Replace all backticks for subshells

All instances where backticks are used to invoke a subshell are replaced with $( ). This standardizes usage around $( ), which can be nested and does not be confused with single quotation marks. Refs: NOAA-EMC#397
WalterKolczynski-NOAA · Dec 11, 2021 · 60ad1b8 · 60ad1b8
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diff --git a/docs/doxygen/compile b/docs/doxygen/compile
@@ -14,7 +14,7 @@ elif [ $machine = "JET" ]; then
 else
     echo "machine $machine is unrecognized, ABORT!"
     echo "try system doxygen"
-    doxygen=`which doxygen`
+    doxygen=$(which doxygen)
 fi
 
 $doxygen

diff --git a/driver/gdas/run_JGDAS_NCEPPOST.sh b/driver/gdas/run_JGDAS_NCEPPOST.sh
@@ -43,7 +43,7 @@ export envir=prod
 
 # set up running dir
 
-export user=`whoami`
+export user=$(whoami)
 export DATA=/gpfs/hps/ptmp/${user}/gdas.${PDY}${cyc}_nemsio_mpiio
 mkdir -p $DATA
 cd $DATA

diff --git a/driver/gdas/test_gdas_analysis_high.sh b/driver/gdas/test_gdas_analysis_high.sh
@@ -25,8 +25,8 @@ export CDATE=2017030806
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_analysis_high_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_enkf_fcst.sh b/driver/gdas/test_gdas_enkf_fcst.sh
@@ -34,8 +34,8 @@ fi
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_fcst_grp${grp}_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_enkf_inflate_recenter.sh b/driver/gdas/test_gdas_enkf_inflate_recenter.sh
@@ -27,8 +27,8 @@ export CDATE=2017011900
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_inflate_recenter_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_enkf_innovate_obs.sh b/driver/gdas/test_gdas_enkf_innovate_obs.sh
@@ -31,8 +31,8 @@ fi
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_innovate_obs_grp${grp}_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_enkf_post.sh b/driver/gdas/test_gdas_enkf_post.sh
@@ -24,8 +24,8 @@ export CDATE=2017011900
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_post_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_enkf_select_obs.sh b/driver/gdas/test_gdas_enkf_select_obs.sh
@@ -24,8 +24,8 @@ export CDATE=2017030806
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_select_obs_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_enkf_update.sh b/driver/gdas/test_gdas_enkf_update.sh
@@ -25,8 +25,8 @@ export CDATE=2017030806
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_enkf_update_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_forecast_high.sh b/driver/gdas/test_gdas_forecast_high.sh
@@ -27,8 +27,8 @@ export CDATE=2017012506
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gdas_forecast_high_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_gdas_gldas.sh b/driver/gdas/test_gdas_gldas.sh
@@ -32,12 +32,12 @@ export CDATE=${CDATE:-2019110700}
 #############################################################
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
-export PDY=`echo $CDATE | cut -c1-8`
+export PDY=$(date -u +%Y%m%d)
+export PDY=$(echo $CDATE | cut -c1-8)
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
-export cyc=`echo $CDATE | cut -c9-10`
+export cyc=$(echo $CDATE | cut -c9-10)
 export cycle=t${cyc}z
 
 set -xa

diff --git a/driver/gdas/test_jgdas_verfozn.sh b/driver/gdas/test_jgdas_verfozn.sh
@@ -23,14 +23,14 @@ export NET=${NET:-gfs}
 export RUN=${RUN:-gdas}
 
 
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfozn.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=${envir:-test}
 
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/${me}d2/emc/da/noscrub/${LOGNAME}/test_data}
 export COMROOT=${COMROOT:-/ptmpp1/${LOGNAME}/com}
 export OZN_WORK_DIR=${OZN_WORK_DIR:-/stmpp1/${LOGNAME}/oznmon.${pid}}

diff --git a/driver/gdas/test_jgdas_verfozn_cray.sh b/driver/gdas/test_jgdas_verfozn_cray.sh
@@ -21,14 +21,14 @@ export NET=${NET:-gfs}
 export RUN=${RUN:-gdas}
 
 
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfozn.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=${envir:-test}
 
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/hps3/emc/da/noscrub/${LOGNAME}/test_data}
 export COMROOT=${COMROOT:-/gpfs/hps2/ptmp/${LOGNAME}/com}
 export OZN_WORK_DIR=${OZN_WORK_DIR:-/gpfs/hps2/stmp/${LOGNAME}/oznmon.${pid}}

diff --git a/driver/gdas/test_jgdas_verfrad.sh b/driver/gdas/test_jgdas_verfrad.sh
@@ -18,13 +18,13 @@ export PDATE=${PDATE:-2018022112}
 #############################################################
 # Specify whether the run is production or development
 #############################################################
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfrad.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=para
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/${me}d2/emc/da/noscrub/${LOGNAME}/test_data}
 export COMROOT=${COMROOT:-/ptmpp1/$LOGNAME/com}
 

diff --git a/driver/gdas/test_jgdas_verfrad_cray.sh b/driver/gdas/test_jgdas_verfrad_cray.sh
@@ -16,8 +16,8 @@ export PDATE=${PDATE:-2016100106}
 #############################################################
 # Specify whether the run is production or development
 #############################################################
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_verfrad.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gdas/test_jgdas_vminmon.sh b/driver/gdas/test_jgdas_vminmon.sh
@@ -18,9 +18,9 @@ export PDATE=${PDATE:-2016030706}
 #############################################################
 # Specify whether the run is production or development
 #############################################################
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
-me=`hostname | cut -c1`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
+me=$(hostname | cut -c1)
 
