Add "dash" options to the bash scripts, and some additional refactoring

scripts/1.install_monan.bash

@@ -17,21 +17,51 @@ umask 022
 #
 #-----------------------------------------------------------------------------#
 
-#Fixed parameters ------------------------------------------------------------#
-github_link_CONVERT_MPAS="https://github.com/monanadmin/convert_mpas.git"
-#-----------------------------------------------------------------------------#
+
+#--- Function that shows usage.
+function show_usage() {
+   echo " Usage: "
+   echo ""
+   echo " ${0} [-h] [-m12] [-bc TAG_CONVERT_MPAS] [-bm TAG_MONAN] [-gm GIT_MONAN] \\"
+   echo "    [-gc GIT_CONVERT_MPAS]"
+   echo ""
+   echo " List of optional flags: "
+   echo ""
+   echo " -h              -- Shows this message."
+   echo " -m12            -- Is this a MONAN run based on 1.2.0-rc and branches derived"
+   echo "                    from this version (e.g., feature/monan-757-NF)? This is a"
+   echo "                    temporary flag that will be removed once the versions"
+   echo "                    containing Noah-MP are merged into the new release. This"
+   echo "                    allows the script to manage older code and still run on jaci."
+   echo ""
+   echo " List of **required** flags: "
+   echo ""
+   echo " -bc TAG_CONVERT -- branch or tag name of the MONAN repository. For example:"
+   echo "                    \"develop\"."
+   echo " -bm TAG_MONAN   -- branch or tag name of the MONAN repository. For example:"
+   echo "                    \"develop\"."
+   echo " -gc GIT_CONVERT -- GitHub handle for MONAN. For example:"
+   echo "                    https://github.com/monanadmin/MONAN-Model.git"
+   echo " -gm GIT_MONAN   -- GitHub handle for MONAN. For example:"
+   echo "                    https://github.com/monanadmin/MONAN-Model.git"
+   echo ""
+}
+#---~---
+
+
+
 
 #Functions -------------------------------------------------------------------#
 function checkout_system() {
   local source_dir=$1
   local github_link=$2
   local tag_or_branch_name=$3
-  if [ -d "${source_dir}" ]; then
+  if [[ -d "${source_dir}" ]]; then
       echo -e  "${GREEN}==>${NC} Source dir already exists, updating it ...\n"
   else
       echo -e  "${GREEN}==>${NC} Cloning your fork repository...\n"
       git clone ${github_link} ${source_dir}
-      if [ ! -d "${source_dir}" ]; then
+      if [[ ! -d "${source_dir}" ]]; then
           echo -e "${RED}==>${NC} An error occurred while cloning your fork. Possible causes:  wrong URL, user or password.\n"
           exit -1
       fi
@@ -51,48 +81,91 @@ function checkout_system() {
 #-----------------------------------------------------------------------------#
 
