rc-qlc 0.3.24__cp311-cp311-win32.whl → 0.3.27__cp311-cp311-win32.whl

qlc/sh/qlc_B2.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 
 # Source the configuration file to load the settings
 . "$CONFIG_FILE"
@@ -64,6 +64,8 @@ for exp in $exps ; do
     mkdir -p "$tpath"
   fi
 
+  log  "----------------------------------------------------------------------------------------"
+
   for name in "${MARS_RETRIEVALS[@]}"; do
 
 	  # Define the corresponding arrays based on the name
@@ -76,12 +78,16 @@ for exp in $exps ; do
 	  ncvar=("${!ncvar_var}")
 	  myvar=("${!myvar_var}")
 
+	  log "ipath : ${ipath}"
+	  log "tpath : ${tpath}"
+
 	  log "name : ${name}"
 	  log "param: ${param}"
 	  log "ncvar: ${ncvar}"
 	  log "myvar: ${myvar}"
 
 	  cd $ipath
+      pwd -P
 
 	  set +e
 	  # List available NC-files
@@ -92,6 +98,7 @@ for exp in $exps ; do
 	  log "ncfiles : ${ncfiles}"
 
 	  cd $tpath
+      pwd -P
 
 	  # Loop through the variables for this $name
 	  for ((i = 0; i < ${#ncvar[@]}; i++)); do

qlc/sh/qlc_C5.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 
 # Source the configuration file to load the settings
 . "$CONFIG_FILE"
@@ -23,21 +23,56 @@ done
 log "$0 ANALYSIS_DIRECTORY = $ANALYSIS_DIRECTORY"
 
 # module load for ATOS
-myOS="`uname -s`"
-HOST=`hostname -s  | awk '{printf $1}' | cut -c 1`
-log   "HOST = ${HOST} | `hostname -s`"
-log   "myOS = ${myOS}"
-if [  "${HOST}" == "a" ] && [ "${myOS}" != "Darwin" ]; then
-	module load ferret/7.6.3
+myOS="$(uname -s)"
+HOST="$(hostname -s | cut -c 1)"
+log "HOST = ${HOST} | $(hostname -s)"
+log "myOS = ${myOS}"
+
+if [ "${HOST}" = "a" ] && [ "${myOS}" != "Darwin" ]; then
+    # Only on ATOS-like hosts (non-macOS, short host starting with 'a')
+    if command -v module >/dev/null 2>&1; then
+        module load ferret/7.6.3
+    else
+        log "[WARN] 'module' command not found; skipping ferret module load"
+    fi
+else
+    # Conda activation for pyferret_env
+    if [ -f "$HOME/miniforge3/etc/profile.d/conda.sh" ]; then
+        . "$HOME/miniforge3/etc/profile.d/conda.sh"
+        conda activate pyferret_env
+    elif [ -f "$HOME/miniforge3/bin/activate" ]; then
+        . "$HOME/miniforge3/bin/activate" "pyferret_env"
+    else
+        log "[WARN] Conda activation scripts not found; relying on PATH for pyferret"
+    fi
 fi
 
-# Check if pyferret exists
-if ! command_exists pyferret; then
-  log  "Error: pyferret command not found" >&2
-  exit 1
-else
-  log  "Success: pyferret command found"
-  which pyferret
+# Determine the pyferret command to use.
+# First, check if pyferret is in the PATH (e.g., from "pip install 'rc-qlc[ferret]'").
+# If not, fall back to the direct path in the conda environment as per the README.
+PYFERRET_CMD=""
+if command -v pyferret &> /dev/null; then
+    log "Using 'pyferret' found in system PATH."
+    PYFERRET_CMD="pyferret"
+elif [ -x "$HOME/miniforge3/envs/pyferret_env/bin/pyferret" ]; then
+    log "Using 'pyferret' from dedicated conda environment."
+    PYFERRET_CMD="$HOME/miniforge3/envs/pyferret_env/bin/pyferret"
+fi
+
+# Check if we found a valid pyferret command
+if [ -z "$PYFERRET_CMD" ]; then
+  log  "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+  log  "WARNING: pyferret command not found."
+  log  "The qlc_C5.sh script requires pyferret for generating global map plots."
+  log  "You can install it as an optional dependency with:"
+  log  "    pip install 'rc-qlc[ferret]'"
+  log  "For more detailed instructions (e.g., for macOS), please see the"
+  log  "'Advanced Topics' section in the main README.md file."
+  log  "Alternatively, you can disable this script by commenting out 'C5' in the"
+  log  "SUBSCRIPT_NAMES array in your qlc.conf file."
+  log  "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+  log  "Skipping pyferret plots and exiting script gracefully."
+  exit 0
 fi
 
