From 6ce273658b5887b73d8f96a393ae607c99359f2e Mon Sep 17 00:00:00 2001
From: Kaushik Malapati <kaushikm@psbuild-rhel7-02.Slac.Stanford.EDU>
Date: Mon, 6 May 2024 13:35:33 -0700
Subject: [PATCH 1/3] MNT: Shellchecking bash scripts

---
 .shellcheckrc                 |   2 +-
 LICENSE.md                    |  62 +++++++-------
 README.md                     |   6 +-
 rc/vimrc                      |   1 -
 scripts/ami_offline_psana     |  22 ++---
 scripts/archive-resume        |   4 +-
 scripts/archive-status        |   4 +-
 scripts/camViewer             |  68 +++++++--------
 scripts/checkcnf              |   1 +
 scripts/configdb_readxtc      |  24 +++---
 scripts/daq_control           |   4 +-
 scripts/daq_waitwin           |  16 ++--
 scripts/dev_conda             |   3 +-
 scripts/eloggrabber           |  36 ++++----
 scripts/get_curr_exp          |  28 +++---
 scripts/get_hutch_name        |  12 +--
 scripts/get_lastRun           |  52 ++++++------
 scripts/grep_ioc              |   6 +-
 scripts/grep_pv               |  12 +--
 scripts/imgr                  |   6 +-
 scripts/iocmanager            |   4 +-
 scripts/ioctool               |  63 +++++++-------
 scripts/ipmConfigEpics        | 130 ++++++++++++++--------------
 scripts/kinit_helper          |   2 +-
 scripts/makepeds              |  80 ++++++++---------
 scripts/makepeds_psana        | 156 +++++++++++++++++-----------------
 scripts/motor-expert-screen   |  49 +++++------
 scripts/motor-typhos          |   8 +-
 scripts/motorInfo             |  89 ++++++++++---------
 scripts/new_bare_repo         |   2 +-
 scripts/pcds_conda            |   1 -
 scripts/pkg_release           |  10 +--
 scripts/pmgr                  |   4 +-
 scripts/pydev_register        |   2 +-
 scripts/restartdaq            |  36 ++++----
 scripts/serverStat            |  37 ++++----
 scripts/set_gem_timing        |   4 +-
 scripts/startami              |  48 +++++------
 scripts/stopami               |  36 ++++----
 scripts/stopdaq               |   5 +-
 scripts/takepeds              |  14 +--
 scripts/verify-hutch          |   4 +-
 scripts/wheredaq              |   2 +-
 scripts/wherepsana            |  43 +++++-----
 scripts/xpp_update_happi_line |   2 +-
 45 files changed, 594 insertions(+), 606 deletions(-)

diff --git a/.shellcheckrc b/.shellcheckrc
index 08c7738e..4db12541 100644
--- a/.shellcheckrc
+++ b/.shellcheckrc
@@ -1 +1 @@
-disable=SC1091  # allow sourcing files that can't immediately be found (pcds_conda)
+disable=SC1091,SC2018,SC2019  # allow sourcing files that can't immediately be found (pcds_conda), disable warnings about supporting accents and foreign languages
diff --git a/LICENSE.md b/LICENSE.md
index 010b5a49..336b168d 100644
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -1,39 +1,39 @@
-Copyright (c) 2018, The Board of Trustees of the Leland Stanford Junior 
-University, through SLAC National Accelerator Laboratory (subject to receipt 
-of any required approvals from the U.S. Dept. of Energy). All rights reserved. 
-Redistribution and use in source and binary forms, with or without 
+Copyright (c) 2018, The Board of Trustees of the Leland Stanford Junior
+University, through SLAC National Accelerator Laboratory (subject to receipt
+of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
- 
-(1) Redistributions of source code must retain the above copyright notice, 
-    this list of conditions and the following disclaimer. 
 
-(2) Redistributions in binary form must reproduce the above copyright notice, 
-    this list of conditions and the following disclaimer in the documentation 
-    and/or other materials provided with the distribution. 
+(1) Redistributions of source code must retain the above copyright notice,
+    this list of conditions and the following disclaimer.
 
-(3) Neither the name of the Leland Stanford Junior University, SLAC National 
-    Accelerator Laboratory, U.S. Dept. of Energy nor the names of its 
-    contributors may be used to endorse or promote products derived from this 
-    software without specific prior written permission. 
+(2) Redistributions in binary form must reproduce the above copyright notice,
+    this list of conditions and the following disclaimer in the documentation
+    and/or other materials provided with the distribution.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER, THE UNITED STATES GOVERNMENT, 
-OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT 
-OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING 
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY 
+(3) Neither the name of the Leland Stanford Junior University, SLAC National
+    Accelerator Laboratory, U.S. Dept. of Energy nor the names of its
+    contributors may be used to endorse or promote products derived from this
+    software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER, THE UNITED STATES GOVERNMENT,
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
 OF SUCH DAMAGE.
 
-You are under no obligation whatsoever to provide any bug fixes, patches, or 
-upgrades to the features, functionality or performance of the source code 
-("Enhancements") to anyone; however, if you choose to make your Enhancements 
-available either publicly, or directly to SLAC National Accelerator Laboratory, 
-without imposing a separate written license agreement for such Enhancements, 
-then you hereby grant the following license: a non-exclusive, royalty-free 
+You are under no obligation whatsoever to provide any bug fixes, patches, or
+upgrades to the features, functionality or performance of the source code
+("Enhancements") to anyone; however, if you choose to make your Enhancements
+available either publicly, or directly to SLAC National Accelerator Laboratory,
+without imposing a separate written license agreement for such Enhancements,
+then you hereby grant the following license: a non-exclusive, royalty-free
 perpetual license to install, use, modify, prepare derivative works, incorporate
-into other computer software, distribute, and sublicense such Enhancements or 
+into other computer software, distribute, and sublicense such Enhancements or
 derivative works thereof, in binary and source code form.
diff --git a/README.md b/README.md
index a6ae291f..c0ad9330 100644
--- a/README.md
+++ b/README.md
@@ -308,7 +308,7 @@ usage: ioctool &lt;ioc&gt;|&lt;pv&gt; [option]<br/>
     telnet : starts a telnet session with the ioc<br/>
     pvs	   : opens the IOC.pvlist file in less<br/>
     </td>
-</tr>          
+</tr>
 
 <tr>
     <td>ipmConfigEpics</td>
@@ -640,9 +640,9 @@ Optional arguments:<br/>
 
 <tr>
     <td> set_gem_timing</td>
-    <td> 
+    <td>
     Usage: set_gem_timing [SC or NC]
     </td>
 </tr>
 
-</table>
\ No newline at end of file
+</table>
diff --git a/rc/vimrc b/rc/vimrc
index 0838aaf0..c5ba6ec3 100644
--- a/rc/vimrc
+++ b/rc/vimrc
@@ -24,4 +24,3 @@ au FileType python
     \     autoindent
     \     fileformat=unix
     \     encoding=utf-8
-
diff --git a/scripts/ami_offline_psana b/scripts/ami_offline_psana
index 389f0e62..bc170e43 100755
--- a/scripts/ami_offline_psana
+++ b/scripts/ami_offline_psana
@@ -7,7 +7,7 @@ usage: $0 options
 We will run ami_offline
 
 OPTIONS:
--e <expnumber> 
+-e <expnumber>
 -R rebinning (binned to 640x640)
 -n no plugins
 EOF
@@ -30,7 +30,7 @@ do
 	R)
 	    REBIN=1
 	    ;;
-	n)  
+	n)
 	    NOPLUG=1
 	    ;;
 	?)
@@ -44,14 +44,14 @@ if [ -z "$EXP" ]; then
     echo getting the experiment "$EXP"
     HUTCH=$(get_hutch_name)
     if [ "$HUTCH" == 'unknown_hutch' ]; then
-	read -p 'please enter an experiment name: ' EXP
+	read -rp 'please enter an experiment name: ' EXP
     else
 	EXP=$(get_curr_exp)
     fi
 fi
 HUTCH=${EXP:0:3}
 
-if [ -z $REBIN ]; then
+if [[ -z $REBIN ]]; then
     ARGSTR=$ARGSTR' -R'
 fi
 
@@ -69,7 +69,7 @@ fi
 ami_base_path=$(grep ami_base_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep -v '#' | grep -v 'ami_base_path+' | tail -n 1 | awk 'BEGIN { FS = "=" }; { print $2}' | sed s/\'//g)
 ami_path=$ami_base_path$(grep ami_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep -v 'ami_path+' | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+//g | sed s/\'//g)
 
-if [ ! -f  $ami_path/offline_ami ]; then
+if [[ ! -f  $ami_path/offline_ami ]]; then
     echo "could not find offline_ami executable in ""$ami_path"
     exit
 fi
@@ -79,7 +79,7 @@ pp=$(grep plugin_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNF" | grep ami_ba
 plugin_path=$ami_base_path$pp
 plugin_str=$plugin_path'/libtimetooldbd.so'
 
-if [ -z $NOPLUG ]; then
+if [[ -z $NOPLUG ]]; then
     ARGSTR=$ARGSTR' -L '$plugin_str
 fi
 #ARGSTR=$ARGSTR -X /reg/neh/operator/$HUTCH\opr/experiments
@@ -91,19 +91,19 @@ if [ "${HOSTNAME:0:5}" == 'psana' ]; then
     if [ "$HAVE_RUNS" == 0 ]; then
 	echo 'did not find any xtc files in /reg/d/psdm/'"$HUTCH"'/'"$EXP"', will exit'
 	exit
-    fi 
+    fi
 elif [ "${HOSTNAME:0:3}" == 'drp' ]; then
     XTCDIR=/cds/data/drpsrcf/$HUTCH/$EXP/xtc/
     HAVE_RUNS=$(find "$XTCDIR"/*r* | wc -l)
     if [ "$HAVE_RUNS" == 0 ]; then
 	echo 'did not find any xtc files in /cds/data/drpsrcf/'"$HUTCH"'/'"$EXP"', will exit'
 	exit
-    fi 
+    fi
 elif  [ "${HOSTNAME:8:3}" == 'rec' ]; then
     XTCDIR=/u2/REC/daq/xtc/
 elif  [ "${HOSTNAME:8:3}" == 'dss' ]; then
     EXPID=$(get_info --setExp "$EXP" --experimentNumber)
-    XTCDIR=/u2/pcds/pds/"$HUTCH"/e"$EXPID"/  
+    XTCDIR=/u2/pcds/pds/"$HUTCH"/e"$EXPID"/
 else
     echo 'Please ssh to a psana, recorder or dss node to see data'
     exit
@@ -124,6 +124,6 @@ LD_LIBRARY_PATH=/reg/g/pcds/dist/pds/"$HUTCH"/current/build/pds/lib/x86_64-linux
 
 #ARGSTR='-p '$XTCDIR $ARGSTR
 echo '----------------------------------------------'
-echo "$ami_path"/offline_ami $ARGSTR -p $XTCDIR 
+echo "$ami_path"/offline_ami "$ARGSTR" -p "$XTCDIR"
 echo '----------------------------------------------'
-$ami_path/offline_ami $ARGSTR -p $XTCDIR 
+"$ami_path"/offline_ami "$ARGSTR" -p "$XTCDIR"
diff --git a/scripts/archive-resume b/scripts/archive-resume
index 9fd8ba8e..05107287 100755
--- a/scripts/archive-resume
+++ b/scripts/archive-resume
@@ -12,7 +12,7 @@ if [[ -z $1 ]]; then
     usage
     exit 1
 fi
-    
+
 if [[ ($1 == "--help") || ($1 == "-h") ]]; then
     usage
     exit 0
@@ -20,5 +20,5 @@ fi
 
 result=$(curl -s "http://pscaa01.slac.stanford.edu:17665/mgmt/bpl/resumeArchivingPV?pv=$1")
 echo
-echo $result | cut -d'{' -f2 | cut -d '}' -f1 | tr ',' '\n'
+echo "$result" | cut -d'{' -f2 | cut -d '}' -f1 | tr ',' '\n'
 echo
diff --git a/scripts/archive-status b/scripts/archive-status
index 1ee864bf..0b525dfc 100755
--- a/scripts/archive-status
+++ b/scripts/archive-status
@@ -12,7 +12,7 @@ if [[ -z $1 ]]; then
     usage
     exit 1
 fi
-    
+
 if [[ ($1 == "--help") || ($1 == "-h") ]]; then
     usage
     exit 0
@@ -20,5 +20,5 @@ fi
 
 result=$(curl -s "http://pscaa01.slac.stanford.edu:17665/mgmt/bpl/getPVStatus?pv=$1")
 echo
-echo $result | cut -d'{' -f2 | cut -d'}' -f1 | tr ',' '\n'
+echo "$result" | cut -d'{' -f2 | cut -d'}' -f1 | tr ',' '\n'
 echo
diff --git a/scripts/camViewer b/scripts/camViewer
index 180d3a7a..65549e80 100755
--- a/scripts/camViewer
+++ b/scripts/camViewer
@@ -23,7 +23,7 @@ VIEWERCFG=/reg/g/pcds/pyps/config/$hutch/camviewer.cfg
 # Match "-" or "_" or " ".
 NAME=$(echo "$1" | sed -e 's/-/ /g' -e 's/_/ /g' -e 's/ /[-_ ]/g')
 #
-# The story here: 
+# The story here:
 # See how many matches we have in the hutch.
 # If 0, try looking in all of the hutches.
 # If 1, then we're done.
@@ -34,11 +34,12 @@ NAME=$(echo "$1" | sed -e 's/-/ /g' -e 's/_/ /g' -e 's/ /[-_ ]/g')
 #
 # Make a temp file with just the PVs and camera names that match.
 tmp=/tmp/cv.$$
-cat "$VIEWERCFG" | grep -i "$NAME" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
+grep -i "$NAME" "$VIEWERCFG" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
 c=$(wc -l <$tmp)
 if [ "$c" -eq 0 ]; then
-    VIEWERCFG=/reg/g/pcds/pyps/config/*/camviewer.cfg
-    cat $VIEWERCFG | grep -i "$NAME" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
+    VIEWERCFG="/reg/g/pcds/pyps/config/*/camviewer.cfg"
+    # shellcheck disable=SC2086
+    grep -i "$NAME" $VIEWERCFG | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
     c=$(wc -l <$tmp)
     if [ "$c" -eq 0 ]; then
 	echo "No match for $1"
@@ -52,14 +53,14 @@ if [ "$c" -eq 1 ]; then
     return
 fi
 # OK, ambiguous.  Look for a complete match on the second word.
-if [ "$(grep -E -i " $NAME\$" < $tmp | wc -l)" -eq 1 ]; then
+if [ "$(grep -E -i -c " $NAME\$" < $tmp)" -eq 1 ]; then
     CAMPVFULL=$(grep -E -i " $NAME\$" < $tmp | awk '{print $1;}')
     rm -f $tmp
     return
 fi
 # What about just a match at the end? (That is, if we are searching
 # for "yag1", prefer "mec_yag1" to "mec_yag11".)
-if [ "$(grep -E -i "$NAME\$" < $tmp | wc -l)" -eq 1 ]; then
+if [ "$(grep -E -i -c "$NAME\$" < $tmp)" -eq 1 ]; then
     CAMPVFULL=$(grep -E -i "$NAME\$" < $tmp | awk '{print $1;}')
     rm -f $tmp
     return
@@ -81,7 +82,7 @@ VIEWERCFG=/reg/g/pcds/pyps/config/$hutch/camviewer.cfg
 printf -v GIGENUM "%02d" "$2"
 GIGEBASE=$HUTCH:GIGE:$GIGENUM
 
-echo "$(grep "$GIGEBASE" "$VIEWERCFG" | grep -v '#' | awk -F, '{print $4}')"
+grep "$GIGEBASE" "$VIEWERCFG" | grep -v '#' | awk -F, '{print $4}'
 }
 
 isNum(){
@@ -103,27 +104,20 @@ fi
 HUTCH=$(echo "$1" | tr a-z A-Z)
 hutch=$(echo "$1" | tr A-Z a-z)
 
-ALLVIEWERCFG=/reg/g/pcds/pyps/config/*/camviewer.cfg
-echo cat $ALLVIEWERCFG | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' 
+ALLVIEWERCFG="/reg/g/pcds/pyps/config/*/camviewer.cfg"
+echo grep -v '#' "$ALLVIEWERCFG" | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }'
 
 VIEWERCFGLFE=/reg/g/pcds/pyps/config/lfe/camviewer.cfg
-VIEWERCFG=/reg/g/pcds/pyps/config/$hutch/camviewer.cfg
 VIEWERCFGXRT=/reg/g/pcds/pyps/config/xrt/camviewer.cfg
-
+VIEWERCFG=/reg/g/pcds/pyps/config/$hutch/camviewer.cfg
 if  [ "$hutch" != 'tmo' ] && [ "$hutch" != 'rix' ]; then
-    for gige_cam in $(grep -v '#' $VIEWERCFGLFE | awk -F, '{print $4 "\n"} '); do
-        echo "$gige_cam"
-    done
-
-    for gige_cam in $(grep -v '#' $VIEWERCFGXRT | awk -F, '{print $4 "\n" }'); do
-	echo "$gige_cam"
-    done
+    grep -v '#' $VIEWERCFGLFE | awk -F, '{if ($4) print $4}' | sed 's/ //g'
+    grep -v '#' $VIEWERCFGXRT | awk -F, '{if ($4) print $4}' | sed 's/ //g'
 fi
 
-for gige_cam in $(grep -v '#' "$VIEWERCFG" | awk -F, '{print $4 "\n" }'); do
-    echo "$gige_cam"
-done
-
+if  [ "$hutch" != 'lfe' ]; then
+grep -v '#' "$VIEWERCFG" | awk -F, '{if ($4) print $4}' | sed 's/ //g'
+fi
 }
 
 iocfpv() {
@@ -138,7 +132,7 @@ iocinfo() {
             iochutch=$(echo "$INFO" | cut -d'/' -f7)
         fi
     done
-}    
+}
 
 usage()
 {
@@ -185,9 +179,10 @@ ACQUIRE=0
 STOP=0
 NUDGE=0
 
-OPTIONS=$(getopt -o lmredasnc:w:u:H: --long list,main,reboot,enable,disable,acquire,stop,nudge,cam:,wait:,rate:,hutch: -n \'$0\' -- "$@")
-
-if [ $? != 0 ] ; then echo "Terminating..." >&2 ; exit 1 ; fi
+if ! OPTIONS=$(getopt -o lmredasnc:w:u:H: --long list,main,reboot,enable,disable,acquire,stop,nudge,cam:,wait:,rate:,hutch: -n \'"$0"\' -- "$@"); then
+    echo "Terminating..." >&2
+    exit 1
+fi
 
 
 
@@ -195,10 +190,10 @@ eval set -- "$OPTIONS"
 
 
 
-while [ : ]
+while [[ $# -gt 0 ]]
 do
     case "$1" in
-        -l|--list)  
+        -l|--list)
             LIST=1
             shift
             ;;
@@ -246,9 +241,9 @@ do
             usage
             break
             ;;
-        --) 
-            shift 
-            break 
+        --)
+            shift
+            break
             ;;
         *)
             echo "Internal Error"
@@ -259,7 +254,7 @@ do
 done
 
 if [ $# -ge 1 ]; then
-    echo "Positional arguments unsupported: $@" >&2
+    echo "Positional arguments unsupported: $*" >&2
     usage
     exit 1
 fi
@@ -320,17 +315,18 @@ name_to_pv "$CAMNAME" "$hutch"
 if [ $MAINSCREEN -gt 0 ]; then
     tmp=/tmp/cv.$$
     list_cams "$hutch" >$tmp
-    c=$(wc <$tmp | grep "$CAMNAME" $tmp | awk '{print $1}')
+
+    c=$(wc $tmp | grep "$CAMNAME" $tmp | awk '{print $1}') # not sure what is happening here
     if [ "$c" == '' ]; then
         echo "Camera name not found in hutch. To see which cameras you can access from your current machine use the '-l/--list' option."
         sleep 3
     elif [ "$c" == "$CAMNAME" ] && [ "$hutch" != "$(get_info --gethutch)" ] ; then
-        echo "To use camera controls, you must be on the same hutch machine as your camera." 
+        echo "To use camera controls, you must be on the same hutch machine as your camera."
         echo "Opening read-only main screen..."
         sleep 3
-    
+
     rm -f $tmp
-    fi    
+    fi
     echo 'try to get the main screen for: ' "$CAMNAME"
     echo 'start the main screen for camera base PV: ' "$CAMPVFULL"
     cmdName=$(caget -St "$CAMPVFULL":LAUNCH_EDM)
diff --git a/scripts/checkcnf b/scripts/checkcnf
index 81e22af1..b9d53e7d 100755
--- a/scripts/checkcnf
+++ b/scripts/checkcnf
@@ -18,6 +18,7 @@ HUTCH=$(get_info --gethutch)
 
