Add proper spacing in comments and loops

jobs/JGLOBAL_EXTRACTVARS

@@ -19,17 +19,17 @@ YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
     "COMIN_ICE_NETCDF:COM_ICE_NETCDF_TMPL" \
     "COMIN_WAVE_GRID:COM_WAVE_GRID_TMPL"
 
-if [[ "${DO_ATM}" == "YES" ]];then
+if [[ "${DO_ATM}" == "YES" ]]; then
   if [[ ! -d "${ARC_RFCST_PROD_ATMOS_F2D}" ]]; then mkdir -p "${ARC_RFCST_PROD_ATMOS_F2D}"; fi
   if [[ ! -d "${ARC_RFCST_PROD_ATMOS_F3D}" ]]; then mkdir -p "${ARC_RFCST_PROD_ATMOS_F3D}"; fi
 fi
-if [[ "${DO_OCN}" == "YES" ]];then
+if [[ "${DO_OCN}" == "YES" ]]; then
   if [[ ! -d "${ARC_RFCST_PROD_OCN}" ]]; then mkdir -p "${ARC_RFCST_PROD_OCN}"; fi
 fi
-if [[ "${DO_ICE}" == "YES" ]];then
+if [[ "${DO_ICE}" == "YES" ]]; then
   if [[ ! -d "${ARC_RFCST_PROD_ICE}" ]]; then mkdir -p "${ARC_RFCST_PROD_ICE}"; fi
 fi
-if [[ "${DO_WAVE}" == "YES" ]];then
+if [[ "${DO_WAVE}" == "YES" ]]; then
   if [[ ! -d "${ARC_RFCST_PROD_WAV}" ]]; then mkdir -p "${ARC_RFCST_PROD_WAV}"; fi
 fi
 

parm/config/gefs/config.extractvars

@@ -9,26 +9,26 @@ echo "BEGIN: config.extractvars"
 
 export COMPRSCMD=${COMPRSCMD:-bzip2}
 
-export compress_ocn=0 #1: compress extracted ocean product, 0: do not compress extracted ocean product
-export compress_ice=0 #1: compress extracted ice product, 0: do not compress extracted ice product
+export compress_ocn=0 #1: Compress extracted ocean product, 0: Do not compress extracted ocean product
+export compress_ice=0 #1: Compress extracted ice product, 0: Do not compress extracted ice product
 
-export ocnres="5p00" #Resolution of ocean products
-export iceres="5p00" #Resolution of ice products
-export wavres="5p00" #Resolution of wave products
+export ocnres="5p00" # Resolution of ocean products
+export iceres="5p00" # Resolution of ice products
+export wavres="5p00" # Resolution of wave products
 
-export depthvar_name="z_l" #name of depth variable in NetCDF ocean products
-export zmin="0." #Minimum depth to extract from NetCDF ocean products
-export zmax="300." #Maximum depth to extract from NetCDF ocean products
+export depthvar_name="z_l" # Name of depth variable in NetCDF ocean products
+export zmin="0." # Minimum depth to extract from NetCDF ocean products
+export zmax="300." # Maximum depth to extract from NetCDF ocean products
 
-export FHOUT_WAV_EXTRACT=6 #Frequency of wave output to be saved on disk
+export FHOUT_WAV_EXTRACT=6 # Frequency of wave output to be saved on disk
 
