Merge pull request #1359 from PecanProject/release/1.4.10.1

Release/1.4.10.1

.travis.yml

@@ -33,6 +33,7 @@ addons:
       - udunits-bin 
       - libgmp-dev
       - libproj-dev
+      - pandoc
       # need to compile documentation
       # BROKEN MISSING FONT
       #- texinfo

CHANGELOG.md

@@ -7,8 +7,14 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [Unreleased]
 
+## [1.4.10.1] - 2017-04-18
+
 ### Changed
 - Bugfix in Fluxnet2015
+- Update Git workflow in Documentation
+- download.CRUNCEP now uses CF-compliant time units (days since start of year instead of "secs")
+- Bugfixes in met.process
+
 
 ## [1.4.10] - 2017-03-27
 Documentation

all/DESCRIPTION

@@ -2,8 +2,8 @@ Package: PEcAn.all
 Type: Package
 Title: PEcAn functions used for ecological forecasts and
     reanalysis
-Version: 1.4.10
-Date: 2017-03-27
+Version: 1.4.10.1
+Date: 2017-04-18
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang,
     Mike Dietze, Carl Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>

book_source/deploy.sh

@@ -6,28 +6,41 @@ set -e
 #check for environment variable
 [ -z "${GITHUB_PAT}" ] && exit 0
 
-# only deploy if this is the master branch build
-branch_name=$(git symbolic-ref -q HEAD)
-branch_name=${branch_name##refs/heads/}
-branch_name=${branch_name:-HEAD}
-[ "${branch_name}" != "master" ] && exit 0
+# don't run on pull requests
+[ "$TRAVIS_PULL_REQUEST" != "false" ]  && exit 0
+
+# find version if we are develop/latest/release and if should be pushed
+if [ "$TRAVIS_BRANCH" = "master" ]; then
+  VERSION="master"
+elif [ "$TRAVIS_BRANCH" = "develop" ]; then
+  VERSION="develop"
+elif [ "$( echo $TRAVIS_BRANCH | sed -e 's#^release/.*$#release#')" = "release" ]; then
+  VERSION="$( echo $TRAVIS_BRANCH | sed -e 's#^release/\(.*\)$#\1#' )"
+else
+  echo "Not Master, Develop, or Release Branch. Will not render Book."
+  exit 0
+fi
 
 #set USER 
 USER=${TRAVIS_REPO_SLUG%/*}
 
-
 # configure your name and email if you have not done so
 git config --global user.email "pecanproj@gmail.com"
 git config --global user.name "TRAVIS-DOC-BUILD"
 
+# clone documentation git repo
 git clone https://${GITHUB_PAT}@github.com/${USER}/pecan-documentation.git book_hosted
+cd book_hosted
 
+## Check if branch named directory exists 
+if [ ! -d $VERSION ]; then
+  mkdir $VERSION
+fi
 
-cp -r _book/* book_hosted
-
+# copy new documentation
+rsync -a --delete ../_book/ $VERSION/
 
-cd book_hosted
+# push updated documentation back up
 git add --all *
-git commit -m"Update the book `date`" || true
+git commit -m "Update the book `date`" || true
 git push -q origin master
-

db/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PEcAn.DB
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
-Version: 1.4.10
-Date: 2017-03-27
+Version: 1.4.10.1
+Date: 2017-04-18
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl
     Davidson, Rob Kooper, Shawn Serbin
 Maintainer: David LeBauer <dlebauer@illinois.edu>

db/R/query.format.vars.R

@@ -4,10 +4,10 @@
 ##' @param con : database connection
 ##' @export query.format.vars
 ##' 
-##' @author Betsy Cowdery , Ankur Desai
+##' @author Betsy Cowdery , Ankur Desai, Istem Fer
 ##' 
 query.format.vars <- function(bety,input.id=NA,format.id=NA,var.ids=NA){
-
+  
   if(is.na(input.id) & is.na(format.id)){PEcAn.utils::logger.error("Must specify input id or format id")}
 
   con <- bety$con
@@ -49,40 +49,42 @@ query.format.vars <- function(bety,input.id=NA,format.id=NA,var.ids=NA){
     colnames(fv) <- c("variable_id", "input_name", "input_units", "storage_type", "column_number")
     fv$variable_id <- as.numeric(fv$variable_id)
     n <- dim(fv)[1]
-
+    
     # get bety names and units 
-    vars <- as.data.frame(matrix(NA, ncol=3, nrow=n))
+    vars <- as.data.frame(matrix(NA, ncol=2, nrow=n))
+    colnames(vars) <- c("bety_name", "bety_units")
+
+    # fv and vars need to go together from now on, 
+    # otherwise when there are more than one of the same variable_id it confuses merge 
+    vars_bety <- cbind(fv, vars)
     for(i in 1:n){
-      vars[i,] <- as.matrix(db.query(paste("SELECT id, name, units from variables where id = ",
-                                 fv$variable_id[i]),con))
+      vars_bety[i, (ncol(vars_bety)-1):ncol(vars_bety)] <- as.matrix(db.query(paste("SELECT name, units from variables where id = ",
+                                                                                    fv$variable_id[i]),con))
     }
-    colnames(vars) <- c("variable_id", "bety_name", "bety_units")
-    vars$variable_id <- as.numeric(fv$variable_id)
 