 LCLS2_HUTCHES="rix, tmo, ued"
 if echo "$LCLS2_HUTCHES" | grep -iw "$HUTCH" > /dev/null; then
+    # shellcheck source=/reg/g/pcds/dist/pds/rix/scripts/setup_env.sh
     source /reg/g/pcds/dist/pds/"$HUTCH"/scripts/setup_env.sh
     PROCMGR='procmgr'
 else
diff --git a/scripts/configdb_readxtc b/scripts/configdb_readxtc
index 453a05f6..80a9d803 100755
--- a/scripts/configdb_readxtc
+++ b/scripts/configdb_readxtc
@@ -8,7 +8,7 @@ We will run configdb_readxtc
 
 OPTIONS:
 -u user (needs to be able to log into the psananeh/feh)
--e expnumber 
+-e expnumber
 EOF
 }
 
@@ -17,7 +17,7 @@ if [[ ($1 == "--help") || ($1 == "-h") ]]; then
 	exit 0
 fi
 
-USER=`whoami`
+USER=$(whoami)
 ARGSTR=''
 
 while getopts "u:e:" OPTION
@@ -37,10 +37,10 @@ do
 done
 
 if [[ $USER =~ "opr" ]]; then
-    printf "Please enter user name (cannot run as xppopr): \n"; read USER
+    printf "Please enter user name (cannot run as xppopr): \n"; read -r USER
 fi
 
-: ${EXP:=`get_curr_exp`}
+: "${EXP:=$(get_curr_exp)}"
 HUTCH=${EXP:0:3}
 
 # check if experiment is passed, then use that
@@ -54,15 +54,13 @@ HUTCH=${EXP:0:3}
 #
 
 opt_dir="/reg/g/pcds/dist/pds/$HUTCH/current/build/pdsapp/bin/x86_64-rhel7-opt"
-eval find $opt_dir/configdb_readxtc
+eval find "$opt_dir"/configdb_readxtc
 ret_code=$?
 if [ $ret_code == 0 ]; then
     EXE='/reg/g/pcds/dist/pds/'$HUTCH'/current/build/pdsapp/bin/x86_64-rhel7-opt/configdb_readxtc'
 else
     dir="/reg/g/pcds/dist/pds/xpp/current/build/pdsapp/bin/x86_64-rhel7"
-    eval find $dir/configdb_readxtc
-    ret_code=$?
-    if [ $ret_code2 == 0 ]; then
+    if eval find $dir/configdb_readxtc; then
 	EXE='/reg/g/pcds/dist/pds/'$HUTCH'/current/build/pdsapp/bin/x86_64-rhel7/configdb_readxtc'
     else
 	echo 'could not find configdb_readxtc executable'
@@ -74,12 +72,10 @@ fi
 # check hostname,only ssh if on control machine.
 #
 if [[ $HOSTNAME =~ "psana" ]]; then
-    $EXE /reg/d/psdm/$HUTCH/$EXP/xtc
+    $EXE /reg/d/psdm/"$HUTCH"/"$EXP"/xtc
 elif  [[ $HOSTNAME =~ "psusr" ]]; then
-    ssh -Y $USER@psana "$EXE /reg/d/psdm/$HUTCH/$EXP/xtc"
+    ssh -Y "$USER"@psana "$EXE /reg/d/psdm/$HUTCH/$EXP/xtc"
 else
-    echo $EXE /reg/d/psdm/$HUTCH/$EXP/xtc
-    ssh -Y $USER@psdev ssh -Y psana "$EXE /reg/d/psdm/$HUTCH/$EXP/xtc"
+    echo "$EXE /reg/d/psdm/$HUTCH/$EXP/xtc"
+    ssh -Y "$USER"@psdev ssh -Y psana "$EXE /reg/d/psdm/$HUTCH/$EXP/xtc"
 fi
- 
-   
diff --git a/scripts/daq_control b/scripts/daq_control
index dca68c5e..a788c9fb 100755
--- a/scripts/daq_control
+++ b/scripts/daq_control
@@ -1,6 +1,6 @@
 #!/bin/bash
 cat << EOF
-This tool is deprecated. Please let your ECS staff 
-know what you were trying to do in case you are not 
+This tool is deprecated. Please let your ECS staff
+know what you were trying to do in case you are not
 aware of a supported alternative
 EOF
diff --git a/scripts/daq_waitwin b/scripts/daq_waitwin
index bba8fa31..1a005cd7 100755
--- a/scripts/daq_waitwin
+++ b/scripts/daq_waitwin
@@ -17,14 +17,14 @@ source /reg/g/pcds/setup/pathmunge.sh
 ldpathmunge /usr/local/lib
 
 
-if [[ $# > 0 ]]; then
+if [[ $# -gt 0 ]]; then
     SEARCHOPT='--onlyvisible --maxdepth 2 --limit 1 --all --desktop '$1' --sync '
-else 
+else
     SEARCHOPT='--onlyvisible --maxdepth 2 --limit 1 --all --sync '
 fi
-proc=`xdotool search $SEARCHOPT --name 'ProcStat'`
-ami=`xdotool search $SEARCHOPT --name 'DAQ Online Monitoring'`
-env=`xdotool search $SEARCHOPT --name 'Env'`
-crwin=`xdotool search $SEARCHOPT --name 'DAQ Control'` 
-echo $proc $ami $env $crwin
-exit
\ No newline at end of file
+proc=$(xdotool search "$SEARCHOPT" --name 'ProcStat')
+ami=$(xdotool search "$SEARCHOPT" --name 'DAQ Online Monitoring')
+env=$(xdotool search "$SEARCHOPT" --name 'Env')
+crwin=$(xdotool search "$SEARCHOPT" --name 'DAQ Control')
+echo "$proc $ami $env $crwin"
+exit
diff --git a/scripts/dev_conda b/scripts/dev_conda
index f23219d7..35762b2d 100755
--- a/scripts/dev_conda
+++ b/scripts/dev_conda
@@ -2,7 +2,7 @@
 usage()
 {
 cat << EOF
-usage: source $0 
+usage: source $0
 
 Source this to activate the latest version a pcds conda environment.
 EOF
@@ -64,4 +64,3 @@ if [ -n "${SSH_CONNECTION}" ]; then
     fi
   fi
 fi
-
diff --git a/scripts/eloggrabber b/scripts/eloggrabber
index 90be0619..c264a30a 100755
--- a/scripts/eloggrabber
+++ b/scripts/eloggrabber
@@ -26,9 +26,9 @@ grab()
 	exit
     fi
     LogBookGrabber_qt \
-	-i $HUTCH \
-	-e $1 \
-	-u $USERNAME \
+	-i "$HUTCH" \
+	-e "$1" \
+	-u "$USERNAME" \
 	-p pcds \
 	-w https://pswww.slac.stanford.edu/ws-auth/lgbk
     exit
@@ -38,21 +38,21 @@ grab()
 grab_script()
 {
 	LogBookGrabber_qt \
-    -i $HUTCH \
-    -e $EXPNAME \
-    -u $USERNAME \
+    -i "$HUTCH" \
+    -e "$EXPNAME" \
+    -u "$USERNAME" \
     -p pcds \
     -w https://pswww.slac.stanford.edu/ws-auth/lgbk \
-    -c $SCRIPT
+    -c "$SCRIPT"
     exit 1
 }
 
 grab_user()
 {
     LogBookGrabber_qt \
-	-i $HUTCH \
-	-e $1 \
-	-u $USERNAME \
+	-i "$HUTCH" \
+	-e "$1" \
+	-u "$USERNAME" \
 	-w https://pswww.slac.stanford.edu/ws-kerb/lgbk
     exit
 }
@@ -67,7 +67,7 @@ grab_instrument()
     LogBookGrabber_qt \
 	-i OPS \
 	-e "$EXPNAME" \
-	-u $USERNAME \
+	-u "$USERNAME" \
 	-p pcds \
 	-w https://pswww.slac.stanford.edu/ws-auth/lgbk
     exit
@@ -79,7 +79,7 @@ grab_controls()
     LogBookGrabber_qt \
 	-i OPS \
 	-e "$EXPNAME" \
-	-u $USERNAME \
+	-u "$USERNAME" \
 	-p pcds \
 	-w https://pswww.slac.stanford.edu/ws-auth/lgbk
     exit
@@ -92,9 +92,9 @@ fi
 
 ##who am I doing this? Why don't just use the actual username?
 #USERNAME=`get_info --gethutch`opr
-USERNAME=`whoami`
-EXPNAME=`get_curr_exp`
-HUTCH=`get_info --gethutch`
+USERNAME=$(whoami)
+EXPNAME=$(get_curr_exp)
+HUTCH=$(get_info --gethutch)
 
 while getopts "e:u:s:xct" OPTION
 do
@@ -105,7 +105,7 @@ do
 	    ;;
 	u)
 	    USERNAME=$OPTARG
-	    grab_user $EXPNAME
+	    grab_user "$EXPNAME"
 	    ;;
 	s)
 	    SCRIPT=$OPTARG
@@ -125,7 +125,7 @@ do
 done
 
 if [[ $USERNAME == *'opr'* ]]; then
-    grab $EXPNAME
+    grab "$EXPNAME"
 else
-    grab_user $EXPNAME
+    grab_user "$EXPNAME"
 fi
diff --git a/scripts/get_curr_exp b/scripts/get_curr_exp
index da2ceeb9..c3595163 100755
--- a/scripts/get_curr_exp
+++ b/scripts/get_curr_exp
@@ -19,10 +19,10 @@ fi
 while getopts "H:i:le" OPTION
 do
     case $OPTION in
-	i) 
+	i)
 	    INSTRUMENT=$OPTARG
 	    ;;
-	H) 
+	H)
 	    INSTRUMENT=$OPTARG
 	    ;;
 	?)
@@ -32,23 +32,23 @@ do
 	esac
 done
 
-DIRTMP=`dirname  "${BASH_SOURCE[0]}"`
-DIR="$( cd $DIRTMP && pwd -P )"
+DIRTMP=$(dirname  "${BASH_SOURCE[0]}")
+DIR=$(cd "$DIRTMP" && pwd -P)
 PATH=$PATH:$DIR
 
-if [ $INSTRUMENT != 'xxx' ]; then
-    CURR_EXP=`get_info --hutch ${INSTRUMENT^^} --exp`
+if [[ $INSTRUMENT != 'xxx' ]]; then
+    CURR_EXP=$(get_info --hutch "${INSTRUMENT^^}" --exp)
 else
-    CURR_EXP=`get_info --exp`
-    if [ $CURR_EXP == 'unknown_hutch' ]; then
-	echo 'Cannot autodetermine hutch, for which hutch would you like to get this information? '
-	read -t 5 hutch
-	if [ $hutch == '' ]; then 
+    CURR_EXP=$(get_info --exp)
+    if [[ $CURR_EXP == 'unknown_hutch' ]]; then
+	echo 'Cannot autodetermine hutch, for which hutch would you like to get this information?'
+	read -rt 5 hutch
+	if [[ $hutch == '' ]]; then
 	    echo 'no response, will quit'
 	    exit 1
 	fi
-	CURR_EXP=`get_info --hutch ${hutch^^} --exp`
+	CURR_EXP=$(get_info --hutch "${hutch^^}" --exp)
     fi
 fi
- 
-echo $CURR_EXP
+
+echo "$CURR_EXP"
diff --git a/scripts/get_hutch_name b/scripts/get_hutch_name
index 84a6fa9e..76d46816 100755
--- a/scripts/get_hutch_name
+++ b/scripts/get_hutch_name
@@ -2,7 +2,7 @@
 usage()
 {
 cat << EOF
-usage: $0 
+usage: $0
 
 Returns the hutch name based on the host it is run on
 EOF
@@ -13,9 +13,9 @@ if [[ ($1 == "--help") || ($1 == "-h") ]]; then
 	exit 0
 fi
 
-DIRTMP=`dirname  "${BASH_SOURCE[0]}"`
-DIR="$( cd $DIRTMP && pwd -P )"
-PATH=$PATH:$DIR
+DIRTMP=$(dirname  "${BASH_SOURCE[0]}")
+DIR=$(cd "$DIRTMP" && pwd -P)
+PATH="$PATH:$DIR"
 
-hutch=`get_info --gethutch`
-echo $hutch
+hutch=$(get_info --gethutch)
+echo "$hutch"
diff --git a/scripts/get_lastRun b/scripts/get_lastRun
index a7442f75..072870af 100755
--- a/scripts/get_lastRun
+++ b/scripts/get_lastRun
@@ -19,23 +19,23 @@ AskLive=0
 Ended=0
 INSTRUMENT='xxx'
 
-DIRTMP=`dirname  "${BASH_SOURCE[0]}"`
-DIR="$( cd $DIRTMP && pwd -P )"
+DIRTMP=$(dirname  "${BASH_SOURCE[0]}")
+DIR=$(cd "$DIRTMP" && pwd -P)
 PATH=$PATH:$DIR
 
 while getopts "H:i:le" OPTION
 do
     case $OPTION in
-	l) 
+	l)
 	    AskLive=1
 	    ;;
-	e) 
+	e)
 	    Ended=1
 	    ;;
-	i) 
+	i)
 	    INSTRUMENT=$OPTARG
 	    ;;
-	H) 
+	H)
 	    INSTRUMENT=$OPTARG
 	    ;;
 	?)
@@ -46,40 +46,40 @@ do
 done
 
 if [ $AskLive -eq 1 ]; then
-    if [ $INSTRUMENT != 'xxx' ]; then
-	CURR_EXP=`get_info --hutch $INSTRUMENT --run --live`    
+    if [[ $INSTRUMENT != 'xxx' ]]; then
+	CURR_EXP=$(get_info --hutch "$INSTRUMENT" --run --live)
     else
-	CURR_EXP=`get_info --run --live`    
+	CURR_EXP=$(get_info --run --live)
 	if [[ $CURR_EXP == *'xxx'* ]]; then
 	    echo 'For which hutch would you like to get this information? '
-	    read hutch
-	    CURR_EXP=`get_info --hutch $hutch --run --live`
+	    read -r hutch
+	    CURR_EXP=$(get_info --hutch "$hutch" --run --live)
 	fi
     fi
 elif [ $Ended -eq 1 ]; then
-    if [ $INSTRUMENT != 'xxx' ]; then
-	CURR_EXP=`get_info --hutch $INSTRUMENT --run --ended`    
+    if [[ $INSTRUMENT != 'xxx' ]]; then
+	CURR_EXP=$(get_info --hutch "$INSTRUMENT" --run --ended)
     else
-	CURR_EXP=`get_info --run --ended`    
+	CURR_EXP=$(get_info --run --ended)
 	if [[ $CURR_EXP == *'xxx'* ]]; then
 	    echo 'For which hutch would you like to get this information? '
-	    read hutch
-	    CURR_EXP=`get_info --hutch $hutch --run --ended`
+	    read -r hutch
+	    CURR_EXP=$(get_info --hutch "$hutch" --run --ended)
 	fi
     fi
 else
-    if [ $INSTRUMENT != 'xxx' ]; then
-	CURR_EXP=`get_info --hutch $INSTRUMENT --run`    
+    if [[ $INSTRUMENT != 'xxx' ]]; then
+	CURR_EXP=$(get_info --hutch "$INSTRUMENT" --run)
     else
-	CURR_EXP=`get_info --run`
+	CURR_EXP=$(get_info --run)
     fi
-    NUM_RET_WORD=`echo $CURR_EXP | wc | awk {'print $2'}`
-    if [ $NUM_RET_WORD == 1 ]; then
-	if [ $CURR_EXP == 'xxx' ]; then
-	    echo 'For which hutch would you like to get this information? '
-	    read hutch
-	    CURR_EXP=`get_info --hutch $hutch --run`
+    NUM_RET_WORD=$(echo "$CURR_EXP" | wc | awk '{print $2}')
+    if [[ $NUM_RET_WORD == 1 ]]; then
+	if [[ $CURR_EXP == 'xxx' ]]; then
+	    echo 'For which hutch would you like to get this information?'
+	    read -r hutch
+	    CURR_EXP=$(get_info --hutch "$hutch" --run)
 	fi
     fi
 fi
-echo $CURR_EXP
+echo "$CURR_EXP"
diff --git a/scripts/grep_ioc b/scripts/grep_ioc
index df78cb38..04d89e5d 100755
--- a/scripts/grep_ioc
+++ b/scripts/grep_ioc
@@ -23,8 +23,8 @@ fi
 if [[ -z $2 ]]; then
     HUTCH="all"
 else
-    for hutchname in "xpp" "xcs" "cxi" "mfx" "mec" "tmo" "rix" "xrt" "aux" "det" "fee" "hpl" "icl" "las" "lfe" "kfe" "tst" "thz" "all"; do 
-        if [[ "${2}" == $hutchname ]]; then
+    for hutchname in "xpp" "xcs" "cxi" "mfx" "mec" "tmo" "rix" "xrt" "aux" "det" "fee" "hpl" "icl" "las" "lfe" "kfe" "tst" "thz" "all"; do
+        if [[ "${2}" == "$hutchname" ]]; then
             HUTCH=$hutchname
         fi
     done
@@ -35,6 +35,6 @@ else
     if [[ $HUTCH == "all" ]]; then
         grep -i "${1}" /reg/g/pcds/pyps/config/*/iocmanager.cfg
     else
-        grep -i "${1}" /reg/g/pcds/pyps/config/${HUTCH}/iocmanager.cfg
+        grep -i "${1}" /reg/g/pcds/pyps/config/"$HUTCH"/iocmanager.cfg
     fi
 fi
diff --git a/scripts/grep_pv b/scripts/grep_pv
index af5d05d4..7ff1cf68 100755
--- a/scripts/grep_pv
+++ b/scripts/grep_pv
@@ -17,20 +17,20 @@ KEYWORD=$1
 
 if [[ -n $KEYWORD ]]; then
     cd /reg/d/iocData/
-    for i in ioc-*; do 
-	cd /reg/d/iocData/$i
+    for i in ioc-*; do
+	cd /reg/d/iocData/"$i"
 	if [ -e ./iocInfo/ ] ; then
      	    cd iocInfo
 	    if [ -e ./IOC.pvlist ] ; then
-		if grep -q $KEYWORD IOC.pvlist
-		then 
+		if grep -q "$KEYWORD" IOC.pvlist
+		then
 		    pwd
-		    grep $KEYWORD IOC.pvlist;
+		    grep "$KEYWORD" IOC.pvlist;
 		    echo ""
 		else
 		    :
 		fi
-	    fi 
+	    fi
 	fi
 	cd ../../
     done
diff --git a/scripts/imgr b/scripts/imgr
index aaf6d0fd..596cd67c 100755
--- a/scripts/imgr
+++ b/scripts/imgr
@@ -18,7 +18,7 @@ imgr IOCNAME [--hutch HUTCH] --upgrade RELEASE_DIR
 imgr IOCNAME [--hutch HUTCH] --move HOST
 imgr IOCNAME [--hutch HUTCH] --move HOST:PORT
 imgr [--hutch HUTCH] --list [--host HOST] [--enabled_only|--disabled_only]
- 
+
 EOF
 }
 if [ $# -lt 1 ]; then
@@ -68,7 +68,7 @@ else
     export IOC_DATA=/cds/data/iocData
     export IOC_COMMON=/cds/data/iocCommon
 fi
-PSPKG_OS=$(${PSPKG_ROOT}/etc/pspkg_os.sh)
+PSPKG_OS=$("$PSPKG_ROOT"/etc/pspkg_os.sh)
 export PSPKG_OS
 if [ "$PSPKG_OS" == rhel5 ]; then
     echo "IocManager 2.0.0 and higher does not run on RHEL5!" >&2
@@ -76,6 +76,6 @@ if [ "$PSPKG_OS" == rhel5 ]; then
 fi
 export QT_XKB_CONFIG_ROOT=/usr/share/X11/xkb
 export PSPKG_RELEASE=controls-0.1.9
-source $PSPKG_ROOT/etc/set_env.sh
+source "$PSPKG_ROOT"/etc/set_env.sh
 
