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

scripts/0.run_all.bash

@@ -1,68 +1,338 @@
 #!/bin/bash 
 
 
-#if [ $# -ne 5 ]
-#then
-#   echo ""
-#   echo "Instructions: execute the command below"
-#   echo ""
-#   echo "${0} GitHubUserRepo EXP_NAME RESOLUTION LABELI FCST"
-#   echo ""
-#   echo "GitHubUserRepo :: GitHub link for your personal fork, eg: https://github.com/MYUSER/MONAN-Model.git"
-#   echo "EXP_NAME       :: Forcing: GFS"
-#   echo "RESOLUTION     :: number of points in resolution model grid, e.g: 1024002  (24 km)"
-#   echo "LABELI         :: Initial date YYYYMMDDHH, e.g.: 2024010100"
-#   echo "FCST           :: Forecast hours, e.g.: 24 or 36, etc."
-#   echo ""
-#   echo "24 hour forcast example:"
-#   echo "${0} https://github.com/MYUSER/MONAN-Model.git GFS 1024002 2024010100 24"
-#   echo ""
-#   exit
-#fi
-
-# Set environment variables exports:
-echo ""
-echo -e "\033[1;32m==>\033[0m Moduling environment for MONAN model...\n"
+
+
+#--- Function that shows usage.
+function show_usage() {
+   echo " Usage: "
+   echo ""
+   echo " ${0} [-o] [-z] [-bc TAG_CONVERT_MPAS] [ -bm TAG_MONAN ] [-d OUTPUT_DIAG_INT] \\"
+   echo "    [-e EXP ] [-f FCST] [-gc GIT_CONVERT_MPAS] [-gm GIT_MONAN ] [-i INPUT_PATH] \\"
+   echo "    [-l NLEV] [-r RES] [-s STEP] [-t YYYYMMDDHH] [-v VARTABLE]"
+   echo ""
+   echo " List of optional flags: "
+   echo ""
+   echo " -bc TAG_CONVERT     -- branch or tag name of the MONAN repository. For example:"
+   echo "                        \"develop\". This is used only by step 1."
+   echo " -bm TAG_MONAN       -- branch or tag name of the MONAN repository. For example:"
+   echo "                        \"develop\". This is used only by step 1."
+   echo " -d OUTPUT_DIAG_INT  -- Output interval for diagnostic. The format must be"
+   echo "                        \"HH:MM:SS\". This is used by steps 3 and 4."
+   echo " -e EXP              -- Meteorological drivers. For example, GFS"
+   echo " -f FCST             -- Simulation length in hours, e.g., 24 or 48."
+   echo " -gc GIT_CONVERT     -- GitHub handle for MONAN. For example:"
+   echo "                        https://github.com/monanadmin/MONAN-Model.git"
+   echo "                        This is used only by step 1."
+   echo " -gm GIT_MONAN       -- GitHub handle for MONAN. For example:"
+   echo "                        https://github.com/monanadmin/MONAN-Model.git"
+   echo "                        This is used only by step 1."
+   echo " -i INPUT_PATH       -- Path containing input data for MONAN. If left empty, the"
+   echo "                        default path defined in setenv.bash will be used"
+   echo " -l NLEV             -- Number of vertical levels for the output. This is used"
+   echo "                        by steps 3 and 4."
+   echo " -o                  -- Overwrite static files. This is used only by step 2."
+   echo " -r RES              -- grid resolution. Supported options are:"
+   echo "                        5898242 (~ 10 km)"
+   echo "                        2621442 (~ 15 km)"
+   echo "                        1024002 (~ 24 km)"
+   echo "                        40962   (~ 120 km)"
+   echo " -s STEP             -- Step to run. Options are:"
+   echo "                        1 - Compile MONAN executables."
+   echo "                        2 - Run pre-processing."
+   echo "                        3 - Run atmospheric model."
+   echo "                        4 - Run post-processing."
+   echo "                        0 - Run all steps 1-4."
+   echo " -t YYYYMMDDHH       -- Initial time. For example if 22 Sept 2025 00 UTC, the"
+   echo "                        argument should be 2025092200. This is used by steps"
+   echo "                        2, 3 and 4."
+   echo " -v VARTABLE         -- Suffix for defining which version of the"
+   echo "                        stream_list_atmosphere.diagnostics template to use."
+   echo "                        The default is to not use any suffix. This is used only"
+   echo "                        by steps 3 and 4."
+   echo " -z                  -- This will remove all files generated by all scripts and"
+   echo "                        reset the directory to the original state, except for"
+   echo "                        directory \"scripts\"."
+   echo ""
+   echo " All settings can be defined directly in the script."
+   echo ""
+}
+#---~---
+
+
+#--- Set environment variables exports:
 . setenv.bash
+#---~---
+
+
+
+
+#--- Default input variables:
+STEP=1
+OVERWRITE=""
+github_link_MONAN="https://github.com/monanadmin/MONAN-Model.git"
+tag_or_branch_name_MONAN="release/1.4.1-rc"
+github_link_CONVERT_MPAS="https://github.com/monanadmin/convert_mpas.git"
+tag_or_branch_name_CONVERT_MPAS="release/1.2.0"
+EXP="GFS"
+INPUT_PATH=""
+RES=1024002
+YYYYMMDDHHi=2024010100
+FCST=24
+NLEV=55
+OUTPUT_DIAG_INTERVAL="03:00:00"
+VARTABLE=""
+ZERO_STATE=false
+#---~---
 