 # Create output directory if not existent
@@ -59,6 +94,7 @@ sDate="${sDat//[-:]/}"
 eDate="${eDat//[-:]/}"
 mDate="$sDate-$eDate"
 ext="$PLOTEXTENSION"
+ulev="$UTLS"
 
 hpath="$PLOTS_DIRECTORY/${exp1}-${exp2}_${mDate}"
 
@@ -80,14 +116,15 @@ for exp in $exps ; do
 	log "Processing ${PLOTTYPE} plot for experiment: $exp"
 
 	log "QLTYPE           : $QLTYPE"
-	log "TEAM_PREFIX      : $TEAM_PREFIX"
-	log "EVALUATION_PREFIX: $EVALUATION_PREFIX"
-	log "MODEL_RESOLUTION : $MODEL_RESOLUTION"
-	log "TIME_RESOLUTION  : $TIME_RESOLUTION"
+	log "TEAM_PREFIX      : ${TEAM_PREFIX}"
+	log "EVALUATION_PREFIX: ${EVALUATION_PREFIX}"
+	log "MODEL_RESOLUTION : ${MODEL_RESOLUTION}"
+	log "TIME_RESOLUTION  : ${TIME_RESOLUTION}"
 	log "mDate            : $mDate"
 	log "ext              : $ext"
 	log "exp1             : $exp1"
 	log "exp2             : $exp2"
+	log "ulev             : $ulev"
 
 	# definition of plot file base name
 	pfile="${TEAM_PREFIX}_${exp1}-${exp2}_${mDate}_${QLTYPE}"
@@ -198,7 +235,7 @@ for exp in $exps ; do
 			else
 				plev="${nlev}"
 			fi
-			log "${plev} plot for: $pvar"
+			log "Model level array index ${plev} for: $pvar"
 
 			# definition of plot files for each exp + variable (log, diff for exp1)
 #			tfile="${pfile}_${name}_${pvar}_${exp}"
@@ -213,15 +250,7 @@ for exp in $exps ; do
 			lat='`lat`'
 			lev='`lev`'
 			tim='`tim`'
-			# crude workaround, needs to be implemented properly
- 			# plev="21"    # 1000 hPa
-			if [ "${plev}" == "21" ]; then
-  				ulev="11:15" # 100:300 hPa
-			elif [ "${plev}" == "16" ]; then
-  				ulev="11:13" # 100:300 hPa
-  			else
-  				ulev="11:12" # default
-  			fi
+  			ulev="${ulev}"
 			facS="1*"
 			facB="1*"
 			facZ="1*"
@@ -618,51 +647,51 @@ EOF
 			if [ -f  "$ferret.jnl" ]; then
 			    cp -p $ferret.jnl  .
 				rm -f ${tfile}_burden.${ext} ${tfile}_burden_log.${ext}
-				log "pyferret -nodisplay -script $ferret.jnl ${ifile} ${pvar} ${MODEL_RESOLUTION} ${exp} ${tfile}_burden ${ext}"
-					 pyferret -nodisplay -script $ferret.jnl ${ifile} ${pvar} ${MODEL_RESOLUTION} ${exp} ${tfile}_burden ${ext}
+				log "$PYFERRET_CMD -nodisplay -script $ferret.jnl ${ifile} ${pvar} ${MODEL_RESOLUTION} ${exp} ${tfile}_burden ${ext}"
+					 $PYFERRET_CMD -nodisplay -script $ferret.jnl ${ifile} ${pvar} ${MODEL_RESOLUTION} ${exp} ${tfile}_burden ${ext}
 			else
 			 	# ferret plots for default journal file
 				rm -f ${tfile}_burden.${ext} ${tfile}_burden_log.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_burden_1x1.jnl"
-					 pyferret -nodisplay -script  ${tfile}_burden_1x1.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_burden_1x1.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_burden_1x1.jnl
 