 /reg/g/pcds/pyps/config/"${HUTCH,,}"/iocmanager/imgr.py "$@" --hutch "${HUTCH,,}"
diff --git a/scripts/iocmanager b/scripts/iocmanager
index fd8eaf82..3d241826 100755
--- a/scripts/iocmanager
+++ b/scripts/iocmanager
@@ -38,7 +38,7 @@ else
     export IOC_DATA=/reg/d/iocData
     export IOC_COMMON=/reg/d/iocCommon
 fi
-PSPKG_OS=$(${PSPKG_ROOT}/etc/pspkg_os.sh)
+PSPKG_OS=$("$PSPKG_ROOT"/etc/pspkg_os.sh)
 export PSPKG_OS
 if [ "$PSPKG_OS" == rhel5 ]; then
     echo "IocManager 2.0.0 and higher does not run on RHEL5!"
@@ -46,7 +46,7 @@ if [ "$PSPKG_OS" == rhel5 ]; then
 fi
 export QT_XKB_CONFIG_ROOT=/usr/share/X11/xkb
 export PSPKG_RELEASE=controls-0.1.9
-source $PSPKG_ROOT/etc/set_env.sh
+source "$PSPKG_ROOT"/etc/set_env.sh
 ulimit -c unlimited
 
 /reg/g/pcds/pyps/config/"${HUTCH,,}"/iocmanager/IocManager.py --hutch "${HUTCH,,}" > /dev/null &
diff --git a/scripts/ioctool b/scripts/ioctool
index 78f71e7d..ed915e4b 100755
--- a/scripts/ioctool
+++ b/scripts/ioctool
@@ -4,10 +4,10 @@ function iocfpv {
    ioc=""
    ioc=$(grep_pv "$1" | cut -d'/' -f5 -s)
    if [ -z "$ioc" ]; then
-      echo "Did not find an ioc associated with this PV." >&2 
+      echo "Did not find an ioc associated with this PV." >&2
       exit 1
    elif [[ $ioc = *[[:space:]]* ]]; then # multiple iocs found if space present
-      ioccount=$(echo $ioc | wc -w)
+      ioccount=$(echo "$ioc" | wc -w)
       echo "$1 is found in $ioccount places"
       echo "Which ioc do you care about here? (press enter to exit)"
       printf '%s\n' "$ioc" >&2
@@ -17,8 +17,8 @@ function iocfpv {
          exit 0
       fi
       ioc=$chosenioc
-   fi   
-   
+   fi
+
 }
 
 function iocdir {
@@ -29,9 +29,9 @@ function iocdir {
       echo "Did not find ${ioc} running anywhere. Exiting..." >&2
       exit 1
    fi
-   
+
    if [[ ! $iocpath =~ ^/.* ]]; then
-      iocpath=/reg/g/pcds/epics/"${iocpath}"  
+      iocpath=/reg/g/pcds/epics/"${iocpath}"
    fi
 
 }
@@ -51,7 +51,7 @@ function ioccfg {
 
 
 function camname_to_pv {
-   #A function that will loop through camviewer.cfg files throughout all hutches to find the name then use that to search for its PV 
+   #A function that will loop through camviewer.cfg files throughout all hutches to find the name then use that to search for its PV
    campv=""
    hutch="$1"
    if [ "$1" == "" ]; then
@@ -62,13 +62,13 @@ function camname_to_pv {
          exit 1
       fi
    fi
-         
+
    VIEWERCFG=/reg/g/pcds/pyps/config/$hutch/camviewer.cfg
    CAMNAME=$(echo "$2" | sed -e 's/-/ /g' -e 's/_/ /g' -e 's/ /[-_ ]/g')
-   
-   
 
-   # The story here: 
+
+
+   # The story here:
    # See how many matches we have in the hutch.
    # If 0, try looking in all of the hutches.
    # If 1, then we're done.
@@ -79,17 +79,17 @@ function camname_to_pv {
    #
    # Make a temp file with just the PVs and camera names that match.
    tmp=/tmp/cv.$$
-   cat $VIEWERCFG | grep -i "$CAMNAME" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
+   grep -i "$CAMNAME" "$VIEWERCFG" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
    c=$(wc -l <$tmp)
-   if [ "$c" -eq 0 ]; then 
-      VIEWERCFG=/reg/g/pcds/pyps/config/*/camviewer.cfg
-      cat $VIEWERCFG | grep -i "$CAMNAME" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
-      c=$(wc -l <$tmp)
-      if [ "$c" -eq 0 ]; then
-         echo "No match for $2"
-         rm -f $tmp
-         exit
-      fi    
+   if [ "$c" -eq 0 ]; then
+       VIEWERCFG="/reg/g/pcds/pyps/config/*/camviewer.cfg"
+       grep -i "$CAMNAME" "$VIEWERCFG" | grep -v '#' | awk -F, '{ if (split($2,a,";")==1) n=$2; else n=a[2]; gsub(" ","",n); gsub(" ","",$4); printf "%s %s\n", n, $4; }' >$tmp
+       c=$(wc -l <$tmp)
+       if [ "$c" -eq 0 ]; then
+           echo "No match for $2"
+           rm -f $tmp
+           exit
+       fi
    fi
    if [ "$c" -eq 1 ]; then
       campv=$(awk '{print $1;}' <$tmp)
@@ -97,14 +97,14 @@ function camname_to_pv {
       return
    fi
    # OK, ambiguous.  Look for a complete match on the second word.
-   if [ "$(grep -E -i "$CAMNAME\$" < $tmp | wc -l)" -eq 1 ]; then
+   if [ "$(grep -E -i -c "$CAMNAME\$" < $tmp)" -eq 1 ]; then
       campv=$(grep -E -i "$CAMNAME\$" < $tmp | awk '{print $1;}')
       rm -f $tmp
       return
    fi
    # What about just a match at the end? (That is, if we are searching
    # for "yag1", prefer "mec_yag1" to "mec_yag11".)
-   if [ "$(grep -E -i "$CAMNAME\$" < $tmp | wc -l)" -eq 1 ]; then
+   if [ "$(grep -E -i -c "$CAMNAME\$" < $tmp)" -eq 1 ]; then
       campv=$(grep -E -i "$CAMNAME\$" < $tmp | awk '{print $1;}')
       rm -f $tmp
       return
@@ -143,8 +143,7 @@ if [[ ($1 == "--help") || ($1 == "-h") ]]; then
    exit 0
 fi
 
-OPTIONS=$(getopt -o H: --long hutch: -n \'$0\' -- "$@")
-if [ $? != 0 ]; then
+if OPTIONS=$(getopt -o H: --long hutch: -n \'"$0"\' -- "$@"); then
    echo "Terminating..." >&2
    exit 1
 fi
@@ -194,22 +193,22 @@ if [[ $NAME == *':'* ]]; then #we are assuming that PVs have a colon in them
 #2) If so, then search for ioc using grep_ioc
 #3) If that returns nothing, try converting the camera name to a PV and search for that
 #4) If neither of those produce results return "Did not find name anywhere"
-elif [[ $NAME == *'-'* || $NAME == *'_'* || ^[[:alnum:]]+$ ]]; then 
+elif [[ $NAME == *'-'* || $NAME == *'_'* || $NAME =~ ^[[:alnum:]]+$ ]]; then
    INFO=$(grep_ioc "$NAME" all | grep "id:'$NAME'")
       if [ -z "$INFO" ]; then
          #echo "Hutch = $hutch"
          camname_to_pv "$hutch" "$NAME"
          iocfpv "$campv"
          NAME="$ioc"
-        
+
       elif [[ -z "$NAME" ]]; then
          echo "Did not find ${NAME} running anywhere. Exiting..." >&2
          exit 1
-      fi 
+      fi
 
 elif [[ ! $NAME == *'-'* ]]; then #We are assuming that ioc names contain a dash in them
    echo "${NAME} does not match the format for PVs or IOC names. Exiting..." >&2
-   exit 1 
+   exit 1
 fi
 
 
@@ -232,9 +231,9 @@ elif [ "$CMD" == "cddir" ]; then
       echo "Script is not being sourced. Start with 'source $0' before calling script with this option." >&2
       exit 1
    fi
-   cd "${iocpath}" 
+   cd "${iocpath}"
+
 
- 
 #################################################################
 
 elif [ "$CMD" == "cfg" ]; then
@@ -306,7 +305,7 @@ elif [ "$CMD" == "telnet" ]; then
    echo "$HOST":"$PORT"
    telnet "$HOST" "$PORT"
 
-#################################################################                                                                           
+#################################################################
 
 elif [ "$CMD" == "pvs" ]; then
    pvlistfile=/cds/data/iocData/"${NAME}"/iocInfo/IOC.pvlist
diff --git a/scripts/ipmConfigEpics b/scripts/ipmConfigEpics
index 66eed76e..ad1fc5e0 100755
--- a/scripts/ipmConfigEpics
+++ b/scripts/ipmConfigEpics
@@ -16,18 +16,18 @@ lfeIpm='um6_ipm hfxdg2_ipm pim3m'
 ipmList()
 {
 printf 'Possible boxes:\n'
-if [ $hutch == 'xcs' ]; then
-   for box in $hx2Ipm $um6Ipm $dg2Ipm $xcsIpm; do echo $box; done
-elif [ $hutch == 'xpp' ]; then
-   for box in $hx2Ipm $xppIpm; do echo $box; done
-elif [ $hutch == 'cxi' ]; then
-   for box in $hx2Ipm $um6Ipm $dg2Ipm $cxiIpm; do echo $box; done
-elif [ $hutch == 'mfx' ]; then
-   for box in $hx2Ipm $um6Ipm $mfxIpm; do echo $box; done
-elif [ $hutch == 'mec' ]; then
-   for box in $hx2Ipm $um6Ipm $mecIpm; do echo $box; done
-elif [ $hutch == 'lfe' ]; then
-   for box in $lfeIpm; do echo $box; done
+if [[ $hutch == 'xcs' ]]; then
+   for box in $hx2Ipm $um6Ipm $dg2Ipm $xcsIpm; do echo "$box"; done
+elif [[ $hutch == 'xpp' ]]; then
+   for box in $hx2Ipm $xppIpm; do echo "$box"; done
+elif [[ $hutch == 'cxi' ]]; then
+   for box in $hx2Ipm $um6Ipm $dg2Ipm $cxiIpm; do echo "$box"; done
+elif [[ $hutch == 'mfx' ]]; then
+   for box in $hx2Ipm $um6Ipm $mfxIpm; do echo "$box"; done
+elif [[ $hutch == 'mec' ]]; then
+   for box in $hx2Ipm $um6Ipm $mecIpm; do echo "$box"; done
+elif [[ $hutch == 'lfe' ]]; then
+   for box in $lfeIpm; do echo "$box"; done
 else
     echo 'hutch cannot be determined, quit'
     exit
@@ -42,189 +42,189 @@ if [ $# -lt 1 ]; then
 fi
 
 # Shared IPMs
-if [ $1 == 'hx2_ipm' ]; then
+if [[ $1 == 'hx2_ipm' ]]; then
     IOC="IOC:HX2:SB1:BMMON"
     BASE='HX2:SB1:BMMON'
     EVR='HX2:SB1:BMMON:EVR'
     WAVE8='hx2_ipm'
-elif [ $1 == 'um6_ipm' ]; then		#aka xcs ipm1
+elif [[ $1 == 'um6_ipm' ]]; then        #aka xcs ipm1
     BASE="XCS:DG1:IMB:01"
     IOC="XCS:R04:IOC:34"
     EVR="XCS:R04:EVR:34"
-elif [ $1 == 'um6_dio' ]; then		#aka xcs ipm1
+elif [[ $1 == 'um6_dio' ]]; then	#aka xcs ipm1
     BASE="XCS:DG1:IMB:02"
     IOC="XCS:R04:IOC:34"
     EVR="XCS:R04:EVR:34"
-elif [ $1 == 'hfxdg2_ipm' ]; then	#aka xcs ipm2
+elif [[ $1 == 'hfxdg2_ipm' ]]; then	#aka xcs ipm2
     IOC="IOC:HFX:DG2:BMMON"
     BASE='HFX:DG2:BMMON'
     EVR='HFX:DG2:BMMON:EVR'
     WAVE8='hfxipm'
-elif [ $1 == 'pim3m' ]; then
+elif [[ $1 == 'pim3m' ]]; then
     BASE="HFX:DG3:IMB:02"
     IOC="XCS:R38:IOC:43"
     EVR="XCS:R38:EVR:43"
 fi
 
 # Hutch-specific IPMs
-if [ $hutch == 'xcs' ]; then
-    if [ $1 == 'decmono' ]; then
+if [[ $hutch == 'xcs' ]]; then
+    if [[ $1 == 'decmono' ]]; then
 	BASE="HFX:MON:IMB:03"
 	IOC="XCS:R38:IOC:43"
 	EVR="XCS:R38:EVR:43"
-    elif [ $1 == 'diomono' ]; then
+    elif [[ $1 == 'diomono' ]]; then
 	BASE="HFX:MON:IMB:02"
 	IOC="XCS:R38:IOC:43"
 	EVR="XCS:R38:EVR:43"
-    elif [ $1 == 'ipmmono' ]; then
+    elif [[ $1 == 'ipmmono' ]]; then
 	BASE="HFX:MON:IMB:01"
 	IOC="XCS:R38:IOC:43"
 	EVR="XCS:R38:EVR:43"
-    elif [ $1 == 'pim3' ]; then
+    elif [[ $1 == 'pim3' ]]; then
 	BASE="XCS:DG3:IMB:04"
 	IOC="XCS:R38:IOC:43"
 	EVR="XCS:R38:EVR:43"
-    elif [ $1 == 'ipm3' ]; then
+    elif [[ $1 == 'ipm3' ]]; then
 	BASE="XCS:DG3:IMB:03"
 	IOC="XCS:R38:IOC:43"
 	EVR="XCS:R38:EVR:43"
-    elif [ $1 == 'ipm4' ]; then
+    elif [[ $1 == 'ipm4' ]]; then
 	IOC="IOC:XCS:SB1:BMMON"
 	BASE='XCS:SB1:BMMON'
 	EVR='XCS:SB1:BMMON:EVR'
 	WAVE8='sb1bmmon'
-    elif [ $1 == 'pim4' ]; then
+    elif [[ $1 == 'pim4' ]]; then
 	BASE="XCS:SB1:IMB:02"
 	IOC="IOC:XCS:IPM"
 	EVR="XCS:R44:EVR:01"
-    elif [ $1 == 'ipm5' ]; then
+    elif [[ $1 == 'ipm5' ]]; then
 	IOC="IOC:XCS:SB2:BMMON"
 	BASE='XCS:SB2:BMMON'
 	EVR='XCS:SB2:BMMON:EVR'
 	WAVE8='sb2bmmon'
-    elif [ $1 == 'pim5' ]; then
+    elif [[ $1 == 'pim5' ]]; then
 	BASE="XCS:SB2:IMB:02"
 	IOC="IOC:XCS:IPM"
 	EVR="XCS:R44:EVR:01"
-    elif [ $1 == 'ipmgonLD' ]; then
+    elif [[ $1 == 'ipmgonLD' ]]; then
 	BASE="XCS:USR:IMB:01"
 	IOC="IOC:XCS:USR:IPM"
 	EVR="XCS:R42:EVR:01"
-    elif [ $1 == 'ipmlamLD' ]; then
+    elif [[ $1 == 'ipmlamLD' ]]; then
 	BASE="XCS:LAM:IMB:02"
 	IOC="IOC:XCS:IPM"
 	EVR="XCS:R44:EVR:01"
-    elif [ $1 == 'snddio' ]; then
+    elif [[ $1 == 'snddio' ]]; then
 	IOC="IOC:XCS:SND:DIO"
 	BASE='XCS:SND:DIO'
 	EVR='XCS:SND:DIO:EVR'
 	WAVE8='snddio'
     fi
-elif [ $hutch == 'cxi' ]; then
-    if [ $1 == 'dg2ipm' ]; then
+elif [[ $hutch == 'cxi' ]]; then
+    if [[ $1 == 'dg2ipm' ]]; then
 	IOC="IOC:CXI:DG2:BMMON"
 	BASE='CXI:DG2:BMMON'
 	EVR='CXI:DG2:BMMON:EVR'
 	WAVE8='dg2ipm'
-    elif [ $1 == 'dg3ipm' ]; then
+    elif [[ $1 == 'dg3ipm' ]]; then
 	IOC="IOC:CXI:DG3:BMMON"
 	BASE='CXI:DG3:BMMON'
 	EVR='CXI:DG3:BMMON:EVR'
 	WAVE8='dg3ipm'
-    elif [ $1 == 'usrdio' ]; then
+    elif [[ $1 == 'usrdio' ]]; then
         IOC="IOC:CXI:USR:DIO"
         BASE='CXI:USR:DIO'
         EVR='CXI:USR:DIO:EVR'
         WAVE8='usrdio'
     fi
-elif [ $hutch == 'mfx' ]; then
-    if [ $1 == 'dg1ipm' ]; then
+elif [[ $hutch == 'mfx' ]]; then
+    if [[ $1 == 'dg1ipm' ]]; then
 	IOC="IOC:MFX:DG1:BMMON"
 	BASE='MFX:DG1:BMMON'
 	EVR='MFX:DG1:BMMON:EVR'
 	WAVE8='dg1ipm'
-    elif [ $1 == 'dg2ipm' ]; then
+    elif [[ $1 == 'dg2ipm' ]]; then
 	IOC="IOC:MFX:DG2:BMMON"
 	BASE='MFX:DG2:BMMON'
 	EVR='MFX:DG2:BMMON:EVR'
 	WAVE8='dg2ipm'
-    elif [ $1 == 'usrdio' ]; then
+    elif [[ $1 == 'usrdio' ]]; then
         IOC="IOC:MFX:USR:DIO"
         BASE='MFX:USR:DIO'
         EVR='MFX:USR:DIO:EVR'
         WAVE8='usrdio'
     fi
-elif [ $hutch == 'xpp' ]; then
-    if [ $1 == 'diomono' ]; then
+elif [[ $hutch == 'xpp' ]]; then
+    if [[ $1 == 'diomono' ]]; then
 	IOC="IOC:XPP:IPM"
 	BASE='XPP:MON:IPM:02'
 	EVR='XPP:IPM:EVR'
-    elif [ $1 == 'decmono' ]; then
+    elif [[ $1 == 'decmono' ]]; then
 	IOC="IOC:XPP:IPM"
 	BASE='XPP:MON:IPM:01'
 	EVR='XPP:IPM:EVR'
-    elif [ $1 == 'ipm2' ]; then
+    elif [[ $1 == 'ipm2' ]]; then
 	IOC="IOC:XPP:SB2:BMMON"
 	BASE='XPP:SB2:BMMON'
 	EVR='XPP:SB2:BMMON:EVR'
 	WAVE8='sb2bmmon'
-    elif [ $1 == 'ipm3' ]; then
+    elif [[ $1 == 'ipm3' ]]; then
 	IOC="IOC:XPP:SB3:BMMON"
 	BASE='XPP:SB3:BMMON'
 	EVR='XPP:SB3:BMMON:EVR'
 	WAVE8='sb3bmmon'
-    elif [ $1 == 'pim3' ]; then
+    elif [[ $1 == 'pim3' ]]; then
 	IOC="IOC:XPP:IPM"
 	BASE='XPP:SB3:IPM:02'
 	EVR='XPP:IPM:EVR'
-    elif [ $1 == 'diodeU' ]; then
+    elif [[ $1 == 'diodeU' ]]; then
 	IOC="IOC:XPP:IPM"
 	BASE='XPP:USR:IPM:01'
 	EVR='XPP:IPM:EVR'
     fi
-elif [ $hutch == 'mec' ]; then
-    if [ $1 == 'ipm1' ]; then
+elif [[ $hutch == 'mec' ]]; then
+    if [[ $1 == 'ipm1' ]]; then
 	IOC="XRT:R33:IOC:39"
 	BASE='MEC:HXM:IPM:01'
 	EVR='XRT:R44:EVR:39'
-    elif [ $1 == 'hxm_pim' ]; then
+    elif [[ $1 == 'hxm_pim' ]]; then
 	IOC="XRT:R33:IOC:39"
 	BASE='MEC:HXM:PIM:01'
 	EVR='XRT:R44:EVR:39'
-    elif [ $1 == 'pim2' ]; then
+    elif [[ $1 == 'pim2' ]]; then
 	IOC="IOC:MEC:IMB02"
 	BASE='MEC:XT2:PIM:02'
 	EVR='MEC:XT2:EVR:01'
-    elif [ $1 == 'pim3' ]; then
+    elif [[ $1 == 'pim3' ]]; then
 	IOC="IOC:MEC:IMB02"
 	BASE='MEC:XT2:PIM:03'
 	EVR='MEC:XT2:EVR:01'
-    elif [ $1 == 'tc1_imb1' ]; then
+    elif [[ $1 == 'tc1_imb1' ]]; then
 	IOC="IOC:MEC:IPIMB01"
 	EVR='MEC:TC1:EVR:01'
 	BASE='MEC:TC1:IMB:01'
-    elif [ $1 == 'usr_imb1' ]; then
+    elif [[ $1 == 'usr_imb1' ]]; then
 	IOC="IOC:MEC:IPIMB01"
 	EVR='MEC:TC1:EVR:01'
 	BASE='MEC:USR:IMB:01'
-    elif [ $1 == 'usr_imb2' ]; then
+    elif [[ $1 == 'usr_imb2' ]]; then
 	IOC="IOC:MEC:IPIMB01"
 	EVR='MEC:TC1:EVR:01'
 	BASE='MEC:USR:IMB:02'
-    elif [ $1 == 'las_imb1' ]; then
+    elif [[ $1 == 'las_imb1' ]]; then
 	IOC="IOC:MEC:IPIMB01"
 	EVR='MEC:TC1:EVR:01'
 	BASE='MEC:LAS:IMB:01'
-    elif [ $1 == 'las_imb2' ]; then
+    elif [[ $1 == 'las_imb2' ]]; then
 	IOC="IOC:MEC:IPIMB01"
 	EVR='MEC:TC1:EVR:01'
 	BASE='MEC:LAS:IMB:02'
-    elif [ $1 == 'ipm2' ]; then
+    elif [[ $1 == 'ipm2' ]]; then
 	IOC="IOC:MEC:XT2-1:BMMON"
 	EVR="MEC:XT2-1:BMMON:EVR"
 	BASE="MEC:XT2-1:BMMON"
 	WAVE8='xt2-1bmmon'
-    elif [ $1 == 'ipm3' ]; then
+    elif [[ $1 == 'ipm3' ]]; then
 	IOC="IOC:MEC:XT2-2:BMMON"
 	EVR="MEC:XT2-2:BMMON:EVR"
 	BASE="MEC:XT2-2:BMMON"
@@ -240,11 +240,11 @@ fi
 