 export job=gdas_vminmon.${cyc}
 export pid=${pid:-$$}

diff --git a/driver/gdas/test_jgdas_vminmon_cray.sh b/driver/gdas/test_jgdas_vminmon_cray.sh
@@ -16,8 +16,8 @@ export PDATE=${PDATE:-2016030700}
 #############################################################
 # Specify whether the run is production or development
 #############################################################
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gdas_vminmon.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gfs/test_gfs_analysis.sh b/driver/gfs/test_gfs_analysis.sh
@@ -25,8 +25,8 @@ export CDATE=2017040700
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gfs_analysis_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gfs/test_gfs_forecast_high.sh b/driver/gfs/test_gfs_forecast_high.sh
@@ -27,8 +27,8 @@ export CDATE=2017012506
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gfs_forecast_high_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gfs/test_gfs_forecast_low.sh b/driver/gfs/test_gfs_forecast_low.sh
@@ -27,8 +27,8 @@ export CDATE=2017012506
 # Specify whether the run is production or development
 #############################################################
 export RUN_ENVIR=para
-export PDY=`echo $CDATE | cut -c1-8`
-export cyc=`echo $CDATE | cut -c9-10`
+export PDY=$(echo $CDATE | cut -c1-8)
+export cyc=$(echo $CDATE | cut -c9-10)
 export job=gfs_forecast_low_${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/gfs/test_jgfs_vminmon.sh b/driver/gfs/test_jgfs_vminmon.sh
@@ -17,14 +17,14 @@ export NET='gfs'
 export RUN='gfs'
 export PDATE=${PDATE:-2016030206}
 
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gfs_vminmon.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}
 export envir=para
 export Z=${Z:-gz}
-me=`hostname | cut -c1`
+me=$(hostname | cut -c1)
 export DATAROOT=${DATAROOT:-/gpfs/${me}d2/emc/da/noscrub/Edward.Safford/test_data}
 export COMROOT=${COMROOT:-/ptmpp1/$LOGNAME/com}
 

diff --git a/driver/gfs/test_jgfs_vminmon_cray.sh b/driver/gfs/test_jgfs_vminmon_cray.sh
@@ -16,8 +16,8 @@ export PDATE=${PDATE:-2016030800}
 #############################################################
 # Specify whether the run is production or development
 #############################################################
-export PDY=`echo $PDATE | cut -c1-8`
-export cyc=`echo $PDATE | cut -c9-10`
+export PDY=$(echo $PDATE | cut -c1-8)
+export cyc=$(echo $PDATE | cut -c9-10)
 export job=gfs_vminmon.${cyc}
 export pid=${pid:-$$}
 export jobid=${job}.${pid}

diff --git a/driver/product/change_gfs_downstream_date.sh b/driver/product/change_gfs_downstream_date.sh
@@ -3,9 +3,9 @@ set -x
 # export cyc=12
 # export cyc=18
 export fhr=012
-export dir=` pwd `
-export PDY=`date -u +%Y%m%d`
-export PDY1=`expr $PDY - 1`
+export dir=$( pwd )
+export PDY=$(date -u +%Y%m%d)
+export PDY1=$(expr $PDY - 1)
 
 export olddate=20200712
 export newdate=20200922

diff --git a/driver/product/change_gfs_downstream_envir.sh b/driver/product/change_gfs_downstream_envir.sh
@@ -3,9 +3,9 @@ set -x
 # export cyc=12
 # export cyc=18
 export fhr=012
-export dir=` pwd `
-export PDY=`date -u +%Y%m%d`
-export PDY1=`expr $PDY - 1`
+export dir=$( pwd )
+export PDY=$(date -u +%Y%m%d)
+export PDY1=$(expr $PDY - 1)
 
 export olddate=20200106
 export newdate=20200712

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_00 b/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_00
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=00
 export cycle=t${cyc}z

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_06 b/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_06
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=06
 export cycle=t${cyc}z

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_12 b/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_12
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=12
 export cycle=t${cyc}z

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_18 b/driver/product/run_JGDAS_ATMOS_GEMPAK_META_NCDC_dell.sh_18
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=18
 export cycle=t${cyc}z

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_dell.sh_00 b/driver/product/run_JGDAS_ATMOS_GEMPAK_dell.sh_00
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=00
 export cycle=t${cyc}z

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_dell.sh_06 b/driver/product/run_JGDAS_ATMOS_GEMPAK_dell.sh_06
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=06
 export cycle=t${cyc}z

diff --git a/driver/product/run_JGDAS_ATMOS_GEMPAK_dell.sh_12 b/driver/product/run_JGDAS_ATMOS_GEMPAK_dell.sh_12
@@ -12,10 +12,10 @@
 
 export KMP_AFFINITY=disabled
 
-export PDY=`date -u +%Y%m%d`
+export PDY=$(date -u +%Y%m%d)
 export PDY=20200922
 
-export PDY1=`expr $PDY - 1`
+export PDY1=$(expr $PDY - 1)
 
 export cyc=12
 export cycle=t${cyc}z