The help function of the bash scripts was somewhat clunky, and has now been...

The help function of the bash scripts was somewhat clunky, and has now been updated to give more verbose information on how to use them. This concerns:

start_ctdas.sh
clone_ctdas.sh

clone_ctdas.sh

@@ -14,39 +14,47 @@
 #!/bin/bash
 set -e
 
-cat > heredocfile.txt <<_EOF_
-    where <rootdir> is a base folder for the project
-    where <projectsource> is a source folder for the project, to clone
-    and <projectclone> is a name to use for the cloned project.
-
-    !! A folder rootdir/projectclone will be created !!
-_EOF_
-
-while getopts "h" opt; do
-  case $opt in
-    h) cat heredocfile.txt
-      exit 1
-    ;;
-    \?) echo "Invalid option: -$OPTARG" >&2
-      exit 1
-    ;;
-    *) cat heredocfile.txt
-      exit 1
-    ;;
+usage="$basename "$0" [arg1] [arg2] [arg3]  [-h] 
+
+-- script to clone an existing CTDAS run and take aover all its settings. This allows a run to be forked, or continued separate from its origin
+
+where:
+     arg1: base directory with original project (i.e., /scratch/"$USER"/)
+     arg2: original project name (i.e, test_ctdas)
+     arg3: cloned project name (i.e, real_ctdas_run)
+     -h  shows this help text
+
+     ! A new folder will then be created and populated:
+
+     /scratch/"$USER"/real_ctdas_run/
+
+    "
+
+while getopts ':hs:' option; do
+  case "$option" in
+    h) echo "$usage"
+       exit
+       ;;
+    :) printf "missing argument for -%s\n" "$OPTARG" >&3
+       echo "$usage" >&3
+       exit 1
+       ;;
+   \?) printf "illegal option: -%s\n" "$OPTARG" >&3
+       echo "$usage" >&3
+       exit 1
+       ;;
   esac
 done
 
 EXPECTED_ARGS=3
-E_BADARGS=666
-
-if [ $# -ne $EXPECTED_ARGS ]
-then
-  echo ""
-  echo "Usage: `basename $0` rootdir projectsource projectclone"
-  cat heredocfile.txt
-  exit $E_BADARGS
+
+if [[ $# -ne $EXPECTED_ARGS ]]; then
+    printf "Missing arguments to function, need $EXPECTED_ARGS \n\n"
+    echo "$usage"
+    exit 2
 fi
 
+
 echo "New project to be started in folder $1"
 echo "               ...........with name $3"
 echo "             ...........cloned from $1/$2"
@@ -83,3 +91,4 @@ echo ""
 cd ${rundir}
 pwd
 
+

start_ctdas.sh

-# CarbonTracker Data Assimilation Shell (CTDAS) Copyright (C) 2017 Wouter Peters. 
+# CarbonTracker Data Assimilation Shell (CTDAS) Copyright (C) 2017,2018,2019 Wouter Peters. 
 # Users are recommended to contact the developers (wouter.peters@wur.nl) to receive
 # updates of the code. See also: http://www.carbontracker.eu. 
 #
@@ -11,41 +11,49 @@
 # You should have received a copy of the GNU General Public License along with this 
 # program. If not, see <http://www.gnu.org/licenses/>. 
 
+# CTDAS code can be downloaded from https://git.wur.nl/woude033/test_CTDAS.git
+
 #!/bin/bash
 set -e
 
-cat > heredocfile.txt <<_EOF_
-    where <projectdir> is a base folder for the project
-    and <projectname> is a name to use for the project.
-
-    !! A folder projectdir/projectname will be created !!
-_EOF_
-
-while getopts "h" opt; do
-  case $opt in
-    h) cat heredocfile.txt
-      exit 1
-    ;;
-    \?) echo "Invalid option: -$OPTARG" >&2
-      exit 1
-    ;;
-    *) cat heredocfile.txt
-      exit 1
-    ;;
+usage="$basename "$0" [arg1] [arg2]  [-h] -- script to start a new CTDAS run  
+
+where:
+     arg1: directory to run from (i.e., /scratch/"$USER"/)
+     arg2: project name (i.e, test_ctdas)
+     -h  shows this help text
+
+     ! A new folder will then be created and populated:
+
+     /scratch/"$USER"/test_ctdas/
+
+    "
+
+while getopts ':hs:' option; do
+  case "$option" in
+    h) echo "$usage"
+       exit
+       ;;
+    :) printf "missing argument for -%s\n" "$OPTARG" >&2
+       echo "$usage" >&2
+       exit 1
+       ;;
+   \?) printf "illegal option: -%s\n" "$OPTARG" >&2
+       echo "$usage" >&2
+       exit 1
+       ;;
   esac
 done
 
 EXPECTED_ARGS=2
-E_BADARGS=666
-
-if [ $# -ne $EXPECTED_ARGS ]
-then
-  echo ""
-  echo "Usage: `basename $0` projectdir projectname"
-  cat heredocfile.txt
-  exit $E_BADARGS
+
+if [[ $# -ne $EXPECTED_ARGS ]]; then
+    printf "Missing arguments to function, need $EXPECTED_ARGS \n\n"
+    echo "$usage"
+    exit 2
 fi
 
+
 echo "New project to be started in folder $1"
 echo "               ...........with name $2"
 
@@ -63,12 +71,9 @@ rsync -au --cvs-exclude * ${rundir}/
 cd ${rundir}
 
 echo "Creating jb file, py file, and rc-file"
-sed -e "s/template/$2/g" template.jb > $2.jb
-sed -e "s/template/$2/g" template.py > $2.py
-sed -e "s,template,${rootdir},g" template.rc > $2.rc
-rm -f template.py
-rm -f template.jb
-rm -f template.rc
+sed -e "s/template/$2/g" templates/template.jb > $2.jb
+sed -e "s/template/$2/g" templates/template.py > $2.py
+sed -e "s,template,${rootdir},g" templates/template.rc > $2.rc
 rm -f start_ctdas.sh
 
 chmod u+x $2.jb
@@ -81,3 +86,4 @@ echo ""
 cd ${rundir}
 pwd
 
+