 # Attempt to read the :SUM PV and open a GUI if successful and exits if not. Uses wave8 or ipimb accordingly
 ipmGUI(){
-    if caget ${BASE}:SUM > /dev/null 2>&1; then
+    if caget "$BASE":SUM > /dev/null 2>&1; then
         if [ ${#WAVE8} -gt 0 ]; then
-            /reg/g/pcds/pyps/apps/wave8/latest/wave8 --base $BASE --evr $EVR --ioc $IOC
+            /reg/g/pcds/pyps/apps/wave8/latest/wave8 --base "$BASE" --evr "$EVR" --ioc "$IOC"
         else
-            /reg/g/pcds/controls/pycaqt/ipimb/ipimb --base $BASE --ioc $IOC --evr $EVR
+            /reg/g/pcds/controls/pycaqt/ipimb/ipimb --base "$BASE" --ioc "$IOC" --evr "$EVR"
         fi
     else
         echo "Could not connect to ${BASE}. Exiting..."
@@ -254,8 +254,8 @@ ipmGUI(){
 # Get hutch name, if not given, using get_info
 get_hutch(){
     if [ -z "$HUTCH" ]; then
-        hutch=`get_info --gethutch`
-        if [ $hutch = unknown_hutch ]; then
+        hutch=$(get_info --gethutch)
+        if [[ $hutch = unknown_hutch ]]; then
 	    echo 'unknown hutch, cannot use ipmConfigEpics script'
 	    exit 1
         fi
@@ -287,7 +287,7 @@ helpBld(){
         # Attempt to caput values
         caput HFX:DG3:CVV:01:Stats2:EnableCallbacks 0
         caput XCS:DG3:CVV:02:Stats2:EnableCallbacks 0
-        # Check if actually set      
+        # Check if actually set
         if [[ $(caget -nt HFX:DG3:CVV:01:Stats2:EnableCallbacks 2> /dev/null) == 0 ]] && [[ $(caget -nt XCS:DG3:CVV:02:Stats2:EnableCallbacks 2> /dev/null) == 0 ]]; then
             echo 'Turned off statsPlugin for XCS ipm3 and dio3'
         else
@@ -334,10 +334,10 @@ done
 get_hutch
 if [ ${#BOXNAME} == 0 ]; then
     ipmList
-    printf 'Enter box name from above list:\n'; read BOXNAME
+    printf 'Enter box name from above list:\n'; read -r BOXNAME
 fi
 
-ipmSetEnvPars $BOXNAME
+ipmSetEnvPars "$BOXNAME"
 if [ $HELPDAQBLD -gt 0 ]; then
     helpBld
 else
diff --git a/scripts/kinit_helper b/scripts/kinit_helper
index bb7076ee..1af37d91 100755
--- a/scripts/kinit_helper
+++ b/scripts/kinit_helper
@@ -15,7 +15,7 @@ function kauth {
 }
 
 function afsauth {
-    # need to be in g-pcds afs grup                                                                                                                  
+    # need to be in g-pcds afs grup
     if ! pts membership g-pcds 2>&1 | grep -q "$(whoami)"
     then
         echo "You do not have permission to use afs. See https://confluence.slac.stanford.edu/display/PCDS/Onboarding+Staff+Members"
diff --git a/scripts/makepeds b/scripts/makepeds
index 203f9ebd..b2f1458d 100755
--- a/scripts/makepeds
+++ b/scripts/makepeds
@@ -1,6 +1,6 @@
 #! /bin/bash
 
-DIR=`dirname $(readlink -f $0)`
+DIR=$(dirname "$(readlink -f "$0")")
 PATH=$PATH:$DIR
 
 usage()
@@ -11,25 +11,25 @@ usage: $0 options
 Make a pedestal file for offline use
 
 OPTIONS:
-        -u|--user        
+        -u|--user
                user (needs to be able to log into the s3df)
-        -p|--post <text>  
+        -p|--post <text>
                add <text> to elog post
         -t|--test
                 do not deploy pedestals (epix10k only)
-        -r|--run         
+        -r|--run
                runnumber for pedestal
-        -e|--experiment <expname> 
+        -e|--experiment <expname>
                in case you do not want pedestals for the ongoing experiment
-        -O|--opal         
+        -O|--opal
                make pedestals for Opals (default only cspad/EPIX detectors)
-        -Z|--zyla         
+        -Z|--zyla
                make pedestals for Zyla (default only cspad/EPIX detectors)
         -R|--Rayonix
                make pedestals for Rayonix (please note that this is not the correct procedure for this detector)
         -U|--uxi
                make pedestals for Uxi/Icarus detector
-        -j|--jungfrau3     
+        -j|--jungfrau3
                make pedestals for Jungfrau - 3 run version(default only cspad/EPIX detectors)
         -q|--queue <queue>
                queue for batch submisson
@@ -39,19 +39,19 @@ OPTIONS:
                lasing off run for XTCAV
         -v|--validity_start <val_run>
                validity range (set to <val_run>-end)
-        -N|--nevents <#>  
+        -N|--nevents <#>
                 use this number of events (default 1000). Needed when using -c as original events are counted
-        -c|--eventcode <evtcode x> 
+        -c|--eventcode <evtcode x>
                 use events with eventcode <x> set
-        -n|--noise_max <#> 
+        -n|--noise_max <#>
                 if you have created a noise file, then write pixel mask file for pixels with noise above #sigmas
-        -C|--noise_min <#> 
+        -C|--noise_min <#>
                 if noise filecreated, write pixel mask file for pixels with noise below xxx (currently integer only)
-        -m|--adu_min <#> 
+        -m|--adu_min <#>
                 write pixel mask file for pixels with pedestal below xxx (currently integer only)
-        -x|--adu_max <#>  
+        -x|--adu_max <#>
                 write pixel mask file for pixels with pedestal above xxx )currently integer only)
-        -i|--interactive 
+        -i|--interactive
                 start calibman. -r 0: show all darks, -r n: show runs (n-25) - 25
         -d|--calibdir
                 give path for alternative calibdir
@@ -84,7 +84,7 @@ do
             shift
             ;;
         -L|--xtcav_lasingoff)
-            POSITIONAL+=" $1"
+            POSITIONAL+=("$1")
             elogMessage="Lasing off for XTCAV"
             shift
             ;;
@@ -163,43 +163,43 @@ INTERACTIVE=${INTERACTIVE:=0}
 # also put 'xxx' (default q name) as S3DF so that even if no queue is given,
 # it goes to S3DF
 SDFQUEUES=('milano' 'roma' 'xxx')
-for SDFQUEUE in ${SDFQUEUES[@]}; do
-    if [[ $QUEUE == $SDFQUEUE ]]; then 
+for SDFQUEUE in "${SDFQUEUES[@]}"; do
+    if [[ $QUEUE == "$SDFQUEUE" ]]; then
 	S3DF=1
     fi
 done
 
 if [[ $RUN == 0 ]]; then
     if [[ $INTERACTIVE == 0 ]]; then
-        printf "Please enter a run number: \n"; read RUN
-        set -- "$@" '--run ' $RUN
+        printf "Please enter a run number: \n"; read -r RUN
+        set -- "$@" '--run ' "$RUN"
     fi
 fi
 
 if [[ $EXP == 'xxx' ]]; then
-    HUTCH=`get_info --gethutch`
-    EXP=`get_info --exp --hutch $HUTCH`
-    set -- "$@" '--experiment ' $EXP
+    HUTCH=$(get_info --gethutch)
+    EXP=$(get_info --exp --hutch "$HUTCH")
+    set -- "$@" '--experiment ' "$EXP"
 else
     HUTCH=${EXP:0:3}
 fi
 
 if [[ $HOSTNAME =~ "sdf" ]]; then
     #echo $DIR/makepeds_psana $@
-    $DIR/makepeds_psana $@
+    "$DIR"/makepeds_psana "$@"
 else
     if [[ $USER =~ "opr" ]]; then
-        printf "Please enter user name (cannot run as from operator account): \n"; read USER
+        printf "Please enter user name (cannot run as from operator account): \n"; read -r USER
     fi
-    echo calling on SDF system: makepeds_psana $@
+    echo calling on SDF system: makepeds_psana "$@"
     # We need to change paths here as the S3DF filesytem is completely independent
     if [ -v SDFDIR  ]; then
         DIR=$SDFDIR
     else
-        DIR=`echo $DIR | sed 's/\/cds\/group\/pcds/\/sdf\/group\/lcls\/ds\/tools/g' | sed 's/\/reg\/g\/pcds/\/sdf\/group\/lcls\/ds\/tools/g'`
+        DIR=$(echo "$DIR" | sed 's/\/cds\/group\/pcds/\/sdf\/group\/lcls\/ds\/tools/g' | sed 's/\/reg\/g\/pcds/\/sdf\/group\/lcls\/ds\/tools/g')
     fi
-    echo ssh -Y $USER@s3dflogin ssh -Y psana "$DIR/makepeds_psana $@"
-    ssh -Y $USER@s3dflogin ssh -Y psana "$DIR/makepeds_psana $@"
+    echo ssh -Y "$USER"@s3dflogin ssh -Y psana "$DIR/makepeds_psana" "$@"
+    ssh -Y "$USER"@s3dflogin ssh -Y psana "$DIR/makepeds_psana" "$@"
 fi
 
 if [[ $HOSTNAME =~ "sdf" ]]; then
@@ -208,11 +208,11 @@ else
     source pcds_conda
 fi
 
-elog_par_post --file pedestal -e "$EXP" -r $RUN
+elog_par_post --file pedestal -e "$EXP" -r "$RUN"
 
 #if this is a default pedestal run, then do not post as this is handled in takepeds
-if [[ $elogMessage == 'DARK' ]] && [[ $ELOGTXT == '' ]] ; then
-    echo ---- Done processing pedestals for Run $RUN -----
+if [[ $elogMessage == 'DARK' ]] && [[ $ELOGTEXT == '' ]] ; then
+    echo ---- Done processing pedestals for Run "$RUN" -----
     exit 0
 fi
 
@@ -223,21 +223,21 @@ fi
 
 PYCMD=LogBookPost.py
 echo -- Now posting special message to elog --
-echo -- $elogMessage --
+echo -- "$elogMessage" --
 
 elogMessage+=$ELOGTEXT
-if [[ `whoami` =~ "opr" ]]; then
-    echo $BINPATH $PYCMD -i "${HUTCH^^}" -u `whoami` -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage"
+if [[ $(whoami) =~ "opr" ]]; then
+    echo "$BINPATH" $PYCMD -i "${HUTCH^^}" -u "$(whoami)" -e "$EXP"  -t DARK  -r "$RUN" -m "$elogMessage"
     if [[ $HOSTNAME == 'cxi-monitor' ]]; then
-        $BINPATH $PYCMD -i "${HUTCH^^}" -u `whoami` -p pcds -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage" -s 1&
+        $BINPATH $PYCMD -i "${HUTCH^^}" -u "$(whoami)" -p pcds -e "$EXP"  -t DARK  -r "$RUN" -m "$elogMessage" -s 1&
     else
-        $BINPATH $PYCMD -i "${HUTCH^^}" -u `whoami` -p pcds -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage"&
+        $BINPATH $PYCMD -i "${HUTCH^^}" -u "$(whoami)" -p pcds -e "$EXP"  -t DARK  -r "$RUN" -m "$elogMessage"&
     fi
 else
-    echo $BINPATH $PYCMD -i "${HUTCH^^}" -e "$EXP"  -t DARK -r $RUN -m "$elogMessage"
+    echo "$BINPATH" $PYCMD -i "${HUTCH^^}" -e "$EXP"  -t DARK -r "$RUN" -m "$elogMessage"
     if [[ $HOSTNAME == 'cxi-monitor' ]]; then
-        $BINPATH $PYCMD -i "${HUTCH^^}" -e "$EXP" -t DARK -r $RUN -m "$elogMessage" -s 1&
+        $BINPATH $PYCMD -i "${HUTCH^^}" -e "$EXP" -t DARK -r "$RUN" -m "$elogMessage" -s 1&
     else
-        $BINPATH $PYCMD -i "${HUTCH^^}" -e "$EXP" -t DARK -r $RUN -m "$elogMessage"&
+        $BINPATH $PYCMD -i "${HUTCH^^}" -e "$EXP" -t DARK -r "$RUN" -m "$elogMessage"&
     fi
 fi
diff --git a/scripts/makepeds_psana b/scripts/makepeds_psana
index 9d60bf8d..df117c08 100755
--- a/scripts/makepeds_psana
+++ b/scripts/makepeds_psana
@@ -13,19 +13,19 @@ usage: $0 options
 Make a pedestal file for offline use
 
 OPTIONS:
-        -r|--run         
+        -r|--run
                runnumber for pedestal
-        -e|--experiment <expname> 
+        -e|--experiment <expname>
                in case you do not want pedestals for the ongoing experiment
-        -O|--opal         
+        -O|--opal
                make pedestals for Opals (default only cspad/EPIX detectors)
-        -Z|--zyla         
+        -Z|--zyla
                make pedestals for Zyla (default only cspad/EPIX detectors)
         -R|--Rayonix
                make pedestals for Rayonix (please note that this is not the correct procedure for this detector)
         -U|--uxi
                make pedestals for Uxi detectors
-        -j|--jungfrau3     
+        -j|--jungfrau3
                make pedestals for Jungfrau - 3 run version(default only cspad/EPIX detectors)
         -q|--queue <queue>
                queue for batch submisson
@@ -35,19 +35,19 @@ OPTIONS:
                lasing off run for XTCAV
         -v|--validity_start <val_run>
                validity range (set to <val_run>-end)
-        -N|--nevents <#>  
+        -N|--nevents <#>
                 use this number of events (default 1000). Needed when using -c as original events are counted
-        -c|--eventcode <evtcode x> 
+        -c|--eventcode <evtcode x>
                 use events with eventcode <x> set
-        -n|--noise_max <#> 
+        -n|--noise_max <#>
                 if you have created a noise file, then write pixel mask file for pixels with noise above #sigmas
-        -C|--noise_min <#> 
+        -C|--noise_min <#>
                 if noise filecreated, write pixel mask file for pixels with noise below xxx (currently integer only)
-        -m|--adu_min <#> 
+        -m|--adu_min <#>
                 write pixel mask file for pixels with pedestal below xxx (currently integer only)
-        -x|--adu_max <#>  
+        -x|--adu_max <#>
                 write pixel mask file for pixels with pedestal above xxx )currently integer only)
-        -i|--interactive 
+        -i|--interactive
                 start calibman. -r 0: show all darks, -r n: show runs (n-25) - 25
         -d|--calibdir
                 give path for alternative calibdir
@@ -119,7 +119,7 @@ xtcav_dark()
    else
        tmpScript=$(mktemp -p "$WORKDIR" xtcav_dark_tmpXXXXX.sh)
        chmod u+x "$tmpScript"
-       printf '#!/bin/bash\nsource $SIT_ENV_DIR/manage/bin/psconda.sh\n' > "$tmpScript"
+       printf "#!/bin/bash\nsource %s/manage/bin/psconda.sh\n" "$SIT_ENV_DIR" > "$tmpScript"
        CMD="xtcavDark $EXP $RUN"
        printf '%s\n' "${CMD}" >> "$tmpScript"
        xtcavCmd="sbatch --exclusive  --account lcls:$EXP -p $QUEUE -o $WORKDIR/xtcav_${EXP}_Run${RUN}_%J.out $tmpScript"
@@ -154,7 +154,7 @@ xtcav_lasOff()
    else
        tmpScript=$(mktemp -p "$WORKDIR" xtcav_dark_tmpXXXXX.sh)
        chmod u+x "$tmpScript"
-       printf '#!/bin/bash\nsource $SIT_ENV_DIR/manage/bin/psconda.sh\n' > "$tmpScript"
+       printf "#!/bin/bash\nsource %s/manage/bin/psconda.sh\n" "$SIT_ENV_DIR" > "$tmpScript"
        CMD="xtcavLasingOff $EXP $RUN"
        printf '%s\n' "${CMD}" >> "$tmpScript"
        xtcavCmd="sbatch --exclusive  --account lcls:$EXP -p $QUEUE -o $WORKDIR/xtcav_${EXP}_Run${RUN}_%J.out $tmpScript"
@@ -177,11 +177,12 @@ xtcav_lasOff()
    exit
 }
 