 				rm -f ${tfile}_zonal.${ext} ${tfile}_zonal_log.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_zonal_1x1.jnl"
-					 pyferret -nodisplay -script  ${tfile}_zonal_1x1.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_zonal_1x1.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_zonal_1x1.jnl
 
 				rm -f ${tfile}_meridional.${ext}  ${tfile}_meridional_log.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_meridional_1x1.jnl"
-					 pyferret -nodisplay -script  ${tfile}_meridional_1x1.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_meridional_1x1.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_meridional_1x1.jnl
 
 				rm -f ${tfile}_surface.${ext}     ${tfile}_surface_log.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_surface_1x1.jnl"
-					 pyferret -nodisplay -script  ${tfile}_surface_1x1.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_surface_1x1.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_surface_1x1.jnl
 
 				rm -f ${tfile}_utls.${ext}        ${tfile}_utls_log.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_utls_1x1.jnl"
-					 pyferret -nodisplay -script  ${tfile}_utls_1x1.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_utls_1x1.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_utls_1x1.jnl
 			fi
 					 
 			if [ "${exp}" == "${exp1}" ]; then
 				rm -f ${tfile}_burden_diff.${ext} ${tfile}_burden_log_diff.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_burden_1x1_diff.jnl"
-					 pyferret -nodisplay -script  ${tfile}_burden_1x1_diff.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_burden_1x1_diff.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_burden_1x1_diff.jnl
 
 				rm -f ${tfile}_zonal_diff.${ext}  ${tfile}_zonal_log_diff.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_zonal_1x1_diff.jnl"
-					 pyferret -nodisplay -script  ${tfile}_zonal_1x1_diff.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_zonal_1x1_diff.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_zonal_1x1_diff.jnl
 
 				rm -f ${tfile}_meridional_diff.${ext} ${tfile}_meridional_log_diff.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_meridional_1x1_diff.jnl"
-					 pyferret -nodisplay -script  ${tfile}_meridional_1x1_diff.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_meridional_1x1_diff.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_meridional_1x1_diff.jnl
 
 				rm -f ${tfile}_surface_diff.${ext} ${tfile}_surface_log_diff.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_surface_1x1_diff.jnl"
-					 pyferret -nodisplay -script  ${tfile}_surface_1x1_diff.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_surface_1x1_diff.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_surface_1x1_diff.jnl
 
 				rm -f ${tfile}_utls_diff.${ext}   ${tfile}_utls_log_diff.${ext}
-				log "pyferret -nodisplay -script  ${tfile}_utls_1x1_diff.jnl"
-					 pyferret -nodisplay -script  ${tfile}_utls_1x1_diff.jnl
+				log "$PYFERRET_CMD -nodisplay -script  ${tfile}_utls_1x1_diff.jnl"
+					 $PYFERRET_CMD -nodisplay -script  ${tfile}_utls_1x1_diff.jnl
 
 #				files=("${tfile}" "${tfile}_log" "${tfile}_diff" "${tfile}_log_diff")
 				files=("${tfile}_surface"    "${tfile}_surface_log"    "${tfile}_surface_diff"    "${tfile}_surface_log_diff"    \
@@ -736,20 +765,15 @@ file_name="${file_name%.*}"   # Remove extension
 # Split the file name into parts
 IFS="_" read -ra parts <<< "$file_name"
 