     # Fill in input names and units with bety names and units if they are missing
 
     ind1 <- fv$input_name == ""
-    fv$input_name[ind1] <- vars$bety_name[ind1]
+    vars_bety$input_name[ind1] <- vars_bety$bety_name[ind1]
     ind2 <- fv$input_units == ""
-    fv$input_units[ind2] <- vars$bety_units[ind2]
-      
+    vars_bety$input_units[ind2] <- vars_bety$bety_units[ind2]
+
     # Fill in CF vars
     # This will ultimately be useful when looking at met variables where CF != Bety
     # met <- read.csv(system.file("/data/met.lookup.csv", package= "PEcAn.data.atmosphere"), header = T, stringsAsFactors=FALSE)
-
+    
     #Fill in MstMIP vars 
     #All pecan output is in MstMIP variables 
-
+    
     bety_mstmip <- read.csv(system.file("bety_mstmip_lookup.csv", package= "PEcAn.DB"), header = T, stringsAsFactors=FALSE)
-
-    vars_full <- merge(fv, merge(vars, bety_mstmip, by = "bety_name", all.x = TRUE), by="variable_id", all=TRUE) # not sure if all=TRUE is appropriate here or not.
-
+    vars_full <- merge(vars_bety, bety_mstmip, by = "bety_name", all.x = TRUE)
+
     vars_full$pecan_name <- vars_full$mstmip_name
     vars_full$pecan_units <- vars_full$mstmip_units
     ind <- is.na(vars_full$pecan_name)
     vars_full$pecan_name[ind] <- vars_full$bety_name[ind]
     vars_full$pecan_units[ind] <- vars_full$bety_units[ind]
-
+    
     header <- as.numeric(f$header)
     skip <- ifelse(is.na(as.numeric(f$skip)),0,as.numeric(f$skip))
 
@@ -105,7 +107,7 @@ query.format.vars <- function(bety,input.id=NA,format.id=NA,var.ids=NA){
                    site = site.id,
                    lat = site.lat,
                    lon = site.lon
-                   )
+    )
   } else {
     format <- list(file_name = f$name,
                    mimetype = f$mimetype,

models/biocro/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PEcAn.BIOCRO
 Type: Package
 Title: PEcAn package for integration of the BioCro model
-Version: 1.4.10
-Date: 2017-03-27
+Version: 1.4.10.1
+Date: 2017-04-18
 Author: David LeBauer, Deepak Jaiswal
 Maintainer: David LeBauer <dlebauer@illinois.edu>
 Description: This module provides functions to link BioCro to PEcAn.

models/clm45/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PEcAn.CLM45
 Type: Package
 Title: PEcAn package for integration of CLM4.5 model
-Version: 1.4.10
-Date: 2017-03-27
+Version: 1.4.10.1
+Date: 2017-04-18
 Author: Mike Dietze
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific

models/dalec/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PEcAn.DALEC
 Type: Package
 Title: PEcAn package for integration of the DALEC model
-Version: 1.4.10
-Date: 2017-03-27
+Version: 1.4.10.1
+Date: 2017-04-18
 Author: Mike Dietze, Tristain Quaife
 Maintainer: Mike Dietze <dietze@bu.edu>
 Description: This module provides functions to link DALEC to PEcAn.

models/ed/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: PEcAn.ED2
 Type: Package
 Title: PEcAn package for integration of ED2 model
-Version: 1.4.10
-Date: 2017-03-27
+Version: 1.4.10.1
+Date: 2017-04-18
 Author: David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Mike Dietze, Carl
     Davidson, Rob Kooper, Shawn Serbin
 Maintainer: Mike Dietze <dietze@bu.edu>

models/ed/NAMESPACE

@@ -10,6 +10,7 @@ export(read.output.ED2)
 export(read.output.file.ed)
 export(read_restart.ED2)
 export(remove.config.ED2)
+export(veg2model.ED2)
 export(write.config.ED2)
 export(write.config.jobsh.ED2)
 export(write.config.xml.ED2)

models/ed/R/model2netcdf.ED2.R

@@ -21,7 +21,7 @@
 ##' @importFrom PEcAn.utils logger.info
 ##' @export
 ##'
-##' @author Michael Dietze, Shawn Serbin, Rob Kooper, Toni Viskari
+##' @author Michael Dietze, Shawn Serbin, Rob Kooper, Toni Viskari, Istem Fer
 ## modified M. Dietze 07/08/12 modified S. Serbin 05/06/13
 model2netcdf.ED2 <- function(outdir, sitelat, sitelon, start_date, end_date) {
 
