Merge branch 'improve_bash_help' into 'master'

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

See merge request !3

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. 
 #
@@ -11,43 +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
 
-echo "Welcome $USER"
-
-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"
 
@@ -65,12 +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
@@ -83,3 +86,4 @@ echo ""
 cd ${rundir}
 pwd
 
+