V492 dev18 shellcheck info

.github/workflows/CI.yml

@@ -40,4 +40,4 @@ jobs:
 
       - name: ShellCheck
         run: |
-          find scripts -name "*.sh" | sort | xargs shellcheck --severity=warning
+          find scripts -name "*.sh" | sort | xargs shellcheck --severity=info

scripts/ANALYSIS.anasum.sh

@@ -2,7 +2,7 @@
 # script to analyse data files with anasum
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=8:00:00; h_vmem=4000M; tmpdir_size=10G
 
 if [[ $# -lt 3 ]]; then
@@ -37,8 +37,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 FLIST=$1
@@ -55,7 +54,7 @@ if [[ ! -f "$FLIST" ]]; then
 fi
 
 # Check that run parameter file exists
-if [[ "$RUNP" == `basename $RUNP` ]]; then
+if [[ "$RUNP" == $(basename "$RUNP") ]]; then
     RUNP="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNP"
 fi
 if [[ ! -f "$RUNP" ]]; then
@@ -64,7 +63,7 @@ if [[ ! -f "$RUNP" ]]; then
 fi
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/$DATE/ANASUM.ANADATA"
 echo -e "Log files will be written to:\n $LOGDIR"
 mkdir -p "$LOGDIR"
@@ -76,7 +75,7 @@ mkdir -p "$ODIR"
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.anasum_sub"
 
-TIMETAG=`date +"%s"`
+TIMETAG=$(date +"%s")
 
 FSCRIPT="$LOGDIR/ANA.$ONAME-$(date +%s)"
 sed -e "s|FILELIST|$FLIST|" \
@@ -90,13 +89,14 @@ echo "$FSCRIPT.sh"
 
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
 # run locally or on cluster (expand shell variables in submission string)
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT".sh)
 
     # account for -terse changing the job number format
     if [[ $SUBC != *-terse* ]] ; then
@@ -106,11 +106,12 @@ if [[ $SUBC == *qsub* ]]; then
     echo "RUN $AFILE JOBID $JOBID"
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-    condor_submit $FSCRIPT.sh.condor
+    condor_submit "$FSCRIPT".sh.condor
 elif [[ $SUBC == *parallel* ]]; then
-    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> $LOGDIR/runscripts.$TIMETAG.dat
-    cat $LOGDIR/runscripts.$TIMETAG.dat | $SUBC
+    echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR"/runscripts."$TIMETAG".dat
+    # shellcheck disable=SC2086
+    cat "$LOGDIR"/runscripts."$TIMETAG".dat | $SUBC
 
 elif [[ $SUBC == *simple* ]]; then
-	"$FSCRIPT.sh" |& tee $FSCRIPT.log
+	"$FSCRIPT.sh" |& tee "$FSCRIPT".log
 fi

scripts/ANALYSIS.anasum_allcuts.sh

@@ -28,8 +28,8 @@ EPOCH="${3:-V6}"
 IGNORETYPE="IGNOREACCEPTANCE"
 # set this to zero to force reprocessing
 SKIPIFPROCESSED="1"
-EDVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFMINORVERSION)
-EDMAJORVERSION=$(cat $VERITAS_EVNDISP_AUX_DIR/IRFVERSION)
+EDVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFMINORVERSION)
+EDMAJORVERSION=$(cat "$VERITAS_EVNDISP_AUX_DIR"/IRFVERSION)
 
 # anasum file are writing into this directory
 TMPDIR="$VERITAS_DATA_DIR/tmp/${EDVERSION}/${VERITAS_ANALYSIS_TYPE:0:2}/"
@@ -47,12 +47,12 @@ if [[ ${RUNTYPE} == "PRECUTS" ]]; then
 fi
 
 PREDIR="$VERITAS_PREPROCESSED_DATA_DIR/${VERITAS_ANALYSIS_TYPE:0:2}/mscw/"
-echo $PREDIR
+echo "$PREDIR"
 echo "TMP $TMPDIR"
 