-# Arg: DETECTOR class.  This could be a comma-separated list, but we're 
+# Arg: DETECTOR class.  This could be a comma-separated list, but we're
 # matching it in the config file as a string.
 get_config()
 {
     awk 'BEGIN{n=0;}/'"$1"' \{/{n=1;next;}/\}/{n=0;next;}{if(n)print;}' <"$CFGFILE" >/tmp/script.$$
+    # shellcheck disable=SC1090
     source /tmp/script.$$
     rm /tmp/script.$$
     #overwrite if argument is passed
@@ -213,8 +214,7 @@ deploy_geometry()
         fi
 
         echo calling "$CMD"
-        $CMD
-        if [ "$?" != "0" ]; then
+        if $CMD; then
             echo Error: Geometry not deployed!
         else
             echo Geometry now deployed.
@@ -239,8 +239,7 @@ deploy_gain()
         CMD=$CMD' -x :dir='$XTCDIR'/:stream=0-79'
 
         echo calling "$CMD"
-        $CMD
-        if [ "$?" != "0" ]; then
+        if $CMD; then
             echo Error: Gain file not deployed!
         else
             echo Gain file deployed.
@@ -390,8 +389,8 @@ NUMBUNCH=${NUMBUNCH:=1}
 #one setting to run each process on an own server (currently faster) or not (if we had to use reservations)
 EXCLUSIVE=0
 
-if [ $RUN == 0 ]; then
-    if [ $INTERACTIVE -ne 1 ]; then
+if [[ $RUN == 0 ]]; then
+    if [[ $INTERACTIVE -ne 1 ]]; then
         printf "Please enter a run number HERE: \n"; read -r RUN
     fi
 fi
@@ -399,7 +398,7 @@ fi
 PCDSDIR='/sdf/group/lcls/ds/tools/'
 SIT_ENV_DIR="/sdf/group/lcls/ds/ana/sw"
 
-if [ $EXP == 'xxx' ]; then
+if [[ $EXP == 'xxx' ]]; then
     echo 'no experiment passed!!!'
     HUTCH=$($PCDSDIR/engineering_tools/latest-released/scripts/get_info --gethutch)
     echo HUTCH "$HUTCH"
@@ -421,7 +420,7 @@ fi
 LCLS2_HUTCHES="rix, tmo, ued"
 if echo "$LCLS2_HUTCHES" | grep -iw "$HUTCH" > /dev/null; then
     echo "This is a LCLS-II experiment"
-    
+
     SIT_ENV_DIR=$SIT_ENV_DIR'/conda2/'
     LCLS2=1
 else
@@ -430,7 +429,7 @@ else
 fi
 source $SIT_ENV_DIR/manage/bin/psconda.sh
 
-#if you don't pass the queue, it'll run interactively 
+#if you don't pass the queue, it'll run interactively
 if [[ $QUEUE == 'xxx' ]]; then
     RUNLOCAL=1
 fi
@@ -442,8 +441,8 @@ ARG=' -n '$NUMEVT' -Z 1000000 -U 1000000 -z 1000000 -u 1000000 '
 # find xtc directory
 # look for xtc w/o in progress if not using live mode. TOBEIMPLEMENTED
 ###########
-RUNSTR=$(printf '%04d' $RUN)
-RUNSTR=$EXP-r$RUNSTR*.xtc
+RUNSTR=$(printf '%04d' "$RUN")
+RUNSTR="$EXP-r$RUNSTR*.xtcx"
 XTCDIR=/sdf/data/lcls/ds/"$HUTCH"/"$EXP"/xtc
 # If inprogress files use FFB location
 if compgen -G "$XTCDIR/$RUNSTR.inprogress" > /dev/null; then
@@ -459,7 +458,7 @@ echo "Use XTC files from  $XTCDIR."
 ###########
 # deduce calibdir.
 ###########
-if [ $CALIBDIR != 'xxx' ]; then
+if [[ $CALIBDIR != 'xxx' ]]; then
     ARG=$ARG' -c '$CALIBDIR
     JFARG=' -C '$CALIBDIR
 else
@@ -489,17 +488,18 @@ fi
 if [ ! -w "$WORKDIR" ]; then
     echo 'Typical directory to store calib logfiles & results is not writeable, will attempt to work from /tmp, but things may fail'
     WORKDIR='/tmp'
-fi 
+fi
 cd "$WORKDIR"
 
 ######################
 # work on the XTCAV
 ######################
 
-if [ $XTCAV == 1 ]; then
+if [[ $XTCAV == 1 ]]; then
     xtcav_dark
 fi
-if [ $XTCAV == 2 ]; then
+
+if [[ $XTCAV == 2 ]]; then
     xtcav_lasOff
 fi
 ######################
@@ -509,15 +509,15 @@ fi
 ###########
 # few generic parameters
 ###########
-if [ $INTERACTIVE == 1 ]; then
+if [[ $INTERACTIVE == 1 ]]; then
     echo 'now calling calibman (GUI) - switch to old release for now'
     source /reg/g/psdm/etc/psconda.sh.old
     calibman
     exit
 fi
 
-if [ $CALIBCODE -ne 0 ]; then
-    if [ $NUMEVT -le 1000 ]; then
+if [[ $CALIBCODE -ne 0 ]]; then
+    if [[ $NUMEVT -le 1000 ]]; then
         NUMEVT=1000000
     fi
     ARG=$ARG' -f '$CALIBCODE
@@ -530,7 +530,7 @@ fi
 #    ARG=$ARG' -q '$QUEUE
 #fi
 
-if [ $DEPLOY == 1 ]; then
+if [[ $DEPLOY == 1 ]]; then
     ARG=$ARG' -D '
 fi
 
@@ -538,7 +538,7 @@ fi
 CREATE_TIME=$(date '+%m_%d_%Y_%H:%M:%S')
 printf -v RUNSTR "%04g" "$RUN"
 
-echo Check detectors: 
+echo Check detectors:
 
 ls -ltr "$XTCDIR"/*r"$RUNSTR"*s*xtc*
 if [[ $LCLS2 -gt 0 ]]; then
@@ -552,12 +552,12 @@ echo 'XTC files contain:'
 cat /tmp/detnames_"$EXP"_"$CREATE_TIME"
 echo "-----------------------"
 
-#### 
+####
 # Section for LCLS2 detectors.
 ####
 if [[ $LCLS2 -gt 0 ]]; then
     ####
-    # epix100 in LCLS2 related stuff. 
+    # epix100 in LCLS2 related stuff.
     ####
     #check if epix100 detectors are present
     HAVE_EPIX100=$(grep -c epix100 /tmp/detnames_"$EXP"_"$CREATE_TIME")
@@ -598,7 +598,7 @@ if [[ $LCLS2 -gt 0 ]]; then
                     CMD="epix10ka_pedestals_calibration -d $EPIX10K -e $EXP -r $RUN --stepnum $calibcycle --stepmax $nextcycle -L INFO -x dir=$XTCDIR"
                     echo "---------------EPIX10K PEDESTALS FOR CYCLE $calibcycle --------------------"
                     if [[ $RUNLOCAL != 1 ]]; then
-                        tmpScript=$(mktemp -p $WORKDIR epix10ka_pedestals_tmpXXXXX.sh)
+                        tmpScript=$(mktemp -p "$WORKDIR" epix10ka_pedestals_tmpXXXXX.sh)
                         #trap "rm -f $tmpScript" EXIT
                         chmod u+x "$tmpScript"
                         printf '#!/bin/bash\n' > "$tmpScript"
@@ -616,7 +616,7 @@ if [[ $LCLS2 -gt 0 ]]; then
                         THISJOBID=$(echo "$SUBMISSION" | awk '{print $4}')
                         JOBIDS+=( "$THISJOBID" )
                         NJOBS=$((NJOBS+1))
-                    else            
+                    else
                         echo "$cmd"
                         $CMD
                     fi
@@ -634,7 +634,7 @@ if [[ $LCLS2 -gt 0 ]]; then
                 done
                 echo 'All jobs finished'
                 # and now check that none of the jobs have existed with an error code:
-                # currently, the epix10k jobs print DONE at the end. 
+                # currently, the epix10k jobs print DONE at the end.
                 # Second check necessary as jobs can fail without printing an exit code to the logfile
                 for JOBID in "${ALLJOBIDS[@]}"; do
                     echo "Checking job $JOBID"
@@ -644,22 +644,22 @@ if [[ $LCLS2 -gt 0 ]]; then
                         NFAILEDJOBS=$((NFAILEDJOBS+1))
                     fi
                 done
-    
+
             fi
 
             echo "---------------EPIX10K PEDESTALS CALCULATED NOW DEPLOY     --------------------"
-            if [ $DEPLOY == 1 ]; then
+            if [[ $DEPLOY == 1 ]]; then
                 if [ $NFAILEDJOBS -gt 0 ]; then
                     read -r -p "$NFAILEDJOBS of the calibration tasks failed, do you want to continue anyways (y/n)?"
                     if [ "$REPLY" != "y" ];then
                         exit 1
                     fi
                 fi
- 
+
                 for EPIX10K in $DETNAMES; do
                     CMD="epix10ka_deploy_constants -D -d $EPIX10K -e $EXP -r $RUN -L INFO -x :dir=$XTCDIR"
-                    echo 'setting validity....' $VALSTR
-                    if [ $VALSTR != 'xxx' ]; then
+                    echo "setting validity...$VALSTR"
+                    if [[ $VALSTR != 'xxx' ]]; then
                         CMD=$CMD' -t '$VALSTR
                     fi
                     echo "$cmd"
@@ -669,7 +669,7 @@ if [[ $LCLS2 -gt 0 ]]; then
                     echo 'Print Information about batch jobs'
                 JOBIDSTR=''
                     for JOBID in "${ALLJOBIDS[@]}"; do
-                if [[ $JOBIDSTR != '' ]]; then 
+                if [[ $JOBIDSTR != '' ]]; then
                      JOBIDSTR=$JOBIDSTR','
                 fi
                 JOBIDSTR=$JOBIDSTR$JOBID
@@ -697,7 +697,7 @@ fi
 #check if jungfrau detectors are present
 HAVE_JUNGFRAU=$(grep -c Jungfrau /tmp/detnames_"$EXP"_"$CREATE_TIME")
 if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) && ( $WANT_RAYONIX -eq 0 )  && ( $WANT_UXI -eq 0 ) ]]; then
-    
+
     DETNAMES=$(grep Jungfrau /tmp/detnames_"$EXP"_"$CREATE_TIME" | awk  'BEGIN { FS = "|"}; {print $1}' | paste -d " " -s)
 
     DSNAME='exp='$EXP':run='$RUN':smd:stream=0-79'
@@ -711,7 +711,7 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
 
     #default arguments.
     JFARG=$JFARG' -d '$DSNAME
-    if [ $CALIBCODE -ne 0 ]; then
+    if [[ $CALIBCODE -ne 0 ]]; then
         JFARG=$JFARG' -c '$CALIBCODE' --evstep '$NUMEVT
     fi
     JFARG=$JFARG' --events '$NUMEVT
@@ -730,7 +730,7 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
         JOBIDS=()
         NJOBS=0
     fi
- 
+
     for JUNGFRAU in $DETNAMES; do
         echo "jungfrau loop $JUNGFRAU  -- $RUNLOCAL"
         CMD="jungfrau_dark_proc $JFARG -s $JUNGFRAU"
@@ -738,25 +738,27 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
         for calibcycle in {0..2}; do
             if [ -v OLD_JUNGFRAU ]; then
                 CMDC=$CMD
-            elif  [ $CALIBCODE -eq 0 ]; then
+            elif [[ $CALIBCODE -eq 0 ]]; then
                 CMDC=$CMD' --stepnum '$calibcycle
             else
                 CMDC=$CMD
             fi
             if [[ $RUNLOCAL != 1 ]]; then
-                tmpScript=$(mktemp -p $WORKDIR jungfrau_multi_tmpXXXXX.sh)
+                tmpScript=$(mktemp -p "$WORKDIR" jungfrau_multi_tmpXXXXX.sh)
                 #trap "rm -f $tmpScript" EXIT
                 chmod u+x "$tmpScript"
                 printf '#!/bin/bash\n' > "$tmpScript"
-                printf 'source %s/manage/bin/psconda.sh\n' "${SIT_ENV_DIR}" >> "$tmpScript"
-                printf 'echo $HOSTNAME\n' >> "$tmpScript"
-                printf '%s\n' "${CMDC}" >> "$tmpScript"
+                {
+		    printf 'source %s/manage/bin/psconda.sh\n' "$SIT_ENV_DIR"
+                    printf "echo %s\n" "$HOSTNAME"
+                    printf '%s\n' "${CMDC}"
+		} >> "tmpScript"
                 if [[ $EXCLUSIVE == 1 ]]; then
                     jfCmd="sbatch --exclusive --account lcls:$EXP -p $QUEUE -o $WORKDIR/jungfrau_${EXP}_RUN${RUN}_%J.out $tmpScript"
                 else
                     jfCmd="sbatch --mem 8GB --cpus-per-task 1 --account lcls:$EXP -p $QUEUE -o $WORKDIR/jungfrau_${EXP}_RUN${RUN}_%J.out $tmpScript"
                 fi
-                echo "run in queue: $jfCmd"        
+                echo "run in queue: $jfCmd"
                 SUBMISSION=$($jfCmd)
                 check_for_submit_error
                 echo "$SUBMISSION"
@@ -770,7 +772,7 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
             if [ -v OLD_JUNGFRAU ]; then
                 break
             fi
-            if [ $CALIBCODE -ne 0 ]; then
+            if [[ $CALIBCODE -ne 0 ]]; then
                 break
             fi
         done
@@ -781,7 +783,7 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
     if [[ $RUNLOCAL != 1 ]]; then
         echo 'Wait for 1/2 minutes before checking jobs:'
         sleep 30
-        echo Running $NJOBS jobs are PIDS: "${JOBIDS[@]}"
+        echo "Running $NJOBS jobs are PIDS: ${JOBIDS[*]}"
         until check_running_jobs; do
                 echo 'Checking again in 10s'
                 sleep 10
@@ -799,8 +801,8 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
     fi
 
     #Now deploy.
-    if [ $DEPLOY == 1 ]; then
-        if [ $NFAILEDJOBS -gt 0 ]; then
+    if [[ $DEPLOY == 1 ]]; then
+        if [[ $NFAILEDJOBS -gt 0 ]]; then
             read -r -p "$NFAILEDJOBS of the calibration tasks failed, do you want to continue (y/n)?"
             if [ "$REPLY" != "y" ];then
                 exit 1
@@ -809,8 +811,8 @@ if [[ ( $HAVE_JUNGFRAU -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &
         for JUNGFRAU in $DETNAMES; do
             #this is also where -t should be used, just as for the validity range
             CMD="jungfrau_deploy_constants -D -d $JUNGFRAU -e $EXP -r $RUN -x :dir=$XTCDIR"
-            if [ $VALSTR != 'xxx' ]; then
-                # this does not work before ana-.....    
+            if [[ $VALSTR != 'xxx' ]]; then
+                # this does not work before ana-.....
                 #CMD=$CMD' -t '$VALSTR'-end'
                 CMD=$CMD' -t '$VALSTR
             fi
@@ -839,7 +841,7 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
         JOBIDS=()
         NJOBS=0
     fi
-    
+
     for EPIX10K in $DETNAMES; do
         echo "Epix10ka name for $EXP is: $EPIX10K"
         ##run all at once - do not use
@@ -850,7 +852,7 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
             CMD="epix10ka_pedestals_calibration -d $EPIX10K -e $EXP -r $RUN -c $calibcycle -x :dir=$XTCDIR:live:stream=0-79 -L INFO"
             echo "---------------EPIX10K PEDESTALS FOR CYCLE $calibcycle --------------------"
             if [[ $RUNLOCAL != 1 ]]; then
-                tmpScript=$(mktemp -p $WORKDIR epix10ka_pedestals_tmpXXXXX.sh)
+                tmpScript=$(mktemp -p "$WORKDIR" epix10ka_pedestals_tmpXXXXX.sh)
                 #trap "rm -f $tmpScript" EXIT
                 chmod u+x "$tmpScript"
                 printf '#!/bin/bash\n' > "$tmpScript"
@@ -868,7 +870,7 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
                 THISJOBID=$(echo "$SUBMISSION" | awk '{print $4}')
                 JOBIDS+=( "$THISJOBID" )
                 NJOBS=$((NJOBS+1))
-            else            
+            else
                 echo "$CMD"
                 $CMD
             fi
@@ -878,14 +880,14 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
     if [[ $RUNLOCAL != 1 ]]; then
         echo 'Wait for 1/2 minute before checking jobs:'
         sleep 30
-        echo Running $NJOBS jobs are PIDS: "${JOBIDS[@]}"
+        echo "Running $NJOBS jobs are PIDS: ${JOBIDS[*]}"
         until check_running_jobs; do
             echo 'Checking again in 10s'
             sleep 10
         done
         echo 'All jobs finished'
         # and now check that none of the jobs have existed with an error code:
-        # currently, the epix10k jobs print DONE at the end. 
+        # currently, the epix10k jobs print DONE at the end.
     # Second check necessary as jobs can fail without printing an exit code to the logfile
         NFAILEDJOBS=0
         for JOBID in "${ALLJOBIDS[@]}"; do
@@ -895,12 +897,12 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
             elif ! grep -q 'DONE' "$WORKDIR"/*"$JOBID".out; then
                 NFAILEDJOBS=$((NFAILEDJOBS+1))
             fi
-        done    
+        done
     fi
 
     echo "---------------EPIX10K PEDESTALS CALCULATED NOW DEPLOY     --------------------"
-    if [ $DEPLOY == 1 ]; then
-        if [ $NFAILEDJOBS -gt 0 ]; then
+    if [[ $DEPLOY == 1 ]]; then
+        if [[ $NFAILEDJOBS -gt 0 ]]; then
             read -r -p "$NFAILEDJOBS of the calibration tasks failed, do you want to continue anyways (y/n)?"
             if [ "$REPLY" != "y" ];then
                 exit 1
@@ -909,8 +911,8 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
 
         for EPIX10K in $DETNAMES; do
             CMD="epix10ka_deploy_constants -D -d $EPIX10K -e $EXP -r $RUN -L INFO -x :dir=$XTCDIR:stream=0-79"
-            if [ $VALSTR != 'xxx' ]; then
-                echo 'setting validity....' $VALSTR
+            if [[ $VALSTR != 'xxx' ]]; then
+                echo "setting validity...$VALSTR"
                 CMD=$CMD' -t '$VALSTR
             fi
             echo "$CMD"
@@ -920,7 +922,7 @@ if [[ ( $HAVE_EPIX10K -ge 1 ) && ( $WANT_ZYLA -eq 0 ) && ( $WANT_OPAL -eq 0 ) &&
             echo 'Print Information about batch jobs'
             JOBIDSTR=''
             for JOBID in "${ALLJOBIDS[@]}"; do
-                if [[ $JOBIDSTR != '' ]]; then 
+                if [[ $JOBIDSTR != '' ]]; then
                     JOBIDSTR=$JOBIDSTR','
                 fi
                 JOBIDSTR=$JOBIDSTR$JOBID
@@ -939,7 +941,7 @@ fi
 # Make list of detectors to treat with calibrun
 ###########
 