 #Paramater Tables used
-export varlist_2d="${PARMgfs}/product/gefs_shortparmlist_2d.parm" #Parameter table for surface variables
-export varlist_3d="${PARMgfs}/product/gefs_shortparmlist_3d_h.parm" #Parameter table for upper air instantaneous variables
-export varlist_3d_d="${PARMgfs}/product/gefs_shortparmlist_3d_d.parm" #Parameter table for upper air daily-averaged variables
-export varlist_wav="${PARMgfs}/product/gefs_wav_shortparmlist.parm" #Parameter table for wave variables
-export varlist_ocn_netcdf="${PARMgfs}/product/gefs_ocn_shortparmlist.parm" #Parameter table for ocean netcdf variables
-export varlist_ice_netcdf="${PARMgfs}/product/gefs_ice_shortparmlist.parm" #Parameter table for ice netcdf variables
+export varlist_2d="${PARMgfs}/product/gefs_shortparmlist_2d.parm" # Parameter table for surface variables
+export varlist_3d="${PARMgfs}/product/gefs_shortparmlist_3d_h.parm" # Parameter table for upper air instantaneous variables
+export varlist_3d_d="${PARMgfs}/product/gefs_shortparmlist_3d_d.parm" # Parameter table for upper air daily-averaged variables
+export varlist_wav="${PARMgfs}/product/gefs_wav_shortparmlist.parm" # Parameter table for wave variables
+export varlist_ocn_netcdf="${PARMgfs}/product/gefs_ocn_shortparmlist.parm" # Parameter table for ocean netcdf variables
+export varlist_ice_netcdf="${PARMgfs}/product/gefs_ice_shortparmlist.parm" # Parameter table for ice netcdf variables
 
 #Directory to save extracted variables
 export ARC_RFCST_PROD="${ARCDIR}/rfcst/${PDY:0:4}/${PDY:0:6}/${PDY:0:8}/mem${ENSMEM}"

scripts/exglobal_extractvars.sh

@@ -28,24 +28,24 @@ if (( FHOUT_WAV_EXTRACT % FHOUT_WAV != 0 )); then
 fi
 
 # Extract variables for atmosphere
-if [[ "${DO_ATM}" == "YES" ]];then
+if [[ "${DO_ATM}" == "YES" ]]; then
   ${EXTRCTVARA} "${DATA}/atmos"
 fi
 
 # Extract variables for ocean
-if [[ "${DO_OCN}" == "YES" ]];then
+if [[ "${DO_OCN}" == "YES" ]]; then
   export component_name="ocn"
   ${EXTRCTVARO} "${DATA}/ocn" "${varlist_ocn_netcdf}" "${ocnres}" "${compress_ocn}" "${FHOUT_OCN_GFS}" "${ARC_RFCST_PROD_OCN}"
 fi
 
 # Extract variables for ice
-if [[ "${DO_ICE}" == "YES" ]];then
+if [[ "${DO_ICE}" == "YES" ]]; then
   export component_name="ice"
   ${EXTRCTVARO} "${DATA}/ice" "${varlist_ice_netcdf}" "${iceres}" "${compress_ice}" "${FHOUT_ICE_GFS}" "${ARC_RFCST_PROD_ICE}"
 fi
 
 # Extract variables for wave
-if [[ "${DO_WAVE}" == "YES" ]];then
+if [[ "${DO_WAVE}" == "YES" ]]; then
   export component_name="wav"
   ${EXTRCTVARW} "${DATA}/wav"
 fi

ush/atmos_extractvars.sh

@@ -69,7 +69,7 @@ for outtype in "f2d" "f3d"; do
     check_atmos "${infile1}" "${infile2}" "${varlist}" "${fnh}"
     copy_to_comout "${outfile}" "${ARC_RFCST_PROD_ATMOS}"
 
-    #Compute daily average for a subset of variables
+    # Compute daily average for a subset of variables
     if (( nh % 6 == 0 )) && (( nh != 0 )) && [[ "${outtype}" == "f3d" ]]; then
       outfile=${subdata}/vartmp_raw_vari_ldy${dcnt}.grib2
       for infile in "${infile1}" "${infile2}"; do
@@ -87,12 +87,12 @@ for outtype in "f2d" "f3d"; do
         dcnt=$(( dcnt + 1 ))
       else
         fcnt=$(( fcnt + 1 ))
-      fi #If at final lead hour of a given day
-    fi #if lead hour is divisible by 6 and outtype is f3d
+      fi # If at final lead hour of a given day
+    fi # if lead hour is divisible by 6 and outtype is f3d
 
     nh=$(( nh + outfreq ))
-  done #fhr
+  done # nh
 
-done #f2d,f3d
+done # f2d,f3d
 
 exit 0

ush/extractvars_tools.sh

@@ -40,14 +40,14 @@ daily_avg_atmos() {
     ${WGRIB2} "${davgtmp}" | ${WGRIB2} -i "${davgtmp}" -append -grib "${davg_file}"
     rm -f "${davgtmp}"
     vcnt=$(( vcnt + 1 ))
-  done <"${varlist_d}" #variable
+  done <"${varlist_d}" # variable
 }
 