 
-if [ $# -lt 1 ]
+#---~---
+#   Retrieve configuration.
+#---~---
+#--- Default settings (all empty)
+MONAN_ONETWO=""
+github_link_MONAN=""
+tag_or_branch_name_MONAN=""
+github_link_CONVERT_MPAS=""
+tag_or_branch_name_CONVERT_MPAS=""
+#---~---
+
+
+#---~---
+#   Parse arguments
+#---~---
+while [[ ${#} > 0 ]]
+do
+   key="${1}"
+   case ${key} in
+   -bc)
+      tag_or_branch_name_CONVERT_MPAS="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -bm)
+      tag_or_branch_name_MONAN="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -gc)
+      github_link_CONVERT_MPAS="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -gm)
+      github_link_MONAN="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -h)
+      show_usage
+      exit 0
+      ;;
+   -m12)
+      MONAN_ONETWO="${key}"
+      shift 1 # past flag
+      ;;
+   *)
+      echo ""
+      echo " Option \"${key}\" is not valid."
+      echo ""
+      show_usage
+      echo ""
+      echo " *** FATAL ERROR! ***"
+      echo " Unknown key or key-value argument pair."
+      echo ""
+      exit 2
+      ;;
+   esac
+done
+#---~---
+
+#---~---
+#   Make sure all required settings were provided.
+#---~---
+if [[ "${tag_or_branch_name_CONVERT_MPAS}" == "" ]] ||
+   [[ "${tag_or_branch_name_MONAN}"        == "" ]] ||
+   [[ "${github_link_CONVERT_MPAS}"        == "" ]] ||
+   [[ "${github_link_MONAN}"               == "" ]]
 then
-   echo ""
-   echo "Instructions: execute the command below"
-   echo ""
-   echo "${0} [G] [M] [C]"
-   echo ""
-   echo "G   :: MONAN GitHub link of your personal fork, eg: https://github.com/MYUSER/MONAN-Model.git"
-   echo "M   :: MONAN tag or branch name of your personal fork. (will be used 'develop' if not informed)" 
-   echo "C   :: Convert_MPAS tag from ${github_link_CONVERT_MPAS} (will be used 'develop' if not informed)"
-   echo ""
-   exit
+   echo " This script requires arguments to be set through flags."
+   show_usage
+   exit 2
 fi
+#---~---
 
 
-# Set environment variables exports:
-echo ""
-echo -e "\033[1;32m==>\033[0m Moduling environment for MONAN model...\n"
-. setenv.bash
+#--- Set environment variables exports:
+. setenv.bash ${MONAN_ONETWO}
+#---~---
+
 echo ""
 echo "---- Installing the Model ----"
 echo ""
 
-# Standart directories variables:---------------------------------------
-DIRHOMES=${DIR_SCRIPTS}/scripts_CD-CT;  mkdir -p ${DIRHOMES}  
-DIRHOMED=${DIR_DADOS}/scripts_CD-CT;    mkdir -p ${DIRHOMED}  
-SCRIPTS=${DIRHOMES}/scripts;            mkdir -p ${SCRIPTS}
-DATAIN=${DIRHOMED}/datain;              mkdir -p ${DATAIN}
-DATAOUT=${DIRHOMED}/dataout;            mkdir -p ${DATAOUT}
-SOURCES=${DIRHOMES}/sources;            mkdir -p ${SOURCES}
-EXECS=${DIRHOMED}/execs;                mkdir -p ${EXECS}
-#----------------------------------------------------------------------
-
 
 # Input variables:-----------------------------------------------------
-github_link_MONAN=${1};   #github_link=https://github.com/monanadmin/MONAN-Model.git
-tag_or_branch_name_MONAN=${2}
-tag_or_branch_name_MONAN=${tag_or_branch_name_MONAN:="1.4.3-rc"}
-echo "MONAN branch name in use: ${tag_or_branch_name_MONAN}"
-
-tag_or_branch_name_CONVERT_MPAS=${3}
-tag_or_branch_name_CONVERT_MPAS=${tag_or_branch_name_CONVERT_MPAS:="1.2.0"}
+tag_or_branch_name_MONAN=${tag_or_branch_name_MONAN:="release/1.4.3-rc"}
+tag_or_branch_name_CONVERT_MPAS=${tag_or_branch_name_CONVERT_MPAS:="release/1.2.0"}
 echo "convert_mpas branch name in use: ${tag_or_branch_name_CONVERT_MPAS}"
 #----------------------------------------------------------------------
 
@@ -105,7 +178,7 @@ CONVERT_MPAS_DIR=${SOURCES}/convert_mpas_${tag_or_branch_name_CONVERT_MPAS}
 #$(sed -i "s;DIR_DADOS=.*$;DIR_DADOS=$(dirname $(dirname $(pwd)));" setenv.bash)
 $(sed -i "s;MONANDIR=.*$;MONANDIR=$MONANDIR;" setenv.bash)
 chmod 755 ${SCRIPTS}/setenv.bash
-. ${SCRIPTS}/setenv.bash
+. ${SCRIPTS}/setenv.bash ${MONAN_ONETWO}
 