-#check if detectors are present    
+#check if detectors are present
 HAVE_EPIX=$(grep -c Epix100 /tmp/detnames_"$EXP"_"$CREATE_TIME")
 HAVE_CSPAD=$(grep -c Cspad /tmp/detnames_"$EXP"_"$CREATE_TIME")
 HAVE_ZYLA=$(grep -c Zyla /tmp/detnames_"$EXP"_"$CREATE_TIME")
@@ -1011,10 +1013,10 @@ if [[ ( $HAVE_RAYONIX -ge 1 ) && ( $WANT_RAYONIX -ge 1 ) ]]; then
     if [ $SPECIFIED_CUTS -eq -4 ]; then
         DETS="$DETS Rayonix"
     else
-        DETS='Rayonix'    
+        DETS='Rayonix'
     fi
     ARG=$ARG' --zeropeds'
-    
+
     DETNAMES=$(grep Rayonix /tmp/detnames_"$EXP"_"$CREATE_TIME" | awk  'BEGIN { FS = "|"}; {print $1}' | paste -d " " -s)
     for RAYONIX in $DETNAMES; do
         deploy_geometry "$RAYONIX"
@@ -1037,7 +1039,7 @@ echo "for the following detectors: $DETS"
 for MYDET in $DETS; do
     #set thresholds for the detector in question
     #ADU minimum, maximum
-    get_config $MYDET
+    get_config "$MYDET"
 
     LOCARG=$ARG' --thr_int_min '$ADUMIN' --thr_int_max '$ADUMAX' --thr_rms_min '$NOISESIGMIN' --thr_rms_max '$NOISESIGMAX
     #this was likely to work with runs where the zyla rate was < readout rate....
@@ -1045,7 +1047,7 @@ for MYDET in $DETS; do
         LOCARG=$LOCARG' -m 100'
     fi
 
-    if [ $VALSTR != 'xxx' ]; then
+    if [[ $VALSTR != 'xxx' ]]; then
         LOCARG=$LOCARG' -v '$VALSTR'-end'
     fi
 
diff --git a/scripts/motor-expert-screen b/scripts/motor-expert-screen
index fd5800c1..ca92cba5 100755
--- a/scripts/motor-expert-screen
+++ b/scripts/motor-expert-screen
@@ -17,9 +17,9 @@ if [[ ($1 == "--help") || ($1 == "-h") || (-z $1) ]]; then
 	exit 0
 fi
 
-shift $(($OPTIND - 1))
+shift $((OPTIND - 1))
 
-PREFIX=`echo $1 | cut -d . -f 1`
+PREFIX=$(echo "$1" | cut -d . -f 1)
 
 # Setup edm environment
 source /reg/g/pcds/setup/epicsenv-3.14.12.sh
@@ -36,7 +36,7 @@ isbeckhoff=false
 
 # Choose title so we can move the right window.
 # If this script hangs later, titles probably changed.
-rtyp=`caget -t $PREFIX.RTYP` > /dev/null 2>&1
+rtyp=$(caget -t "$PREFIX".RTYP) > /dev/null 2>&1
 if [ "${rtyp}" == 'xps8p' ]; then
     title='Newport XPS Positioner'
 elif [ "${rtyp}" == 'ims' ]; then
@@ -45,16 +45,14 @@ elif [ "${rtyp}" == 'motor' ]; then
     # Check to see if this is a Beckhoff axis
     #   caget will return exit code 0 if :PLC:nErrorId_RBV exists,
     #   we set isbeckhoff based on this.
-    caget "${PREFIX}:PLC:nErrorId_RBV" > /dev/null 2>&1
-    if [ $? -eq 0 ]; then
+    if caget "${PREFIX}:PLC:nErrorId_RBV" > /dev/null 2>&1; then
         title="Typhos Suite - ${PREFIX}"
         isbeckhoff=true;
     else
         title='Aerotech motor'
     fi
 else
-    caget "$PREFIX.PN" > /dev/null 2>&1
-    if [ $? -eq 0 ]; then
+    if caget "$PREFIX.PN" > /dev/null 2>&1; then
         title='IMS Motor Control -- Main'
     else
         title='IMS Motor Control'
@@ -65,16 +63,16 @@ fi
 # if xdotool is not installed, the move window commands will skip
 
 # Check already open windows
-oldwins=`xdotool search --onlyvisible --maxdepth 2 --all --name "$title" 2> /dev/null`
+oldwins=$(xdotool search --onlyvisible --maxdepth 2 --all --name "$title" 2> /dev/null)
 
 # Open new window
 if [ ${isbeckhoff} == true ]; then
-    motor-typhos ${PREFIX} > /dev/null 2>&1 &
+    motor-typhos "$PREFIX" > /dev/null 2>&1 &
 elif [ "${rtyp}" == 'xps8p' ]; then
     # If we have a Newport motor, we need to parse the PV to get the macro
     # substitutions for the edm screen
-    base=`echo $PREFIX | cut -d':' -f 1,2,3`
-    num=`echo $PREFIX | cut -d':' -f 4`
+    base=$(echo "$PREFIX" | cut -d':' -f 1,2,3)
+    num=$(echo "$PREFIX" | cut -d':' -f 4)
     if [ "$num" -ge 1 ] && [ "$num" -le 8 ]; then
         ext=0108
     elif [ "$num" -ge 9 ] && [ "$num" -le 16 ]; then
@@ -83,7 +81,7 @@ elif [ "${rtyp}" == 'xps8p' ]; then
         ext=1724
     elif [ "$num" -ge 25 ] && [ "$num" -le 32 ]; then
         ext=2532
-    elif [ "$num" -ge 33 ] && [ "$num" -le 40]; then
+    elif [ "$num" -ge 33 ] && [ "$num" -le 40 ]; then
         ext=3340
     else
         # If something went wrong we'll be missing some boring things
@@ -93,13 +91,12 @@ elif [ "${rtyp}" == 'xps8p' ]; then
 elif [ "${rtyp}" == 'mmca' ]; then # MMC-100 axis
     edm -x -eolc -m "MOTOR=$PREFIX" mmc_main.edl > /dev/null 2>&1 &
 elif [ "${rtyp}" == 'motor' ]; then
-    caget "$PREFIX:PN" > /dev/null 2>&1
-    if [ $? -eq 0 ]; then
+    if caget "$PREFIX:PN" > /dev/null 2>&1; then
         /reg/g/pcds/package/epics/3.14//modules/pcds_motion/${OLD_VERSION}/launch-motor.sh "$PREFIX" > /dev/null 2>&1 &
     else
 	# smaracts have "motor" rtyp, so we catch them with the PREFIX or with smaract specific pvs
 	if [[ $PREFIX == *"MCS2"* || $(caget "$PREFIX:PTYPE_RBV" > /dev/null 2>&1) -eq 0 ]]; then
-            enc=$(caget $PREFIX.UEIP)
+            enc=$(caget "$PREFIX".UEIP)
             if [[ $enc == *"Yes"* ]]; then
 		edm -x -eolc -m "MOTOR=$PREFIX" mcs2_main.edl > /dev/null 2>&1 &
             else
@@ -120,13 +117,13 @@ fi
 
 # Accumulate all windows
 sleep 2 # Crudely give the new window enough time to load
-newwins=`xdotool search --onlyvisible --maxdepth 2 --all --sync --name "$title" 2> /dev/null`
+newwins=$(xdotool search --onlyvisible --maxdepth 2 --all --sync --name "$title" 2> /dev/null)
 
 # Find the id of the new window
 for new in $newwins; do
     foundMatch=0
     for old in $oldwins; do
-        if [ $new == $old ]; then
+        if [[ $new == "$old" ]]; then
             foundMatch=1
             break
         fi
@@ -138,7 +135,7 @@ for new in $newwins; do
 done
 
 # Get window location, dimensions
-geom=`xdotool getwindowgeometry $id 2> /dev/null` 
+geom=$(xdotool getwindowgeometry "$id" 2> /dev/null)
 locxy=${geom#*Position: }
 locxy=${locxy%% *}
 winx=${locxy%,*}
@@ -149,17 +146,17 @@ xwidth=${sizexy%x*}
 ywidth=${sizexy#*x}
 
 # Get mouse position
-read x y s w <<<$(xdotool getmouselocation 2> /dev/null)
-xpos=`echo $x | cut -d':' -f 2`
-ypos=`echo $y | cut -d':' -f 2`
+read -r x y s w <<<"$(xdotool getmouselocation 2> /dev/null)"
+xpos=$(echo "$x" | cut -d':' -f 2)
+ypos=$(echo "$y" | cut -d':' -f 2)
 
-if [ -z $xpos ]; then
+if [[ -z $xpos ]]; then
   exit
 # Check if mouse is already on the window. In this case, we wouldn't move it.
-elif [ "$xpos" -lt "$winx" ] || [ "$xpos" -gt $(( ${winx} + ${xwidth}  )) ] || [ "$ypos" -lt "$winy" ] || [ "$ypos" -gt $(( ${winy} + ${ywidth} )) ]; then
+elif [ "$xpos" -lt "$winx" ] || [ "$xpos" -gt $((winx + xwidth)) ] || [ "$ypos" -lt "$winy" ] || [ "$ypos" -gt $((winy + ywidth)) ]; then
     # Adjust xpos and ypos so center of window aligns with cursor.
-    xpos=$(( ${xpos} - ( ${xwidth} / 2 ) ))
-    ypos=$(( ${ypos} - ( ${ywidth} / 2 ) ))
+    xpos=$((xpos - (xwidth / 2)))
+    ypos=$((ypos - (ywidth / 2)))
     # Finally, move the window to our cursor.
-    xdotool windowmove $id $xpos $ypos 2> /dev/null
+    xdotool windowmove "$id" "$xpos" "$ypos" 2> /dev/null
 fi
diff --git a/scripts/motor-typhos b/scripts/motor-typhos
index e3453142..04bed80e 100755
--- a/scripts/motor-typhos
+++ b/scripts/motor-typhos
@@ -14,7 +14,7 @@ if [[ ($1 == "--help") || ($1 == "-h") ]]; then
 	exit 0
 fi
 
-PREFIX=`echo $1 | cut -d . -f 1`
+PREFIX=$(echo "$1" | cut -d . -f 1)
 
 if [ -z "${PREFIX}" ]; then
     usage;
@@ -24,9 +24,7 @@ fi
 # Use the latest tagged environment
 source /reg/g/pcds/pyps/conda/pcds_conda
 
-caget "${PREFIX}:PLC:nErrorId_RBV" > /dev/null 2>&1
-
-if [ $? -eq 0 ]; then
+if caget "${PREFIX}:PLC:nErrorId_RBV" > /dev/null 2>&1; then
     echo "* This looks like a Beckhoff axis."
     DEVICE_CLASS="pcdsdevices.epics_motor.BeckhoffAxis"
     NAME="${PREFIX}"  # maybe we can do better?
@@ -39,4 +37,4 @@ fi
 TYPHOS_ARGS="${DEVICE_CLASS}[{'prefix':'${PREFIX}','name':'${NAME}'}]"
 echo "* Launching typhos with arguments: ${TYPHOS_ARGS}"
 echo "* This may take a bit, please wait..."
-typhos ${TYPHOS_ARGS} > /dev/null 2>&1 &
+typhos "$TYPHOS_ARGS" > /dev/null 2>&1 &
diff --git a/scripts/motorInfo b/scripts/motorInfo
index c65c5fe8..4da9360c 100755
--- a/scripts/motorInfo
+++ b/scripts/motorInfo
@@ -24,8 +24,8 @@ fi
 while getopts "f:s:e:" OPTION
 do
     case $OPTION in
-    f) 
-	PVFIELDS=`echo $OPTARG | sed s/','/' '/g`
+    f)
+	PVFIELDS=${OPTARG//,/}
 	;;
     s)
         STARTTIME=$OPTARG
@@ -33,109 +33,114 @@ do
     e)
         ENDTIME=$OPTARG
 	;;
+    *)
+	echo "Invalid option \"$OPTION\" provided"
+	usage
+	exit 1
+	;;
     esac
 done
 
-shift $(($OPTIND - 1))
+shift $((OPTIND - 1))
 
 if [ $# -lt 2 ]; then
     usage
     exit
 fi
 
-MOTOR_PV=`echo $1 | cut -d . -f 1`
-if [[ $1 ==  $MOTOR_PV ]]; then
+MOTOR_PV=$(echo "$1" | cut -d . -f 1)
+if [[ $1 ==  "$MOTOR_PV" ]]; then
     FIELD=''
 else
-    echo 1: $1
-    echo MOTOR_PV $MOTOR_PV
-    FIELD=`echo $1 | cut -d . -f 2`
+    echo "1: $1"
+    echo "MOTOR_PV: $MOTOR_PV"
+    FIELD=$(echo "$1" | cut -d . -f 2)
 fi
 
 source /reg/g/pcds/setup/pcds_shortcuts.sh
 
 if [[ $PVFIELDS == '' ]] && [[ "$2" != *pmgr* ]]; then
-    IOC_DIR='/reg/g/pcds/epics/'`find_pv $MOTOR_PV | grep DIR | grep ims | awk '{print $2}'`'/build/autosave'
-    PVLIST=`grep $MOTOR_PV $IOC_DIR/*req`
+    IOC_DIR='/reg/g/pcds/epics/'$(find_pv "$MOTOR_PV" | grep DIR | grep ims | awk '{print $2}')'/build/autosave'
+    PVLIST=$("grep $MOTOR_PV $IOC_DIR/*req")
     for pv in $PVLIST; do
-	PVFIELDS=`echo $pv | awk -F "$MOTOR_PV" '{ print $2 }'`' '$PVFIELDS
+	PVFIELDS=$(echo "$pv" | awk -F "$MOTOR_PV" '{ print $2 }')' '$PVFIELDS
     done
 fi
 
-if [ $2 == 'autosave' ]; then
-    IOC_DIR='/reg/d/iocData/'`find_pv $MOTOR_PV | grep IOC: | head -n 1 | awk '{print $2}'`'/autosave'
+if [[ $2 == 'autosave' ]]; then
+    IOC_DIR='/reg/d/iocData/'$(find_pv "$MOTOR_PV" | grep IOC: | head -n 1 | awk '{print $2}')'/autosave'
 
-    files=`ls -t $IOC_DIR/*sav_1*`
+    files=$(ls -t "$IOC_DIR"/*sav_1*)
     for field in $PVFIELDS; do
 	if [[ "$field" == *RBV* ]] || [[ "$field" == *VAL* ]] || [[ "$field" == *DESC* ]]; then
 	    continue
 	fi
-	echo 'Looking at the autosave history for: ' $MOTOR_PV$field
+	echo "Looking at the autosave history for: $MOTOR_PV$field"
 	same_value_dat='now'
-	currVal=`caget -t $MOTOR_PV$field`
-	currValN=`caget -tn $MOTOR_PV$field`
+	currVal=$(caget -t "$MOTOR_PV$field")
+	currValN=$(caget -tn "$MOTOR_PV$field")
 	for file in $files; do
-	    autoVal=`grep $MOTOR_PV$field' ' $file | awk {'print $2'}`
-	    if [[ $autoVal != $currValN ]] && [[ ${#autoVal} > 0 ]]; then
+	    autoVal=$(grep "$MOTOR_PV$field " "$file" | awk '{print $2}')
+	    if [[ $autoVal != "$currValN" ]] && [[ ${#autoVal} -gt 0 ]]; then
 		#if $autoVal #check that this is not empty.
-		file_date=`echo $file | awk -F sav_ '{ print $2 }'` 
-		if [[ $currVal != $currValN ]]; then
-		    echo $MOTOR_PV$field current: $currValN '('$currVal')' -- $autoVal at $file_date , was same last: $same_value_dat
+		file_date=$(echo "$file" | awk -F sav_ '{ print $2 }')
+		if [[ $currVal != "$currValN" ]]; then
+		    echo "$MOTOR_PV$field current: $currValN '('$currVal')' -- $autoVal at $file_date , was same last: $same_value_dat"
 		else
-		    echo $MOTOR_PV$field current: $currValN -- $autoVal at $file_date , was same last: $same_value_dat
+		    echo "$MOTOR_PV$field current: $currValN -- $autoVal at $file_date , was same last: $same_value_dat"
 		fi
 	    else
-		same_value_dat=`echo $file | awk -F sav_ '{ print $2 }'`
+		same_value_dat=$(echo "$file" | awk -F sav_ '{ print $2 }')
 	    fi
 	done
 	echo
     done
-elif [ $2 == 'archive' ]; then
+elif [[ $2 == 'archive' ]]; then
     echo 'Command-line archiver is not implemented yet'
 elif [[ "$2" == *pmgr* ]]; then
-    HUTCH=`echo $MOTOR_PV | cut -d : -f 1`
+    HUTCH=$(echo "$MOTOR_PV" | cut -d : -f 1)
     hutch=${HUTCH,,}
-    ACTION=`echo $2 | cut -d _ -f 2`
+    ACTION=$(echo "$2" | cut -d _ -f 2)
     if [[ $ACTION == 'diff' ]]; then
-	/reg/g/pcds/config/$hutch/pmgr/pmgrUtils.sh $ACTION $MOTOR_PV    
+	/reg/g/pcds/config/"$hutch"/pmgr/pmgrUtils.sh "$ACTION" "$MOTOR_PV"
     elif [[ $ACTION == 'save' ]]; then
-	echo 'Differences of '$MOTOR_PV' to saved config:'
-	/reg/g/pcds/config/$hutch/pmgr/pmgrUtils.sh diff $MOTOR_PV    
-	echo 'Save current config (yes/no)? '; read ANSWER
+	echo "Differences of $MOTOR_PV to saved config:"
+	/reg/g/pcds/config/"$hutch"/pmgr/pmgrUtils.sh diff "$MOTOR_PV"
+	echo 'Save current config (yes/no)? '; read -r ANSWER
 	if [[ $ANSWER == 'yes' ]]; then
 	    echo 'Save now...'
-	    /reg/g/pcds/config/$hutch/pmgr/pmgrUtils.sh save $MOTOR_PV    
+	    /reg/g/pcds/config/"$hutch"/pmgr/pmgrUtils.sh save "$MOTOR_PV"
 	    echo 'Saved.'
 	fi
     else
-	echo $ACTION ' is not yet implemented for the pmgr function of motorInfo'
+	echo "$ACTION is not yet implemented for the pmgr function of motorInfo"
     fi
 else
-    MOTOR2_PV=`echo $2 | cut -d . -f 1`
+    MOTOR2_PV=$(echo "$2" | cut -d . -f 1)
     ADD_MOTOR_PV=$MOTOR2_PV
-    echo 'MOTORS DIFF' $# $ADD_MOTOR_PV
+    echo "MOTORS DIFF $# $ADD_MOTOR_PV"
     while [[ $# -gt 2 ]]; do
 	shift
-	ADD_MOTOR_PV=$ADD_MOTOR_PV' '`echo $2 | cut -d . -f 1`
+	ADD_MOTOR_PV="$ADD_MOTOR_PV $(echo "$2" | cut -d . -f 1)"
     done
 