 # temporary file for output
 TMPLOG="$(pwd)/anasum.submit.$(uuidgen).tmp.txt"
-rm -f ${TMPLOG}
+rm -f "${TMPLOG}"
 
 for C in $CUTS
 do
@@ -61,19 +61,19 @@ do
         if  [[ $RUNTYPE == "PRECUTS" ]]; then
             CDIR=$(echo "$CDIR" | sed -E 's/anasum_(NTel[23])([A-Za-z]+)Pre/\1-\2/')
         fi
-        echo $CDIR
+        echo "$CDIR"
         mkdir -p "$TMPDIR/${CDIR}"
-        "$(dirname "$0")/ANALYSIS.anasum_parallel_from_runlist.sh" ${RUNL} \
+        "$(dirname "$0")/ANALYSIS.anasum_parallel_from_runlist.sh" "${RUNL}" \
             "$TMPDIR/${CDIR}" \
-            ${C} \
+            "${C}" \
             ${IGNORETYPE} \
-            $VERITAS_EVNDISP_AUX_DIR/ParameterFiles/ANASUM.runparameter \
-            $PREDIR $SKIPIFPROCESSED | tee -a ${TMPLOG}
+            "$VERITAS_EVNDISP_AUX_DIR"/ParameterFiles/ANASUM.runparameter \
+            "$PREDIR" $SKIPIFPROCESSED | tee -a "${TMPLOG}"
     elif [[ $RUNTYPE == "V2DL3" ]]; then
         mkdir -p "$TMPDIR/v2dl3_${C}"
-         "$(dirname "$0")/ANALYSIS.v2dl3.sh" ${RUNL} \
+         "$(dirname "$0")/ANALYSIS.v2dl3.sh" "${RUNL}" \
              "$TMPDIR/v2dl3_${C}" \
-             ${C} | tee -a ${TMPLOG}
+             "${C}" | tee -a "${TMPLOG}"
     else
         echo "Error: unknown run type $RUNTYPE (allowed: ANASUM, V2DL3, or PRECUTS)"
         exit
@@ -84,5 +84,5 @@ echo
 echo "===================================================================="
 echo "JOB SUBMISSION"
 echo "===================================================================="
-grep -A 1 "Job submission using HTCondor" ${TMPLOG} | sort -r -u
-rm -f ${TMPLOG}
+grep -A 1 "Job submission using HTCondor" "${TMPLOG}" | sort -r -u
+rm -f "${TMPLOG}"

scripts/ANALYSIS.anasum_combine.sh

@@ -2,7 +2,7 @@
 # script to combine anasum files processed in parallel mode
 
 # qsub parameters
-# shellcheck disable=SC2034
+# shellcheck disable=SC2034  # SGE resource directives, read by job scheduler
 h_cpu=0:59:00; h_vmem=12000M; tmpdir_size=150G
 
 if [[ $# -lt 3 ]]; then
@@ -39,9 +39,8 @@ fi
 
 # Run init script
 if [ ! -n "$EVNDISP_APPTAINER" ]; then
-    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh"
+    bash "$( cd "$( dirname "$0" )" && pwd )/helper_scripts/UTILITY.script_init.sh" || exit 1
 fi
-[[ $? != "0" ]] && exit 1
 
 # Parse command line arguments
 RUNLIST=$1
@@ -57,7 +56,7 @@ if [[ ! -f "$RUNLIST" ]]; then
 fi
 
 # Check that run parameter file exists
-if [[ "$RUNP" == `basename $RUNP` ]]; then
+if [[ "$RUNP" == $(basename "$RUNP") ]]; then
     RUNP="$VERITAS_EVNDISP_AUX_DIR/ParameterFiles/$RUNP"
 fi
 if [[ ! -f "$RUNP" ]]; then
@@ -66,15 +65,15 @@ if [[ ! -f "$RUNP" ]]; then
 fi
 
 # directory for run scripts
-DATE=`date +"%y%m%d"`
+DATE=$(date +"%y%m%d")
 LOGDIR="$VERITAS_USER_LOG_DIR/ANASUM.COMBINE-${DATE}-$(uuidgen)"
 mkdir -p "$LOGDIR"
 echo -e "Log files will be written to:\n $LOGDIR"
 
 # Job submission script
 SUBSCRIPT="$(dirname "$0")/helper_scripts/ANALYSIS.anasum_combine_sub"
 
-FSCRIPT="$LOGDIR/anasum_combine-$DATE-RUN$RUN-$(date +%s)"
+FSCRIPT="$LOGDIR/anasum_combine-$DATE-$(basename "$OUTFILE")-$(date +%s)"
 echo "Run script written to $FSCRIPT"
 