 copy_to_comout() {
   # Function to copy the output file with the extracted product variables to a user-defined destination directory
-  rundir_outfile=$1 #output data file generated in RUNDIR
-  comout_dir=$2 #destination directory to which to copy the data file
-  if [[ -f "${rundir_outfile}" ]];then
+  rundir_outfile=$1 # output data file generated in RUNDIR
+  comout_dir=$2 # destination directory to which to copy the data file
+  if [[ -f "${rundir_outfile}" ]]; then
     cpfs "${rundir_outfile}" "${comout_dir}"
   else
     echo "FATAL ERROR: Output file (${rundir_outfile}) does not exist."

ush/ocnice_extractvars.sh

@@ -24,11 +24,11 @@ comout_rfcst_prod_ocnice=${6}
 for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
   fnh=$(printf "%3.3d" "${nh}")
 
-  if [[ ${component_name} == "ocn" ]];then
+  if [[ ${component_name} == "ocn" ]]; then
     infile=${COMIN_OCEAN_NETCDF}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
     # For ocean products, add an argument to extract a subset of levels
     otherargs=(-d "${depthvar_name},""${zmin},""${zmax}")
-  elif [[ ${component_name} == "ice" ]];then
+  elif [[ ${component_name} == "ice" ]]; then
     infile=${COMIN_ICE_NETCDF}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc
     otherargs=()
   fi
@@ -39,20 +39,20 @@ for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
     varsinfile=$(cdo -showname "${infile}")
     varsavailable=""
     for i in ${varsrequested}; do
-      #check if variable from parm file is available in netcdf file. If variable is not in netcdf file, do not try to extract that variable. 
+      # Check if variable from parm file is available in netcdf file. If variable is not in netcdf file, do not try to extract that variable.
       if [[ ${varsinfile} == *"${i}"* ]]; then
         varsavailable+="${i},"
       else
         echo "WARNING: ${i} is not available in ${infile}."
       fi
     done
-    if [[ -z "${varsavailable}" ]];then
+    if [[ -z "${varsavailable}" ]]; then
       echo "WARNING: No variables from parm file ${varlist} are available in netcdf file ${infile}."
     else
       ocnice_vars=${varsavailable::-1}
       ncks -v "${ocnice_vars}" "${otherargs[@]}" "${infile}" "${outfile}"
     fi
-    if [[ ${datacompress} -eq 1 ]];then
+    if [[ ${datacompress} -eq 1 ]]; then
       ${COMPRSCMD} "${outfile}"
       copy_to_comout "${outfile}.bz2" "${comout_rfcst_prod_ocnice}"
     else
@@ -61,6 +61,6 @@ for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
   else
     echo "WARNING: ${infile} does not exist."
   fi
-done
+done # nh
 
 exit 0                                                                                                                                                                                        

ush/wave_extractvars.sh

@@ -20,15 +20,15 @@ for (( nh = FHOUT_WAV_EXTRACT; nh <= FHMAX_WAV; nh = nh + FHOUT_WAV_EXTRACT ));
 
   infile=${COMIN_WAVE_GRID}/${RUN}wave.t${cyc}z.global.${wavres}.f${fnh}.grib2
   outfile=${subdata}/${RUN}wave.t${cyc}z.global.${wavres}.f${fnh}.grib2
-  rm -f "${outfile}" #remove outfile if it already exists before extraction
+  rm -f "${outfile}" # Remove outfile if it already exists before extraction
 
-  if [[ -f "${infile}" ]]; then #check if input file exists before extraction
+  if [[ -f "${infile}" ]]; then # Check if input file exists before extraction
     # shellcheck disable=SC2312 
     ${WGRIB2} "${infile}" | grep -F -f "${varlist_wav}" | ${WGRIB2} -i "${infile}" -append -grib "${outfile}"
   else
     echo "WARNING: ${infile} does not exist."
   fi 
   copy_to_comout "${outfile}" "${ARC_RFCST_PROD_WAV}"
-done #fhr
+done # nh
 
 exit 0