 
-# Standart directories variables:---------------------------------------
+#--- 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="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -d)
+      OUTPUT_DIAG_INTERVAL="${2}"
+      shift 2 # Past flag and argument
+      ;;
+   -e)
+      EXP="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -f)
+      FCST="${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
+      ;;
+   -i)
+      INPUT_PATH="${2}"
+      shift 2 # Past flag and argument
+      ;;
+   -l)
+      NLEV="${2}"
+      shift 2 # Past flag and argument
+      ;;
+   -o)
+      OVERWRITE="-o"
+      shift 1 # past flag
+      ;;
+   -r)
+      RES="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -s)
+      STEP="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -t)
+      YYYYMMDDHHi="${2}"
+      shift 2 # past flag and argument
+      ;;
+   -v)
+      VFIRST=$(echo ${2} | cut -c 1-1)
+      case "${VFIRST}" in
+         .) VARTABLE="${2}"  ;;
+         *) VARTABLE=".${2}" ;;
+      esac      
+      shift 2 # past flag and argument
+      ;;
+   -z)
+      ZERO_STATE=true
+      shift 1 # past flag
+      ;;
+   *)
+      echo "Unknown key-value argument pair."
+      show_usage
+      exit 2
+      ;;
+   esac
+done
+#---~---
+
+
+#--- Set and create standard directories
 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="https://github.com/monanadmin/MONAN-Model.git"
-monan_branch=release/1.4.1-rc
-convertmpas_branch=release/1.2.0
-EXP=GFS
-RES=1024002
-YYYYMMDDHHi=2024010100
-FCST=24
-#----------------------------------------------------------------------
+
+#---~---
+#   If the user has set -z, we ask for confirmation before all work is deleted...
+#---~---
+if ${ZERO_STATE}
+then
+   echo -e ""
+   echo -e "${ORANGE}!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!${NC}"
+   echo -e "${ORANGE}!!! WARNING !!! WARNING !!! WARNING !!! WARNING !!!${NC}"
+   echo -e "${ORANGE}!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!${NC}"
+   echo -e "${ORANGE}==>${NC} This script is about to reset this working case."
+   read -p "    Are you sure about this? [y|N] " proceed
+   proceed=$(echo ${proceed:-N} | tr [:upper:] [:lower:])
+   case "${proceed}" in
+   y|yes)
+      #---~---
+      #   Give one last chance to avoid accidental file deletion.
+      #---~---
+      echo -e ""
+      echo -e ""
+      echo -e "${ORANGE}==>${NC} Alright, but mind that this cannot be undone."
+      echo -e "${ORANGE}==>${NC} I am giving you a few seconds to cancel this script"
+      echo -e "    in case you change your mind. Hit Ctrl+C before the countdown ends."
+      echo -e ""
+      echo -e ""
+      count=11
+      while [[ ${count} -gt 1 ]]
+      do
+         let count=${count}-1
+         echo -e "${ORANGE}==>${NC} File deletion will begin in ${count} seconds."
+         sleep 1
+      done
+      /bin/rm -frv ${DATAIN}
+      /bin/rm -frv ${DATAOUT}
+      /bin/rm -frv ${SOURCES}
+      /bin/rm -frv ${EXECS}
+      /bin/rm -frv ${DIR_SCRIPTS}/run.??????????
+      ;;
+   *)
+      #--- Keep files.
+      echo -e ""
+      echo -e "${GREEN}==>${NC} Keeping all files. To run MONAN, call this script again"
+      echo -e "    without the \"-z\" option."
+      #---~---
+      ;;
+   esac
+
+   #---~---
+   #   We do not run the scripts when -z is set.
+   #---~---
+   exit 0
+   #---~---
+fi
+#---~---
+
+
+#--- If INPUT_PATH is provided, replace the path in setenv.bash
+if [[ "${INPUT_PATH}" != "" ]] && [[ -d "${INPUT_PATH}" ]]
+then
+   sed -i.bck "s,^export DIRDADOS=.*,export DIRDADOS=${INPUT_PATH},g" ${SCRIPTS}/setenv.bash
+   /bin/rm -f ${SCRIPTS}/setenv.bash.bck
+fi
+#---~---
+
+
+#---~---
+#   Make sure the grid resolution settings are valid.
+#---~---
+case "${RES}" in
+5898242)
+   echo -e "${GREEN}==>${NC} Grid resolution ${RES} (~ 10 km).\n"
+   ;;
+2621442)
+   echo -e "${GREEN}==>${NC} Grid resolution ${RES} (~ 15 km).\n"
+   ;;
+1024002)
+   echo -e "${GREEN}==>${NC} Grid resolution ${RES} (~ 24 km).\n"
+   ;;
+40962)
+   echo -e "${GREEN}==>${NC} Grid resolution ${RES} (~ 120 km).\n"
+   ;;
+*)
+   echo -e "${ORANGE}****** WARNING ******${NC} \n"
+   echo -e "${ORANGE}==>${NC} Provided grid resolution (${RES}) is not recognised.\n"
+   echo -e "${ORANGE}==>${NC} We cannot guarantee that MONAN will run fine.\n"
+   ;;
+esac
+#---~---
 
