Bumping version, correcting paths in Daymet, and adding parsable option

Author: kasra-keshavarz

CHANGELOG

@@ -1,5 +1,19 @@
 Changelog
 =========
+[v0.4.0] - August 11th, 2023
+# Improvements
+ * `--parsable` option now added when the script submits jobs to the SLURM
+   scheduler
+# Fixed
+ * Issue with the `Daymet` dataset is fixed and now subsetting is done properly
+
+[v0.3.0] - June 16th, 2023
+# Improvements
+ * Ensemble members are now processed in parallel mode
+
+# Datasets
+ * AB Government climate projections are added to the dataset (data
+   currently not publicly available)
 
 [v0.2.0] - May 5th, 2023
 

VERSION

@@ -1 +1 @@
-0.3.0
+0.4.0

assets/coord_closest_daymet_idx.ncl

@@ -58,6 +58,8 @@ Script options:
 					on the SLURM system; optional
   -k, --no-chunk			No parallelization, recommended for small domains
   -p, --prefix=STR			Prefix  prepended to the output files
+  -b, --parsable			Parsable SLURM message mainly used
+					for chained job submissions
   -c, --cache=DIR			Path of the cache directory; optional
   -E, [email protected]		E-mail user when job starts, ends, and finishes; optional
   -V, --version				Show version
@@ -113,7 +115,7 @@ shopt -s expand_aliases
 # Parsing input arguments
 # =======================
 # argument parsing using getopt - WORKS ONLY ON LINUX BY DEFAULT
-parsedArguments=$(getopt -a -n extract-dataset -o jhVE:d:i:v:o:s:e:t:l:n:p:c:m:ka: --long submit-job,help,version,email:,dataset:,dataset-dir:,variable:,output-dir:,start-date:,end-date:,time-scale:,lat-lims:,lon-lims:,prefix:,cache:,ensemble:,no-chunk,shape-file: -- "$@")
+parsedArguments=$(getopt -a -n extract-dataset -o jhVbE:d:i:v:o:s:e:t:l:n:p:c:m:ka: --long submit-job,help,version,parsable,email:,dataset:,dataset-dir:,variable:,output-dir:,start-date:,end-date:,time-scale:,lat-lims:,lon-lims:,prefix:,cache:,ensemble:,no-chunk,shape-file: -- "$@")
 validArguments=$?
 # check if there is no valid options
 if [ "$validArguments" != "0" ]; then
@@ -148,6 +150,7 @@ do
     -m | --ensemble)      ensemble="$2"        ; shift 2 ;; # optional
     -k | --no-chunk)      parallel=false       ; shift   ;; # optional
     -p | --prefix)	  prefixStr="$2"       ; shift 2 ;; # required
+    -b | --parsable)	  parsable=true	       ; shift   ;; # optional
     -c | --cache)	  cache="$2"	       ; shift 2 ;; # optional
     -a | --shape-file)    shapefile="$2"       ; shift 2 ;; # optional
 
@@ -180,8 +183,21 @@ fi
 
 # email withought job submission not allowed
 if [[ -n $email ]] && [[ -z $jobSubmission ]]; then
-  echo "$(basename $0): Email is not supported wihtout job submission;"
-  echo "$(basename $0): Continuing without email notification..."
+  echo "$(basename $0): ERROR! Email is not supported wihtout job submission;"
+  exit 1;
+fi
+
+# parsable without job submission not allowed
+if [[ $parsable==true ]] && [[ -z $jobSubmission ]]; then
+  echo "$(basename $0): ERROR! --parsable argument cannot be used without job submission"
+  exit 1;
+fi
+
+# if parsable argument is provided
+if [[ -n $parsable ]]; then
+  parsable="--parsable"
+else
+  parsable=""
 fi
 
 # if shapefile is provided extract the extents from it
@@ -402,12 +418,13 @@ call_processing_func () {
 	#SBATCH --nodes=1
 	#SBATCH --account=rpp-kshook
 	#SBATCH --time=04:00:00
-	#SBATCH --mem=8192M
+	#SBATCH --mem=8000M
 	#SBATCH --job-name=DATA_${scriptName}
 	#SBATCH --error=$logDir/datatool_%A-%a_err.txt
 	#SBATCH --output=$logDir/datatool_%A-%a.txt
 	#SBATCH --mail-user=$email
 	#SBATCH --mail-type=BEGIN,END,FAIL
+	#SBATCH ${parsable}
 	
 	$(declare -p startDateArr)
 	$(declare -p endDateArr)
@@ -430,7 +447,9 @@ call_processing_func () {
 	srun ${script} --start-date="\$tBegin" --end-date="\$tEnd" --cache="${cache}-\${SLURM_ARRAY_JOB_ID}-\${SLURM_ARRAY_TASK_ID}" --ensemble="\${member}"
 	EOF
 
-    echo "$(basename $0): job submission details are printed under $logDir"
+    if [[ -z $parsable ]]; then
+      echo "$(basename $0): job submission details are printed under $logDir"
+    fi
 
   # serial run
   else

assets/coord_daymet_idx.ncl

@@ -125,8 +125,8 @@ latDim="y" # latitude dimension
 lonDim="x" # longitude dimension
 
 # spatial extraction script address
-coordIdxScript="$(dirname $0)/../assets/coord_daymet_idx.ncl"
-coordClosestIdxScript="$(dirname $0)/../assets/coord_closest_daymet_idx.ncl"
+coordIdxScript="$(dirname $0)/../../assets/coord_daymet_idx.ncl"
+coordClosestIdxScript="$(dirname $0)/../../assets/coord_closest_daymet_idx.ncl"
 
 # ===================
 # Necessary Functions