@@ -538,16 +538,21 @@ model2netcdf.ED2 <- function(outdir, sitelat, sitelon, start_date, end_date) {
     nc_var[[3]] <- mstmipvar("CarbPools", lat, lon, t, zg)
     nc_var[[4]] <- mstmipvar("CO2CAS", lat, lon, t, zg)
     nc_var[[5]] <- mstmipvar("CropYield", lat, lon, t, zg)
-    out <- conversion(6, umol2kg_C)  ## umol/m2 s-1 -> kg m-2 s-1
-    nc_var[[6]] <- mstmipvar("GPP", lat, lon, t, zg)
-    out <- conversion(7, umol2kg_C)  ## umol/m2 s-1 -> kg m-2 s-1
-    nc_var[[7]] <- mstmipvar("HeteroResp", lat, lon, t, zg)
-    out <- conversion(8, umol2kg_C)  ## umol/m2 s-1 -> kg m-2 s-1
-    nc_var[[8]] <- mstmipvar("NEE", lat, lon, t, zg)
-    out <- conversion(9, umol2kg_C)  ## umol/m2 s-1 -> kg m-2 s-1
-    nc_var[[9]] <- mstmipvar("NPP", lat, lon, t, zg)
-    out <- conversion(10, umol2kg_C)  ## umol/m2 s-1 -> kg m-2 s-1
-    nc_var[[10]] <- mstmipvar("TotalResp", lat, lon, t, zg)
+    out <- conversion(6, yr2s)  ## kg C m-2 yr-1 -> kg C m-2 s-1
+    nc_var[[6]]<- ncdf4::ncvar_def("GPP", units = "kg C m-2 s-1", dim = list(lon, lat, t), missval = -999, 
+                                   longname = "Gross Primary Productivity")
+    out <- conversion(7, yr2s)  ## kg C m-2 yr-1 -> kg C m-2 s-1
+    nc_var[[7]]<- ncdf4::ncvar_def("HeteroResp", units = "kg C m-2 s-1", dim = list(lon, lat, t), missval = -999, 
+                                   longname = "Heterotrophic Respiration")
+    out <- conversion(8, yr2s)  ## kg C m-2 yr-1 -> kg C m-2 s-1
+    nc_var[[8]]<- ncdf4::ncvar_def("NEE", units = "kg C m-2 s-1", dim = list(lon, lat, t), missval = -999, 
+                                   longname = "Net Ecosystem Exchange")
+    out <- conversion(9, yr2s)  ## kg C m-2 yr-1 -> kg C m-2 s-1
+    nc_var[[9]]<- ncdf4::ncvar_def("NPP", units = "kg C m-2 s-1", dim = list(lon, lat, t), missval = -999, 
+                                   longname = "Net Primary Productivity")
+    out <- conversion(10, yr2s)  ## kg C m-2 yr-1 -> kg C m-2 s-1
+    nc_var[[10]]<- ncdf4::ncvar_def("TotalResp", units = "kg C m-2 s-1", dim = list(lon, lat, t), missval = -999, 
+                                   longname = "Total Respiration")
     nc_var[[11]] <- mstmipvar("TotLivBiom", lat, lon, t, zg)
     nc_var[[12]] <- mstmipvar("TotSoilCarb", lat, lon, t, zg)
     nc_var[[13]] <- mstmipvar("Fdepth", lat, lon, t, zg)
@@ -566,7 +571,9 @@ model2netcdf.ED2 <- function(outdir, sitelat, sitelon, start_date, end_date) {
     nc_var[[25]] <- mstmipvar("Lwnet", lat, lon, t, zg)
     nc_var[[26]] <- mstmipvar("Qg", lat, lon, t, zg)
     nc_var[[27]] <- mstmipvar("Qh", lat, lon, t, zg)
-    nc_var[[28]] <- mstmipvar("Qle", lat, lon, t, zg)
+    out <- conversion(28, get.lv())  ## kg m-2 s-1 -> W m-2
+    nc_var[[28]]<- ncdf4::ncvar_def("Qle", units = "W m-2", dim = list(lon, lat, t), missval = -999, 
+                                    longname = "Latent heat")
     nc_var[[29]] <- mstmipvar("Swnet", lat, lon, t, zg)
     nc_var[[30]] <- mstmipvar("RootMoist", lat, lon, t, zg)
     nc_var[[31]] <- mstmipvar("Tveg", lat, lon, t, zg)