 
-# STEP 1: Installing and compiling the A-MONAN model and utility programs:
-#time ${SCRIPTS}/1.install_monan.bash ${github_link} ${monan_branch} ${convertmpas_branch}
-#exit
+#--- Make sure VARTABLE has the leading "-v" if not empty.
+if [[ "${VARTABLE}" == "" ]]
+then
+   dv_VARTABLE=""
+else
+   dv_VARTABLE="-v ${VARTABLE}"
+fi
+#---~---
 
-# STEP 2: Executing the pre-processing fase. Preparing all CI/CC files needed:
-#time ${SCRIPTS}/2.pre_processing.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST} 
-#exit
 
-# STEP 3: Executing the Model run:
-time ${SCRIPTS}/3.run_model.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST} 
-exit
+#---~---
+#   Select step.
+#---~---
+case ${STEP} in
+0)
+   #---~---
+   #   Call the script itself four times, passing all the configuration.
+   #---~---
+   step_now=0
+   while [[ ${step_now} -lt 4 ]]
+   do
+      #--- Update step
+      let step_now=${step_now}+1
+      #---~---
 
-# STEP 4: Executing the Post of Model run:
-time ${SCRIPTS}/4.run_post.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST} 
-exit
 
-time ${SCRIPTS}/make_template.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+      #--- Run step
+      time ${0} ${OVERWRITE} ${dv_VARTABLE} -bc ${tag_or_branch_name_CONVERT_MPAS}         \
+         -bm ${tag_or_branch_name_MONAN} -d ${OUTPUT_DIAG_INTERVAL} -e ${EXP} -f ${FCST}   \
+         -gc ${github_link_CONVERT_MPAS} -gm ${github_link_MONAN} -l ${NLEV} -r ${RES}     \
+         -s ${step_now} -t ${YYYYMMDDHHi}
+      #---~---
+   done
+   #---~---
+   ;;
+1)
+   #---~---
+   #   STEP 1: Install and compile MONAN and its utility programs.
+   #---~---
+   time 1.install_monan.bash -bc ${tag_or_branch_name_CONVERT_MPAS}                        \
+      -bm ${tag_or_branch_name_MONAN} -gc ${github_link_CONVERT_MPAS}                      \
+      -gm ${github_link_MONAN}
+   #---~---
+   ;;
+2)
+   #---~---
+   #   STEP 2: Run the pre-processing step, and make initial/boundary conditions if needed.
+   #---~---
+   time 2.pre_processing.bash ${OVERWRITE} -e ${EXP} -f ${FCST} -r ${RES} -t ${YYYYMMDDHHi}
+   #---~---
+   ;;
+3)
+   #---~---
+   #   STEP 3: Run the model.
+   #---~---
+   time 3.run_model.bash ${dv_VARTABLE} -d ${OUTPUT_DIAG_INTERVAL} -e ${EXP} -f ${FCST}    \
+      -l ${NLEV} -r ${RES} -t ${YYYYMMDDHHi}
+   #---~---
+   ;;
+4)
+   #---~---
+   # STEP 4: Run the post-processing step.
+   #---~---
+   time 4.run_post.bash ${dv_VARTABLE} -d ${OUTPUT_DIAG_INTERVAL} -e ${EXP} -f ${FCST}     \
+      -l ${NLEV} -r ${RES} -t ${YYYYMMDDHHi}
+   #---~---
+   ;;
+esac
+#---~---