075)
 * Added optional `process_partial` argument to `model2netcdf.ED2()` to allow it to process existing output from failed runs.
 
-# PEcAn.ED2 1.7.2
+# PEcAn.ED2 1.7.2.9000
 
-* Added a `NEWS.md` file to track changes to the package. Prior to this point, PEcAn.ED2 development was tracked in the main PEcAn NEWS file.
+* Added a `NEWS.md` file to track changes to the package. Prior to this point changes are tracked in the main CHANGELOG for the PEcAn repository.
+* Added optional `process_partial` argument to `model2netcdf.ED2()` to allow it to process existing output from failed 

models/ed/R/model2netcdf.ED2.R

@@ -187,7 +187,7 @@ model2netcdf.ED2 <- function(outdir,
     varfile <- file(file.path(outdir, paste(y, "nc", "var", sep = ".")), "w")
     # fill nc file with data
     for (i in seq_along(nc_var)) {
-      ncdf4::ncvar_put(nc, varid = nc_var[[i]], vals = out[[i]])
+      var_put(nc, varid = nc_var[[i]], vals = out[[i]])
       cat(paste(nc_var[[i]]$name, nc_var[[i]]$longname), file = varfile,
           sep = "\n")
     }
@@ -1027,7 +1027,7 @@ read_E_files <- function(yr, yfiles, h5_files, outdir, start_date, end_date,
   for(i in ysel) {
 
     nc <- ncdf4::nc_open(file.path(outdir, h5_files[i]))
-    on.exit(ncdf4::nc_close(nc), add = TRUE)
+    on.exit(ncdf4::nc_close(nc), add = FALSE)
     allvars <- names(nc$var)
     if (!is.null(vars)) allvars <- allvars[ allvars %in% vars ]
 
@@ -1542,5 +1542,16 @@ extract_pfts <- function(pfts) {
   pfts_out
 }
 
+
+# A version of ncvar_put that returns the varid in warning messages
+var_put <- function(nc, varid, vals, start = NA, count = NA) {
+  output <- utils::capture.output(
+    ncdf4::ncvar_put(nc = nc, varid = varid, vals = vals, start = start, count = count)
+  )
+  if(length(output)!=0) {
+    cat(paste0("With '", varid$name, "':"), output, "\n")
+  }
+}
+
 ##-------------------------------------------------------------------------------------------------#
 ### EOF

models/ed/R/read_ed_veg.R

@@ -105,7 +105,7 @@ read_css <- function(filepath, check = TRUE, ...) {
 read_pss <- function(filepath, check = TRUE) {
   pss <- read.table(filepath, header = TRUE)
   if (check) {
-    check_pss(pss, ...)
+    check_pss(pss)
   }
   pss
 }