 # Check that anasum output files exist before combining
@@ -94,29 +93,31 @@ chmod u+x "$FSCRIPT.sh"
 
 # run locally or on cluster
 SUBC=$("$(dirname "$0")/helper_scripts/UTILITY.readSubmissionCommand.sh")
-SUBC=`eval "echo \"$SUBC\""`
+SUBC=$(eval "echo \"$SUBC\"")
 if [[ $SUBC == *"ERROR"* ]]; then
     echo "$SUBC"
     exit
 fi
 if [[ $SUBC == *qsub* ]]; then
-    JOBID=`$SUBC $FSCRIPT.sh`
+    # shellcheck disable=SC2086
+    JOBID=$($SUBC "$FSCRIPT".sh)
     # account for -terse changing the job number format
     if [[ $SUBC != *-terse* ]] ; then
         echo "without -terse!"      # need to match VVVVVVVV  8539483  and 3843483.1-4:2
         JOBID=$( echo "$JOBID" | grep -oP "Your job [0-9.-:]+" | awk '{ print $3 }' )
     fi
 elif [[ $SUBC == *condor* ]]; then
     "$(dirname "$0")/helper_scripts/UTILITY.condorSubmission.sh" "$FSCRIPT.sh" "$h_vmem" "$tmpdir_size"
-    condor_submit $FSCRIPT.sh.condor
-echo "RUN $RUN JOBID $JOBID"
-    echo "RUN $RUN SCRIPT $FSCRIPT.sh"
+    condor_submit "$FSCRIPT".sh.condor
+echo "OUTFILE $OUTFILE JOBID $JOBID"
+    echo "OUTFILE $OUTFILE SCRIPT $FSCRIPT.sh"
     if [[ $SUBC != */dev/null* ]] ; then
-        echo "RUN $RUN OLOG $FSCRIPT.sh.o$JOBID"
-        echo "RUN $RUN ELOG $FSCRIPT.sh.e$JOBID"
+        echo "OUTFILE $OUTFILE OLOG $FSCRIPT.sh.o$JOBID"
+        echo "OUTFILE $OUTFILE ELOG $FSCRIPT.sh.e$JOBID"
     fi
 elif [[ $SUBC == *sbatch* ]]; then
-    $SUBC $FSCRIPT.sh
+    # shellcheck disable=SC2086
+    $SUBC "$FSCRIPT".sh
 elif [[ $SUBC == *parallel* ]]; then
     echo "$FSCRIPT.sh &> $FSCRIPT.log" >> "$LOGDIR/runscripts.$(date +"%s").dat"
 elif [[ "$SUBC" == *simple* ]] ; then

scripts/ANALYSIS.anasum_link_files.sh

@@ -25,8 +25,7 @@ exit
 fi
 
 # Run init script
-bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh"
-[[ $? != "0" ]] && exit 1
+bash "$(dirname "$0")/helper_scripts/UTILITY.script_init.sh" || exit 1
 
 # Parse command line arguments
 RUNLIST=$1
@@ -40,7 +39,7 @@ if [[ ! -f "$RUNLIST" ]]; then
 fi
 
 # output directory
-mkdir -p ${ODIR}
+mkdir -p "${ODIR}"
 # directory schema
 getNumberedDirectory()
 {
@@ -51,17 +50,17 @@ getNumberedDirectory()
     else
         NDIR="${IDIR}/${TRUN:0:2}/"
     fi
-    echo ${NDIR}
+    echo "${NDIR}"
 }
 
-RUNS=`cat "$RUNLIST"`
-NRUNS=`cat "$RUNLIST" | wc -l `
+RUNS=$(cat "$RUNLIST")
+NRUNS=$(cat "$RUNLIST" | wc -l )
 echo "total number of runs to be linked: $NRUNS"
 
 for RUN in "${RUNS[@]}"; do
-    ARCHIVEDIR=$(getNumberedDirectory $RUN $DDIR)
+    ARCHIVEDIR=$(getNumberedDirectory "$RUN" "$DDIR")
     if [ -e "${ARCHIVEDIR}/${RUN}.anasum.root" ]; then
-        ls ${ARCHIVEDIR}/${RUN}.anasum.root
-        ln -f -s ${ARCHIVEDIR}/${RUN}.anasum.root ${ODIR}/${RUN}.anasum.root
+        ls "${ARCHIVEDIR}"/"${RUN}".anasum.root
+        ln -f -s "${ARCHIVEDIR}"/"${RUN}".anasum.root "${ODIR}"/"${RUN}".anasum.root
     fi
 done