 #----------------------------------------------------------------------
 
@@ -134,22 +207,23 @@ echo "*"
 echo "********************************************************************************"
 
 echo ""
+echo -e "${GREEN}==>${NC} github_link_MONAN        = ${github_link_MONAN}"
 echo -e "${GREEN}==>${NC} tag_or_branch_name_MONAN = ${tag_or_branch_name_MONAN}"
 echo ""
-read -p "Are you sure you are installing the right versions scripts x MONAN-Model ? [Y/n]" confirma
-confirma=${confirma:-Y}
-
-if [[ "${confirma}" =~ ^[Yy]$ ]]
-then
+read -p "Are you sure you are installing the right versions scripts x MONAN-Model ? [Y/n] " confirma
+confirma=$(echo ${confirma:-Y} | tr [:upper:] [:lower:])
+case "${confirma}" in
+y|yes)
    echo ""
-   echo -e "${GREEN}==>${NC} OK, so keep going."
+   echo -e "${GREEN}==>${NC} OK, proceeding to installation."
    echo ""
-else
+   ;;
+*)
    echo ""
    echo -e "    ${RED}==>${NC} Please, make the right versions and try again."
    exit
    echo ""
-fi
+esac
 
 
 checkout_system ${MONANDIR} ${github_link_MONAN} ${tag_or_branch_name_MONAN}
@@ -200,7 +274,7 @@ cat << EOF > make-all.sh
 #    SHAREDLIB=true - generate position-independent code suitable for use in a shared library. Default is false.
 
 cd ${SCRIPTS}
-. ${SCRIPTS}/setenv.bash
+. ${SCRIPTS}/setenv.bash ${MONAN_ONETWO}
 cd $MONANDIR
 
 rm -rf $MONANDIR/default_inputs/ $MONANDIR/src/core_atmosphere/physics/physics_wrf/files
@@ -244,7 +318,7 @@ mv ${MONANDIR}/init_atmosphere_model ${EXECS}
 make clean CORE=init_atmosphere
 
 
-if [ -s "${EXECS}/init_atmosphere_model" ] && [ -e "${EXECS}/atmosphere_model" ]; then
+if [[ -s "${EXECS}/init_atmosphere_model" ]] && [[ -e "${EXECS}/atmosphere_model" ]]; then
     echo ""
     echo -e "${GREEN}==>${NC} Files init_atmosphere_model and atmosphere_model generated Successfully in ${EXECS} !"
     echo
@@ -261,14 +335,14 @@ echo -e  "${GREEN}==>${NC} Installing init_atmosphere_model and atmosphere_model
 echo ""
 . ${MONANDIR}/make-all.sh
 
-if [ "$HOSTNAME" == "ian" ]; then
+if [[ "$HOSTNAME" == "ian" ]]; then
 #   echo "hostname=$HOSTNAME"
    export PATH=$NETCDF/bin:$PATH
 fi
 
 # install convert_mpas
 echo ""
-echo -e  "${GREEN}==>${NC} Moduling environment for convert_mpas...\n"
+echo -e  "${GREEN}==>${NC} Loading modules needed by convert_mpas...\n"
 
 cd ${CONVERT_MPAS_DIR}
 make clean
@@ -279,7 +353,7 @@ mv ${CONVERT_MPAS_DIR}/convert_mpas ${EXECS}/
 cp ${CONVERT_MPAS_DIR}/VERSION.txt ${EXECS}/CONVMPAS-VERSION.txt
 
 
-if [ -s "${EXECS}/convert_mpas" ] ; then
+if [[ -s "${EXECS}/convert_mpas" ]] ; then
     echo ""
     echo -e "${GREEN}==>${NC} File convert_mpas generated Sucessfully in ${CONVERT_MPAS_DIR} and copied to ${EXECS} !"
     echo