-pqlc="${parts[5]}"
-pnml="${parts[6]}"
-# files without level type (_pl _ml _sfc)
-#pvar2="${parts[7]}"
-#pexp="${parts[8]}"
-#ptyp="${parts[9]}"
-#pdif="${parts[11]}"
-# files with level type (_pl _ml _sfc)
-tlev="${parts[7]}"
-pvar2="${parts[8]}"
-pexp="${parts[9]}"
-ptyp="${parts[10]}"
-plog="${parts[11]}"
-pdif="${parts[12]}"
+pqlc="${parts[4]}"
+pnml="${parts[5]}"
+tlev="${parts[6]}"
+pvar2="${parts[7]}"
+pexp="${parts[8]}"
+ptyp="${parts[9]}"
+plog="${parts[10]}"
+pdif="${parts[11]}"
+
 if [[ "$pvar2" == *"-"* ]]; then
 # echo "INFO: variable name '$pvar2' contains dash, display as underscore."
   pvar=$pvar2
@@ -779,7 +803,7 @@ fi
 if [ "${tlev}" != "sfc" ] ; then
   GO="GO"
 fi
-
+#log "${GO} = GO | ${pexp} = ${exp1} | ${plog}"
 if [ "${GO}" == "GO" ] && [ "${pexp}" == "${exp1}" ] && [ "${plog}" == "" ] ; then
 plot1="$PLOTS_DIRECTORY/${exp1}/${TEAM_PREFIX}_${exp1}-${exp2}_${mDate}_${QLTYPE}_${pnml}_${tlev}_${pvar}_${exp1}_${ptyp}.${ext}"
 plot2="$PLOTS_DIRECTORY/${exp2}/${TEAM_PREFIX}_${exp1}-${exp2}_${mDate}_${QLTYPE}_${pnml}_${tlev}_${pvar}_${exp2}_${ptyp}.${ext}"
@@ -812,6 +836,7 @@ cat >> ${texFile} <<EOF
 EOF
 fi
 done # plot
+
 log  "----------------------------------------------------------------------------------------"
 log "${texFile}"
 cat  ${texFile}

qlc/sh/qlc_D1.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 
 # Source the configuration file to load the settings
 . "$CONFIG_FILE"
@@ -31,13 +31,13 @@ if [  "${HOST}" == "a" ] && [ "${myOS}" != "Darwin" ]; then
 module load python3/3.10.10-01
 fi
 
-# Check if python exists
-if ! command_exists python; then
-  log  "Error: python command not found" >&2
+# Check if qlc-py exists
+if ! command_exists qlc-py; then
+  log  "Error: qlc-py command not found" >&2
   exit 1
 else
-  log  "Success: python command found"
-  which python
+  log  "Success: qlc-py command found"
+  which qlc-py
 fi
 
 # Create output directory if not existent
@@ -60,68 +60,299 @@ eDate="${eDat//[-:]/}"
 mDate="$sDate-$eDate"
 ext="${QLTYPE}.pdf"
 
-exps="$exp1 $exp2"
-for exp in $exps ; do
-	log "Processing ${PLOTTYPE} plot for experiment: $exp"
-
-	log "TEAM_PREFIX      : $TEAM_PREFIX"
-	log "EVALUATION_PREFIX: $EVALUATION_PREFIX"
-	log "MODEL_RESOLUTION : $MODEL_RESOLUTION"
-	log "TIME_RESOLUTION  : $TIME_RESOLUTION"
-	log "mDate            : $mDate"
-	log "ext              : $ext"
-	log "exp1             : $exp1"
-	log "exp2             : $exp2"
-
-	ipath="$ANALYSIS_DIRECTORY/$exp"
-	tpath="$PLOTS_DIRECTORY/$exp"
-    hpath="$PLOTS_DIRECTORY/${exp1}-${exp2}_${mDate}"
-
-	# Create help directory if not existent
-  	if [  ! -d "$hpath" ]; then
-    	mkdir -p "$hpath"
-	fi
-
-	# Create output directory if not existent
-  	if [  ! -d "$tpath" ]; then
-    	mkdir -p "$tpath"
-	fi
+# Create a temporary list for TeX files and a temporary JSON config
+hpath="$PLOTS_DIRECTORY/${exp1}-${exp2}_${mDate}"
+texPlotsfile="${hpath}/texPlotfiles_${QLTYPE}.list"
+texFile="${texPlotsfile%.list}.tex"
+temp_config_file="${hpath}/temp_qlc_D1_config.json"
 