-    echo Field :  $MOTOR_PV -- $ADD_MOTOR_PV
+    echo Field :  "$MOTOR_PV" -- "$ADD_MOTOR_PV"
     for field in $PVFIELDS; do
 	if [[ "$field" == *RBV* ]] || [[ "$field" == *VAL* ]]; then
 	    continue
 	fi
-	value_mot1=`caget -t $MOTOR_PV$field`
+	value_mot1=$(caget -t "$MOTOR_PV$field")
 	values=''
 	HAS_DIFF=0
 	for PV in $ADD_MOTOR_PV; do
-	    newval=`caget -t $PV$field`
+	    newval=$(caget -t "$PV$field")
 	    values=$values' - '$newval
-	    if [[ $value_mot1 != $newval ]]; then
+	    if [[ $value_mot1 != "$newval" ]]; then
 		HAS_DIFF=1
 	    fi
 	done
-	if [[ $HAS_DIFF > 0 ]]; then
-	    echo $field :  $value_mot1 -- $values
+	if [[ $HAS_DIFF -gt 0 ]]; then
+	    echo "$field" :  "$value_mot1" -- "$values"
 	fi
     done
 fi
diff --git a/scripts/new_bare_repo b/scripts/new_bare_repo
index d5932540..0dee128a 100755
--- a/scripts/new_bare_repo
+++ b/scripts/new_bare_repo
@@ -43,7 +43,7 @@ elif [[ ${CWD} != *${REPO}* ]]; then
 else
     git init
     cp -u /cds/sw/tools/bin/eco_tools/gitignore.template .gitignore
-    git add *.cfg Makefile .gitignore
+    git add -- *.cfg Makefile .gitignore
     git commit -m "Initial commit"
     git-bare-repo /afs/slac.stanford.edu/g/cd/swe/git/repos/package/epics/ioc/"${HUTCH}"/"${REPO}".git
     git remote add origin /afs/slac.stanford.edu/g/cd/swe/git/repos/package/epics/ioc/"${HUTCH}"/"${REPO}".git
diff --git a/scripts/pcds_conda b/scripts/pcds_conda
index 7ad47665..1e794176 100755
--- a/scripts/pcds_conda
+++ b/scripts/pcds_conda
@@ -136,4 +136,3 @@ if [ -n "${SSH_CONNECTION}" ]; then
     fi
   fi
 fi
-
diff --git a/scripts/pkg_release b/scripts/pkg_release
index 570a774f..16a72ed8 100755
--- a/scripts/pkg_release
+++ b/scripts/pkg_release
@@ -42,12 +42,12 @@ if ! ping -c 1 github.com &> /dev/null; then
 fi
 echo "Connection successful."
 TEST_OUTPUT=$(ssh -Tx git@github.com 2>&1) # Test ssh key with github and use ssh if appropriate, https otherwise
-if echo $TEST_OUTPUT | grep "successfully authenticated" > /dev/null; then
+if echo "$TEST_OUTPUT" | grep "successfully authenticated" > /dev/null; then
   echo "Attemping clone using SSH..."
   echo "URL = $SSH_URL"
   set -e  # Catch error in git clone
   git clone "${SSH_URL}" "${TEMP}"
-elif echo $TEST_OUTPUT | grep "Permission denied\|no kex alg" > /dev/null; then
+elif echo "$TEST_OUTPUT" | grep "Permission denied\|no kex alg" > /dev/null; then
   echo "Attemping clone using HTTPS..."
   echo "URL = $URL"
   set -e  # Catch error in git clone
@@ -61,7 +61,7 @@ echo "Checking out tag..."
 pushd "${TEMP}"
 git tag -l | grep "${TAG}" >/dev/null
 if [ "${?}" == "1" ]; then
-  echo "Error: could not find tag "${TAG}". Aborting."
+  echo "Error: could not find tag \"${TAG}.\" Aborting."
   echo "Available tags:"
   git tag -l
   exit
@@ -69,8 +69,8 @@ fi
 set -e  # Catch error in git checkout
 git checkout "${TAG}"
 popd
-echo "Renaming "${TEMP}" directory to ${TAG}"
+echo "Renaming \"${TEMP}\" directory to ${TAG}"
 mv "${TEMP}" "${TAG}"
 echo "Write-protecting directory..."
 chmod -R a-w "${TAG}"
-echo "Created $(readlink -f ${TAG})"
+echo "Created $(readlink -f "$TAG")"
diff --git a/scripts/pmgr b/scripts/pmgr
index 1c4949e0..e368c67d 100755
--- a/scripts/pmgr
+++ b/scripts/pmgr
@@ -18,6 +18,6 @@ if [[ -n $1 && ! $1 =~ '--' ]]; then
     HUTCH=$1
     shift
 else
-    HUTCH=`get_hutch_name`
+    HUTCH=$(get_hutch_name)
 fi
-/reg/g/pcds/pyps/config/${HUTCH}/pmgr/pmgr --type ims_motor --hutch ${HUTCH} $@ &
+/reg/g/pcds/pyps/config/"$HUTCH"/pmgr/pmgr --type ims_motor --hutch "$HUTCH" "$@" &
diff --git a/scripts/pydev_register b/scripts/pydev_register
index 7d039d66..7aefe230 100755
--- a/scripts/pydev_register
+++ b/scripts/pydev_register
@@ -24,7 +24,7 @@ elif [ ! -e "${1}" ]; then
 fi
 
 PYDEV_DIR=~/pydev
-full_path="$(readlink -f $1)"
+full_path=$(readlink -f "$1")
 if [ "${2}" == "module" ]; then
   link="${PYDEV_DIR}"
 elif [ "${2}" == "bin" ]; then
diff --git a/scripts/restartdaq b/scripts/restartdaq
index 1530e9c8..eadd59d1 100755
--- a/scripts/restartdaq
+++ b/scripts/restartdaq
@@ -41,13 +41,13 @@ do
 	s)
 	    SILENT=1
 	    ;;
-	m) 
+	m)
 	    AIMHOST=$OPTARG
 	    ;;
- 	c) 
- 	    CORESIZE=2000000000 
+ 	c)
+ 	    CORESIZE=2000000000
  	    ;;
- 	d) 
+ 	d)
  	    DSSTEST=1
  	    ;;
 	?)
@@ -88,6 +88,7 @@ cd /reg/g/pcds/dist/pds/"$HUTCH"/scripts/ || exit
 DAQNETWORK='fez'
 LCLS2_HUTCHES="rix, tmo, ued"
 if echo "$LCLS2_HUTCHES" | grep -iw "$HUTCH" > /dev/null; then
+    # shellcheck source=/reg/g/pcds/dist/pds/rix/scripts/setup_env.sh
     source /reg/g/pcds/dist/pds/"$HUTCH"/scripts/setup_env.sh
     PROCMGR='procmgr'
     DAQNETWORK='drp'
@@ -101,8 +102,7 @@ if [ "$IS_DAQ_HOST" == 0 ]; then
     WORKINGHOSTS=''
     #make sure at least cds is up.
     for HOST in $HOSTS; do
-	ping -w 2 "$HOST" >/dev/null 2>&1
-	if [[ $? == 0 ]]; then
+	if ping -w 2 "$HOST" >/dev/null 2>&1; then
 	    WORKINGHOSTS=$WORKINGHOSTS' '$HOST
 	fi
     done
@@ -117,12 +117,12 @@ else
     DAQHOST=$(wheredaq)
 fi
 
-PLATFORM=$(grep 'if not platform' /reg/g/pcds/dist/pds/"$HUTCH"/scripts/$CNFFILE | awk '{print $NF}' | sed s/\'//g)
+PLATFORM=$(grep 'if not platform' /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNFFILE" | awk '{print $NF}' | sed s/\'//g)
 if [[ "$DAQHOST" != *$NOTRUNNING* ]]; then
     echo stop the DAQ on "$DAQHOST" from "$HOSTNAME"
     T="$(date +%s%N)"
     $PROCMGR stop \
-	/reg/g/pcds/dist/pds/"$HUTCH"/scripts/$CNFFILE 
+	/reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNFFILE"
 
 
     if [ -f /reg/g/pcds/dist/pds/"$HUTCH"/scripts/p"$PLATFORM"$CNFEXT.running ]; then
@@ -138,7 +138,7 @@ else
 	echo while DAQ reports to not run, will stop the DAQ on "$DAQHOST" from "$HOSTNAME" to clear the p"$PLATFORM"$CNFEXT.running file
 	T="$(date +%s%N)"
 	$PROCMGR stop \
-	    /reg/g/pcds/dist/pds/"$HUTCH"/scripts/$CNFFILE 
+	    /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNFFILE"
 
         if [ -f /reg/g/pcds/dist/pds/"$HUTCH"/scripts/p"$PLATFORM"$CNFEXT.running ]; then
             echo 'the DAQ did not stop properly, exit now and try again follow the escalation procedure'
@@ -156,7 +156,7 @@ T="$(date +%s%N)"
 echo start DAQ on "$AIMHOST"
 if [ "$HOSTNAME" == "$AIMHOST" ]; then
     $PROCMGR start \
-        /reg/g/pcds/dist/pds/"$HUTCH"/scripts/$CNFFILE -c $CORESIZE -o /reg/g/pcds/pds/"$HUTCH"/logfiles
+        /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNFFILE" -c $CORESIZE -o /reg/g/pcds/pds/"$HUTCH"/logfiles
 else
     ssh -Y "$AIMHOST" restartdaq
 fi
@@ -191,7 +191,7 @@ if [ ${#DOWIN} != 0 ] ||  [ ${#SELPART} != 0 ]; then
 	    SELPART=0
 	fi
     fi
-    if [ -f /reg/neh/operator/"$HUTCH"\opr/bin/"$HUTCH"\_cleanup_windows_daq ]; then
+    if [ -f /reg/neh/operator/"$HUTCH"opr/bin/"$HUTCH"_cleanup_windows_daq ]; then
 	if [ ${#DOWIN} != 0 ]; then
 	    echo 'This instrument does not have standard locations for DAQ windows setup'
 	fi
@@ -199,7 +199,7 @@ if [ ${#DOWIN} != 0 ] ||  [ ${#SELPART} != 0 ]; then
     fi
 fi
 
-if [ ${#DOWIN} != 0 ]; then    
+if [ ${#DOWIN} != 0 ]; then
     T="$(date +%s%N)"
     if [ "$HUTCH" == 'xpp' ]; then
 	test=$(xdotool search --sync --onlyvisible --name 'ProcStat')
@@ -208,25 +208,25 @@ if [ ${#DOWIN} != 0 ]; then
 	sleep 2
     fi
     echo 'resorting the windows now using: /reg/neh/operator/'"$HUTCH"'opr/bin/'"$HUTCH"'_cleanup_windows_daq'
-    /reg/neh/operator/"$HUTCH"\opr/bin/"$HUTCH"\_cleanup_windows_daq
+    /reg/neh/operator/"$HUTCH"opr/bin/"$HUTCH"_cleanup_windows_daq
     Tdinter="$(($(date +%s%N)-T))"
     Sinter="$((Tdinter/1000000000))"
     Minter="$((Tdinter/1000000))"
     echo 'and '"$Sinter"'.'"$Minter"' extra seconds for windows'
 fi
 
-if [ ${#SELPART} != 0 ]; then    
+if [ ${#SELPART} != 0 ]; then
     DAQC=$(xdotool search  --onlyvisible --name 'DAQ Control')
     #echo $DAQC
     xdotool mousemove --sync --window "$DAQC" 80 230
     xdotool windowfocus "$DAQC"
-    xdotool click 1 
-    
+    xdotool click 1
+
     PARTSEL=$(xdotool search  --onlyvisible --sync --name 'Partition Selection')
     YLOW=$(xdotool search --name 'Partition Selection' getwindowgeometry %@ | grep Geometry | awk '{print $2}' | sed s/x/" "/g | awk '{print $2}')
         #echo $PARTSEL
-    xdotool mousemove --sync --window "$PARTSEL" 80 $(("$YLOW"-28)) 
-    xdotool click 1 
+    xdotool mousemove --sync --window "$PARTSEL" 80 $(("$YLOW"-28))
+    xdotool click 1
 fi
 
 if [ "$SILENT" == 0 ];then
diff --git a/scripts/serverStat b/scripts/serverStat
index abdd856e..99cc581f 100755
--- a/scripts/serverStat
+++ b/scripts/serverStat
@@ -6,11 +6,11 @@ names_from_name(){
     fi
     INNAME=$1
     if [[ $INNAME == *'-ipmi'* ]]; then
-        INNAME=$(echo "$INNAME" | sed s/-ipmi//g)
+	INNAME=${INNAME//-ipmi/}
     elif [[ $INNAME == *'-fez'* ]]; then
-        INNAME=$(echo "$INNAME" | sed s/-fez//g)
+        INNAME=${INNAME//-fez/}
     elif [[ $INNAME == *'-ana'* ]]; then
-        INNAME=$(echo "$INNAME" | sed s/-ana//g)
+        INNAME=${INNAME//-ana/}
     fi
     CDSNAME=$INNAME
     CDSIP=$(netconfig search "$CDSNAME" | grep IP: | awk '{print $2}')
@@ -79,7 +79,7 @@ done
 
 
 HOST_HAS_FEZ=$(netconfig search "$HOSTNAME"-fez --brief | wc -l)
-let HOST_HAS_FEZ-=1
+(( HOST_HAS_FEZ-=1 ))
 
 if [[ $# -lt 2 ]]; then
     if [[ $# -lt 1 ]]; then
@@ -118,18 +118,18 @@ fi
 
 if [[ $NAME == *'-ipmi'* ]]; then
     NAMEIPMI=$NAME
-    NAME=$(echo "$NAME" | sed s/-ipmi//g)
+    NAME=${NAME//-ipmi/}
     DEV=$NAME
 elif [[ $NAME == *'-fez'* ]]; then
-    NAME=$(echo "$NAME" | sed s/-fez//g)
+    NAME=${NAME//-fez/}
     DEV=$NAME
 elif [[ $NAME == *'-ana'* ]]; then
-    NAME=$(echo "$NAME" | sed s/-ana//g)
+    NAME=${NAME//-ana/}
 fi
 
 if  [[ $NAME == *rec* ]]; then
     if [[ $CMD == "off" ]] || [[ $CMD == "cycle" ]]; then
-        echo "This is a recorder, better not to power cycle unless necessary, try to reset first. Quit? " "$NAME" "$CMD"; read ANSWER
+        echo "This is a recorder, better not to power cycle unless necessary, try to reset first. Quit? " "$NAME" "$CMD"; read -r ANSWER
         if [[ $ANSWER == 'y' ]] || [[ $ANSWER == 'Y' ]] || [[ $ANSWER == 'yes' ]]; then
             printf 'quit now\n'
             exit 0
@@ -147,22 +147,22 @@ if [[ $ISSRV -lt 1 ]] && [[ $HUTCH != 'unknown_hutch' ]]; then
 
     if [[  $DEV =~ 'event' ]]; then
         DSSNODES=$(grep dss_nodes "$CNF" | grep -v '^#' | head -n1 | grep -oE "daq-$HUTCH-dss[[:digit:]]+")
-        NEVENT=$(echo "${DEV:5}")  # grab the index (e.g. 2 if $DEV is event2)
-        SEDNUM=$(($NEVENT+1))  # adjust the number to correctly index the list of dssnodes with sed
+        NEVENT=${DEV:5}  # grab the index (e.g. 2 if $DEV is event2)
+        SEDNUM=$((NEVENT + 1))  # adjust the number to correctly index the list of dssnodes with sed
         NAME=$(echo "$DSSNODES" | sed -n ${SEDNUM}p)
         if [[ -z $NAME ]]; then
             echo "dss node not found for $DEV, exiting..." >&2
             exit 1
         fi
     else
-        NDEV=$(grep "$DEV" "$CNF" | grep -v '#' | grep host | wc -l)
+        NDEV=$(grep "$DEV" "$CNF" | grep -v '#' | grep -c host)
         if [ "$NDEV" -eq 1 ]; then
-            NAME=$(grep "$DEV" "$CNF" | grep -v '#' | grep host | awk '{print $1}' | sed s/{host://g | sed s/,// | sed s/_/-/g | sed s/\'//g | sed s/-fez//g)
+            NAME=$(grep "$DEV" "$CNF" | grep -v '#' | grep host | awk '{print $1}' | sed s/"{host:"//g | sed s/,// | sed s/_/-/g | sed s/\'//g | sed s/-fez//g)
         elif  [ "$NDEV" -eq 0 ]; then
             echo 'No device of this name found, exiting...' >&2
             exit 1
         else
-            NAME=$(grep "$DEV'" "$CNF" | grep -v '#' | grep host | awk '{print $1}' | sed s/{host://g | sed s/,// | sed s/_/-/g)
+            NAME=$(grep "$DEV'" "$CNF" | grep -v '#' | grep host | awk '{print $1}' | sed s/"{host:"//g | sed s/,// | sed s/_/-/g)
         fi
     fi
     if [[ $NAME ]]; then
@@ -204,22 +204,19 @@ elif [[ $CMD == "expert" ]]; then
     echo -e ""
     echo -e "Checking host/ipmi/fez network interfaces are online:"
     echo -e "-------------------------------------------------"
-    ping -w 2 "$NAME" >/dev/null 2>&1
-    if [[ $? == 0 ]]; then
+    if ping -w 2 "$NAME" >/dev/null 2>&1; then
        echo "$NAME pings."
        CDS_ONLINE=1
     else
        echo "$NAME does not ping."
        CDS_ONLINE=0
     fi
-    ping -w 2 "$NAME"-ipmi >/dev/null 2>&1
-    if [[ $? == 0 ]]; then
+    if ping -w 2 "$NAME"-ipmi >/dev/null 2>&1; then
        echo "$NAME-ipmi pings."
     else
        echo "$NAME-ipmi does not ping."
     fi
-    ping -w 2 "$NAME"-fez >/dev/null 2>&1
-    if [[ $? == 0 ]]; then
+    if ping -w 2 "$NAME"-fez >/dev/null 2>&1; then
        echo "$NAME-fez pings."
     else
        echo "$NAME-fez does not ping."
@@ -287,7 +284,7 @@ elif [[ $CMD == "status" ]]; then
         if [[ $HOST_HAS_FEZ -ge 1 ]]; then
             PNGFEZ=$(ping -c 1 "$FEZNAME" | grep transmitted | awk '{print $4}')
             echo "$NAME is a server with IP: $CDSIP (ping success: $PNG), $FEZIP (ping success: $PNGFEZ)"
-            if [[ $(($PNG+$PNGFEZ)) -gt 1 ]]; then
+            if [[ $((PNG + PNGFEZ)) -gt 1 ]]; then
                 echo 'cds&fez interfaces are up'
             fi
         else
diff --git a/scripts/set_gem_timing b/scripts/set_gem_timing
index feb8d59d..d3533b67 100755
--- a/scripts/set_gem_timing
+++ b/scripts/set_gem_timing
@@ -50,7 +50,7 @@ else
 fi
 
 SET_IOC_PATH_CMD="${IMGR_CMD_PATH} ioc-lfe-gasdet-daq --upgrade $IOC_PATH"
-CURR_IOC_PATH=$(${IMGR_CMD_PATH} ioc-lfe-gasdet-daq --info | awk 'FNR == 4 {print $3}') #Warning: make sure your release of imgr supports --info 
+CURR_IOC_PATH=$(${IMGR_CMD_PATH} ioc-lfe-gasdet-daq --info | awk 'FNR == 4 {print $3}') #Warning: make sure your release of imgr supports --info
 if [[ $CURR_IOC_PATH = "$IOC_PATH" ]]; then
   echo "Current IOC path is: $CURR_IOC_PATH which is equiavlent to requested IOC path for the requested switch to $1, not invoking imgr"
 else
@@ -58,4 +58,4 @@ else
   $SET_IOC_PATH_CMD
 fi
 
-exit 0
\ No newline at end of file
+exit 0
diff --git a/scripts/startami b/scripts/startami
index 7e906a65..7c3106b2 100755
--- a/scripts/startami
+++ b/scripts/startami
@@ -33,15 +33,15 @@ do
 	    ;;
 	esac
 done
-shift "$(($OPTIND-1))"
+shift "$((OPTIND-1))"
 
-if [[ `whoami` != *'opr'* ]]; then
+if [[ $(whoami) != *'opr'* ]]; then
     echo "Please run ami from the operator account!"
     exit
 fi
 
