Use a better algorithm in function absolute_path

For function absolute_path in commonFunctionsForTests.sh, we now
use a better algorithm.  If the path exists, we use readlink -f
to get the absolute path.  Otherwise we just replace ~ with $HOME.
This avoids issues with paths that don't exist.

In the intTestCreate.sh scripts, we make sure to call absolute_path
for the root directory again after the root folder is made.

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>

test/GCClassic/intTestCreate.sh

@@ -95,6 +95,10 @@ if [[ ! -d ${root} ]]; then
     mkdir -p ${root}
 fi
 
+# Get the absolute path of the root folder again;
+# now that the folder exists
+root=$(absolute_path ${root})
+
 # Remove everything in the test folde r
 cleanup_files ${root}
 
@@ -137,6 +141,13 @@ cd ${runDir}
 # Create individual run directories: 2x25 - MERRA2 - 72L
 #=============================================================================
 
+if [[ -d ${root} ]]; then
+    extra="y\n"
+else
+    extra=""
+fi
+echo ${extra}
+
 dir="gc_2x25_CH4_merra2"
 create_rundir "3\n1\n2\n1\n${root}\n${dir}\nn\n"          ${root} ${dir} ${log}
 

test/GCHPctm/intTestCreate.sh

@@ -94,6 +94,10 @@ if [[ ! -d ${root} ]]; then
     mkdir -p ${root}
 fi
 
+# Get the absolute path of the root folder again;
+# now that the folder exists
+root=$(absolute_path ${root})
+
 # Remove run directories in the test folder
 cleanup_files ${root}
 

test/shared/commonFunctionsForTests.sh

@@ -46,7 +46,12 @@ function absolute_path() {
     #
     # 1st argument = relative path
     #========================================================================
-    printf "$(cd "$(dirname "${1}")"; pwd -P)/$(basename "${1}")"
+    if [[ -d ${1} ]]; then
+	absPath=$(readlink -f "${1}")   # If directory exists, use readlink
+    else
+	absPath="${1/#\~/$HOME}"        # Otherwise, replace ~ with $HOME
+    fi
+    echo "${absPath}"
 }