-HUTCH=`get_hutch_name`
-EXPNAME=`get_curr_exp`
+HUTCH=$(get_hutch_name)
+EXPNAME=$(get_curr_exp)
 CNFEXT=.cnf
 
 if [[ $HUTCH == 'cxi' ]]; then
@@ -61,46 +61,46 @@ if [[ -z $CONFIG ]]; then
 fi
 
 #
-# this is XPP specific. Don't think we should have local plugins anyways, 
-# only release ones. 
+# this is XPP specific. Don't think we should have local plugins anyways,
+# only release ones.
 #
 source /reg/g/pcds/setup/pathmunge.sh
-if [ $HUTCH == 'xpp' ]; then
+if [[ $HUTCH == 'xpp' ]]; then
     ldpathmunge /reg/neh/operator/xppopr/ami_plugins
-elif [ $HUTCH == 'xcs' ]; then
+elif [[ $HUTCH == 'xcs' ]]; then
     ldpathmunge /reg/neh/operator/xcsopr/online/ami_plugins
 fi
 
 
-DAQHOST=`wheredaq`
-ami_base_path=`grep ami_base_path /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG | grep -v '#' | grep -v 'ami_base_path+'  | awk 'BEGIN { FS = "=" }; { print $2}' | sed s/\'//g`
-ami_path=$ami_base_path`grep ami_path /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG | grep -v 'ami_path+' | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+// | sed s/\'//g`
+DAQHOST=$(wheredaq)
+ami_base_path=$(grep ami_base_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" | grep -v '#' | grep -v 'ami_base_path+'  | awk 'BEGIN { FS = "=" }; { print $2}' | sed s/\'//g)
+ami_path=$ami_base_path$(grep ami_path /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" | grep -v 'ami_path+' | grep -v '#' | awk 'BEGIN { FS = "= " }; { print $2}' | sed s/ami_base_path+// | sed s/\'//g)
 
-proxy_cds=`/reg/g/pcds/dist/pds/$HUTCH/current/tools/procmgr/procmgr status /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG | grep ami_proxy | awk {'print $1'} | sed s/'-fez'/''/g`
+proxy_cds=$(/reg/g/pcds/dist/pds/"$HUTCH"/current/tools/procmgr/procmgr status /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" | grep ami_proxy | awk '{print $1}' | sed s/'-fez'/''/g)
 
-amicmd=`grep ami_client /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG | grep -v '#' |  awk 'BEGIN { FS = ":" }; { print $4}' | sed s/ami_path//g | sed s/\'+proxy_cds/$proxy_cds/g | sed  s:\'+expname:$EXPNAME/:g | sed s/+\'//g | sed s/\'\}\)//g` 
+amicmd=$(grep ami_client /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" | grep -v '#' |  awk 'BEGIN { FS = ":" }; { print $4}' | sed s/ami_path//g | sed s/\'+proxy_cds/"$proxy_cds"/g | sed  s:\'+expname:"$EXPNAME"/:g | sed s/+\'//g | sed s/\'\}\)//g)
 
 if [[ "$DAQHOST" == *"$HOSTNAME" ]]; then  # Check host and daq host line share host name...
     #running on the DAQ host, this will restart the ami_client!
-    read -p "Do you really intend to restart the ami_client on $DAQHOST? (y/n)"
+    read -rp "Do you really intend to restart the ami_client on $DAQHOST? (y/n)"
     if [ "$REPLY" == "y" ];then
 	echo "Restarting the ami_client...";
-	/reg/g/pcds/dist/pds/$HUTCH/current/tools/procmgr/procmgr stop \
-	    /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG ami_client 
-	/reg/g/pcds/dist/pds/$HUTCH/current/tools/procmgr/procmgr start \
- 	    /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG -c 2000000000 -o /reg/g/pcds/pds/$HUTCH/logfiles ami_client 
+	/reg/g/pcds/dist/pds/"$HUTCH"/current/tools/procmgr/procmgr stop \
+	    /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" ami_client
+	/reg/g/pcds/dist/pds/"$HUTCH"/current/tools/procmgr/procmgr start \
+ 	    /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" -c 2000000000 -o /reg/g/pcds/pds/"$HUTCH"/logfiles ami_client
 	exit
     else
-	read -p "Do you want to start a second client on the DAQ host $DAQHOST? (y/n)"
+	read -rp "Do you want to start a second client on the DAQ host $DAQHOST? (y/n)"
 	if [ "$REPLY" == "n" ];then
 	    exit
 	else
-	    echo "Starting another ami_client on "$DAQHOST , calling:
+	    echo "Starting another ami_client on $DAQHOST , calling:"
 	fi
     fi
 else
-    echo --- connect to proxy on: $proxy_cds, calling:
-fi    
+    echo --- "connect to proxy on: $proxy_cds, calling:"
+fi
 
-echo $ami_path$amicmd
-exec $ami_path$amicmd&
+echo "$ami_path$amicmd"
+exec "$ami_path$amicmd&"
diff --git a/scripts/stopami b/scripts/stopami
index 8a25d193..7931ce85 100755
--- a/scripts/stopami
+++ b/scripts/stopami
@@ -13,37 +13,37 @@ if [[ ($1 == "--help") || ($1 == "-h") ]]; then
 	exit 0
 fi
 
-HUTCH=`get_hutch_name`
-DAQHOST=`wheredaq`
-RESCNT=`echo $DAQHOST |wc| awk {'print $2'}`
-if [ $RESCNT -eq 1 ]; then
-    if [ $HOSTNAME == $DAQHOST ]; then
+HUTCH=$(get_hutch_name)
+DAQHOST=$(wheredaq)
+RESCNT=$(echo "$DAQHOST" |wc| awk '{print $2}')
+if [[ $RESCNT -eq 1 ]]; then
+    if [[ $HOSTNAME == "$DAQHOST" ]]; then
         #running on the DAQ host, this will restart the ami_client!
-	read -p "Do you really intend to stop the ami_client on $DAQHOST where the daq is running? (y/n)"
+	read -rp "Do you really intend to stop the ami_client on $DAQHOST where the daq is running? (y/n)"
 	if [ "$REPLY" == "y" ];then
 	    echo "Restarting the ami_client...";
-	    /reg/g/pcds/dist/pds/$HUTCH/current/tools/procmgr/procmgr stop \
-		/reg/g/pcds/dist/pds/$HUTCH/scripts/$HUTCH.cnf ami_client 
+	    /reg/g/pcds/dist/pds/"$HUTCH"/current/tools/procmgr/procmgr stop \
+		/reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$HUTCH".cnf ami_client
 	fi
     fi
 fi
 
-AMI_PROCID=`ps -ef | grep online_ami | grep current | awk {'print $2'}`
-HAVE_ID=`echo $AMI_PROCID | wc | awk {'print $2'}`
-if [ $HAVE_ID -gt 0 ]; then
+AMI_PROCID=$(pgrep online_ami)
+HAVE_ID=$(echo "$AMI_PROCID" | wc | awk '{print $2}')
+if [[ $HAVE_ID -gt 0 ]]; then
     for id in $AMI_PROCID; do
-	echo 'killing ' $id
-	kill $id
+	echo "killing $id"
+	kill "$id"
     done
 fi
 
 sleep 2
 
-AMI_PROCID=`ps -ef | grep online_ami | grep current | awk {'print $2'}`
-HAVE_ID=`echo $AMI_PROCID | wc | awk {'print $2'}`
-if [ $HAVE_ID -gt 0 ]; then
+AMI_PROCID=$(pgrep online_ami)
+HAVE_ID=$(echo "$AMI_PROCID" | wc | awk '{print $2}')
+if [[ $HAVE_ID -gt 0 ]]; then
     for id in $AMI_PROCID; do
-	echo 'kill -9 ' $id
-	kill -9 $id
+	echo "kill -9 $id"
+	kill -9 "$id"
     done
 fi
diff --git a/scripts/stopdaq b/scripts/stopdaq
index a9b59e91..69c3cd13 100755
--- a/scripts/stopdaq
+++ b/scripts/stopdaq
@@ -33,12 +33,13 @@ fi
 unset PYTHONPATH
 unset LD_LIBRARY_PATH
 
-#go to hutches DAQ scripts directory 
+#go to hutches DAQ scripts directory
 #(puts pid file in consistent location - necessary for stopping for LCLS-II DAQ)
 cd /reg/g/pcds/dist/pds/"$HUTCH"/scripts/ || exit
 
 LCLS2_HUTCHES="rix, tmo, ued"
 if echo "$LCLS2_HUTCHES" | grep -iw "$HUTCH" > /dev/null; then
+    # shellcheck source=/reg/g/pcds/dist/pds/rix/scripts/setup_env.sh
     source /reg/g/pcds/dist/pds/"$HUTCH"/scripts/setup_env.sh
     PROCMGR='procmgr'
 else
@@ -49,7 +50,7 @@ PLATFORM=$(grep 'if not platform' /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNFFIL
 if [[ "$DAQHOST" != 'DAQ is not running' ]]; then
     T="$(date +%s%N)"
     echo stop the DAQ from "$HOSTNAME"
-    $PROCMGR stop /reg/g/pcds/dist/pds/"$HUTCH"/scripts/$CNFFILE    
+    $PROCMGR stop /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CNFFILE"
     if [ -f /reg/g/pcds/dist/pds/"$HUTCH"/scripts/p"$PLATFORM""$CNFEXT".running ]; then
 	echo 'the DAQ did not stop properly, exit now and try again or call your POC or the DAQ phone'
 	exit
diff --git a/scripts/takepeds b/scripts/takepeds
index 5502fdb1..6622d3cb 100755
--- a/scripts/takepeds
+++ b/scripts/takepeds
@@ -10,7 +10,7 @@ Takes a run with dark images for use in pedestals, and posts to the elog.
 EOF
 }
 
-if [[($1 == "--help") || ($1 == "-h")]]; then
+if [[ ($1 == "--help") || ($1 == "-h")]]; then
         usage
         exit 0
 fi
@@ -19,16 +19,16 @@ DAQ_RELEASE=/cds/group/pcds/dist/pds/current
 
 # -R: for norecord , -r forces recording
 station=$(get_info --getstation)
-$DAQ_RELEASE/tools/scanning/take_pedestals -p $station -r
+$DAQ_RELEASE/tools/scanning/take_pedestals -p "$station" -r
 
 elogMessage="DARK"
 source pcds_conda
 PYCMD=LogBookPost
 
-EXP=`get_curr_exp`
-RUN=`get_lastRun`
+EXP=$(get_curr_exp)
+RUN=$(get_lastRun)
 HUTCH=${EXP:0:3}
-echo $PYCMD -i "${HUTCH^^}" -u `whoami` -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage"
-$PYCMD -i "${HUTCH^^}" -u `whoami` -p pcds -e "$EXP"  -t DARK  -r $RUN -m "$elogMessage"&
+echo $PYCMD -i "${HUTCH^^}" -u "$(whoami)" -e "$EXP"  -t DARK  -r "$RUN" -m "$elogMessage"
+$PYCMD -i "${HUTCH^^}" -u "$(whoami)" -p pcds -e "$EXP"  -t DARK  -r "$RUN" -m "$elogMessage"&
 
-echo 'Please call: makepeds -q milano -r '`get_lastRun`' -u <userID>'
+echo "Please call: makepeds -q milano -r $(get_lastRun) -u <userID>"
diff --git a/scripts/verify-hutch b/scripts/verify-hutch
index 62c93e12..71cb065b 100755
--- a/scripts/verify-hutch
+++ b/scripts/verify-hutch
@@ -4,7 +4,7 @@ usage(){
 cat << EOF
 usage: ${BASH_SOURCE[0]} <hutch>
 
-Verifies that the passed argument is a known hutch, exit 0 for success and exit 1 for failure. 
+Verifies that the passed argument is a known hutch, exit 0 for success and exit 1 for failure.
 
 EOF
 }
@@ -21,7 +21,7 @@ fi
 
 hutch=${1,,}
 for i in "tmo" "txi" "rix" "xpp" "xcs" "mfx" "cxi" "mec" "ued" "ued" "det" "lfe" "kfe" "tst" "las" "hpl"; do
-    if [[ $hutch == $i ]]; then
+    if [[ $hutch == "$i" ]]; then
         exit 0
     fi
 done
diff --git a/scripts/wheredaq b/scripts/wheredaq
index e760304e..f93b697c 100755
--- a/scripts/wheredaq
+++ b/scripts/wheredaq
@@ -38,6 +38,6 @@ if [[ ! -f /reg/g/pcds/dist/pds/"$HUTCH"/scripts/p"$PLATFORM".cnf.running ]]; th
 	echo 'DAQ is not running in '"$HUTCH"
     fi
 else
-    DAQ_HOST=$(grep "'HOST'" /reg/g/pcds/dist/pds/"$HUTCH"/scripts/p"$PLATFORM".cnf.running | awk {'print $3'} | sed s/\'//g)
+    DAQ_HOST=$(grep "'HOST'" /reg/g/pcds/dist/pds/"$HUTCH"/scripts/p"$PLATFORM".cnf.running | awk '{print $3}' | sed s/\'//g)
     echo 'DAQ is running on '"$DAQ_HOST"
 fi
diff --git a/scripts/wherepsana b/scripts/wherepsana
index 6c1a8323..1d9a41a1 100755
--- a/scripts/wherepsana
+++ b/scripts/wherepsana
@@ -20,14 +20,14 @@ if [[ ($1 == "--help") || ($1 == "-h") ]]; then
 	exit 0
 fi
 
-HUTCH=`get_info --gethutch`
+HUTCH=$(get_info --gethutch)
 for i in "xpp" "xcs" "mfx" "cxi" "mec" "det"; do
-   if [ $HUTCH == $i ]; then
+   if [[ $HUTCH == "$i" ]]; then
       FOUNDHUTCH=1
       break
    fi
 done
-if [ -z $FOUNDHUTCH ]; then
+if [[ -z $FOUNDHUTCH ]]; then
    echo 'could not determine hutch or hutch not implemented, quit'
    exit
 fi
@@ -48,7 +48,7 @@ do
 	    ;;
 	esac
 done
-shift "$(($OPTIND-1))"
+shift "$((OPTIND-1))"
 
 # If specified a config file, then use that
 if [[ -z $CONFIG ]]; then
@@ -63,40 +63,39 @@ if [[ -z $CONFIG ]]; then
         elif [[ -z $CONFIG ]]; then
             echo 'You must provide cxi config file (-c) if not on daq machine'
             exit 1
-        fi 
+        fi
     fi
 
     CONFIG=$HUTCH$CNFEXT
 fi
 
 #create a tempoprary file with the procStatus so we only call that once;
-/reg/g/pcds/dist/pds/$HUTCH/current/tools/procmgr/procmgr status /reg/g/pcds/dist/pds/$HUTCH/scripts/$CONFIG > /tmp/procServStatus.$$
-
-PSANA_NODES=(`grep monreqsrvpsana /tmp/procServStatus.$$ | awk {'print $1'}`)
+/reg/g/pcds/dist/pds/"$HUTCH"/current/tools/procmgr/procmgr status /reg/g/pcds/dist/pds/"$HUTCH"/scripts/"$CONFIG" > /tmp/procServStatus.$$
 
+mapfile -t PSANA_NODES < <(grep monreqsrvpsana /tmp/procServStatus.$$ | awk '{print $1}')
 if [[ -z $DETAIL ]]; then
     NODESTR=''
-    for ((idx=0; idx<${#PSANA_NODES[@]}; ++idx)); do 
-        NODESTR=$NODESTR${PSANA_NODES[idx]}','; 
+    for ((idx=0; idx<${#PSANA_NODES[@]}; ++idx)); do
+        NODESTR=$NODESTR${PSANA_NODES[idx]}',';
     done
-    echo ${NODESTR::-1}
+    echo "${NODESTR::-1}"
 else
-    EVENT=(`grep event /tmp/procServStatus.$$ | awk {'print $1'}`)
-    PSANA_MASKS=(`grep monreqsrvpsana /tmp/procServStatus.$$ | awk -F "-i " {'print $2'} | awk {'print $1'}`)
-    EVENT_MASKS=(`grep event /tmp/procServStatus.$$ | awk -F "-s " '{print $2;}' | awk '{print lshift(1,$1);}'`)
+    mapfile -t EVENT < <(grep event /tmp/procServStatus.$$ | awk '{print $1}')
+    mapfile -t PSANA_MASKS < <(grep monreqsrvpsana /tmp/procServStatus.$$ | awk -F "-i " '{print $2}' | awk '{print $1}')
+    mapfile -t EVENT_MASKS < <(grep event /tmp/procServStatus.$$ | awk -F "-s " '{print $2;}' | awk '{print lshift(1,$1);}')
     echo 'psana runs on the following nodes looking at event nodes '${#EVENT[@]}
     NODESTR=''
-    for ((idx=0; idx<${#PSANA_NODES[@]}; ++idx)); do 
-        echo -n ${PSANA_NODES[idx]}':'
+    for ((idx=0; idx<${#PSANA_NODES[@]}; ++idx)); do
+        echo -n "${PSANA_NODES[idx]}:"
 	MASKS=${PSANA_MASKS[idx]}
-	for ((m=0; m<${#EVENT[@]}; ++m)); do 
-	    if [ $((${MASKS}&${EVENT_MASKS[m]})) != 0 ]; then
-	        echo -n ' '${EVENT[m]} 
-		MASKS=$((${MASKS}&~${EVENT_MASKS[m]}))
+	for ((m=0; m<${#EVENT[@]}; ++m)); do
+	    if [ $((MASKS&EVENT_MASKS[m])) != 0 ]; then
+	        echo -n "${EVENT[m]}"
+		MASKS=$((MASKS&~EVENT_MASKS[m]))
 	    fi
         done
-	if [ ${MASKS} != '0' ]; then
-	    echo " MISSING MON MASK: "$MASKS
+	if [[ ${MASKS} != '0' ]]; then
+	    echo "MISSING MON MASK: $MASKS"
 	fi
 	echo ""
     done
diff --git a/scripts/xpp_update_happi_line b/scripts/xpp_update_happi_line
index 8f2f884e..bc9c098b 100755
--- a/scripts/xpp_update_happi_line
+++ b/scripts/xpp_update_happi_line
@@ -1,4 +1,4 @@
 #!/bin/bash
 source pcds_conda
-cd $ENG_TOOL_SCRIPTS
+cd "$ENG_TOOL_SCRIPTS"
 python xpp_update_happi_line.py "$@"

From 273ecd5c608b20f4f373968274ebb37fa230d1fa Mon Sep 17 00:00:00 2001
From: Kaushik Malapati <kaushikm@psbuild-rhel7-02.Slac.Stanford.EDU>
Date: Mon, 6 May 2024 15:02:52 -0700
Subject: [PATCH 2/3] Tentatively adding shellfmt to precommit

---
 .pre-commit-config.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e8582abb..a947b2cb 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -32,3 +32,8 @@ repos:
     rev: 5.11.5
     hooks:
     -   id: isort
+-   repo: https://github.com/pecigonzalo/pre-commit-shfmt
+    rev: v2.2.0
+    hooks:
+    -   id: shell-fmt-go
+        args: [-l, -d, -s, -fn, -sr, -ci, -i=4]

From 6a5b3290330dfc45435dd0f6f1f39a05bb26f621 Mon Sep 17 00:00:00 2001
From: KaushikMalapati <80156796+KaushikMalapati@users.noreply.github.com>
Date: Mon, 13 May 2024 15:39:42 -0500
Subject: [PATCH 3/3] Update scripts/takepeds

Co-authored-by: Zachary Lentz <ZLLentz@users.noreply.github.com>
---
 scripts/takepeds | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/takepeds b/scripts/takepeds
index 6622d3cb..b3eff728 100755
--- a/scripts/takepeds
+++ b/scripts/takepeds
@@ -10,7 +10,7 @@ Takes a run with dark images for use in pedestals, and posts to the elog.
 EOF
 }
 
-if [[ ($1 == "--help") || ($1 == "-h")]]; then
+if [[ ($1 == "--help") || ($1 == "-h") ]]; then
         usage
         exit 0
 fi