+# Ensure the output directory exists
+mkdir -p "$hpath"
+rm -f "$texPlotsfile" "$temp_config_file" "$texFile"
+touch "$texPlotsfile"
+
+# Dynamically discover variables from config, validated against existing .nc files.
+log "Discovering variables from config and validating against files in ${ANALYSIS_DIRECTORY}/${exp1}..."
+validated_vars=()
+if [[ -z "${MARS_RETRIEVALS[*]}" ]]; then
+    log "Warning: MARS_RETRIEVALS array is not defined in the configuration. Falling back to filename parsing."
+    # Fallback to the old method if config arrays are missing
+    myvar_list_array=($(find "${ANALYSIS_DIRECTORY}/${exp1}" -type f -name "*.nc" ! -name "*_tavg.nc" -print0 | \
+        xargs -0 -n 1 basename | \
+        sed -E 's/.*_[A-Z][0-9]+_[a-z]+_(.*)\.nc/\1/' | \
+        sort -u))
+else
     for name in "${MARS_RETRIEVALS[@]}"; do
+        myvar_array_name="myvar_${name}[@]"
+        myvars=("${!myvar_array_name}")
+
+        for var_name in "${myvars[@]}"; do
+            # Check if a file for this variable exists for the first experiment.
+            # The pattern looks for any file ending in _<var_name>.nc
+            if compgen -G "${ANALYSIS_DIRECTORY}/${exp1}/*_${var_name}.nc" > /dev/null; then
+                validated_vars+=("$var_name")
+            fi
+        done
+    done
+    # De-duplicate the results
+    myvar_list_array=($(printf "%s\n" "${validated_vars[@]}" | sort -u))
+fi
+
+
+if [ ${#myvar_list_array[@]} -eq 0 ]; then
+    log "Error: Could not find any variables to process. Check config and analysis files. Exiting."
+    exit 1
+fi
+myvar_list_string=$(IFS=,; echo "${myvar_list_array[*]}")
+log "Found variables: ${myvar_list_string}"
+
+# Dynamically create a temporary JSON config file with three entries.
+cat > "$temp_config_file" << EOM
+[
+  {
+    "name": "${TEAM_PREFIX}",
+    "logdir": "${QLC_HOME}/log",
+    "workdir": "${QLC_HOME}/run",
+    "output_base_name": "${hpath}/${QLTYPE}",
+    "station_file": "${STATION_FILE:-""}",
+    "obs_path": "${OBS_DATA_PATH:-""}",
+    "obs_dataset_type": "${OBS_DATASET_TYPE:-""}",
+    "obs_dataset_version": "${OBS_DATASET_VERSION:-""}",
+    "start_date": "${sDat}",
+    "end_date": "${eDat}",
+    "variable": "${myvar_list_string}",
+    "plot_region": "${REGION:-""}",
+    "station_radius_deg": ${STATION_RADIUS_DEG:-0.5},
+    "plot_type": "${PLOT_TYPE:-""}",
+    "time_average": "${TIME_AVERAGE:-""}",
+    "station_plot_group_size": ${STATION_PLOT_GROUP_SIZE:-5},
+    "show_stations": false,
+    "show_min_max": true,
+    "log_y_axis": false,
+    "fix_y_axis": true,
+    "show_station_map": true,
+    "load_station_timeseries_obs": true,
+    "show_station_timeseries_obs": true,
+    "show_station_timeseries_mod": false,
+    "show_station_timeseries_com": false,
+    "save_plot_format": "${PLOTEXTENSION}",
+    "save_data_format": "nc",
+    "multiprocessing": ${MULTIPROCESSING:-false},
+    "n_threads": ${N_THREADS:-4},
+    "debug": ${DEBUG:-false},
+    "global_attributes": {
+      "title": "Air pollutants over ${REGION:-""}, ${myvar_list_string}",
+      "summary": "netCDF output: ${OBS_DATASET_TYPE:-""} observations for selected stations.",
+      "author": "$(echo $USER)",
+      "history": "Processed for CAMS2_35bis (qlc_v${QLC_VERSION})",
+      "Conventions": "CF-1.8"
+    }
+  },
+  {
+    "name": "${TEAM_PREFIX}",
+    "logdir": "${QLC_HOME}/log",
+    "workdir": "${QLC_HOME}/run",
+    "output_base_name": "${hpath}/${QLTYPE}",
+    "station_file": "${STATION_FILE:-""}",    
+    "mod_path": "${ANALYSIS_DIRECTORY:-""}",
+    "model": "${MODEL:-""}",
+    "experiments": "${exp1},${exp2}",
+    "exp_labels": "${EXP_LABELS:-""}",
+    "start_date": "${sDat}",
+    "end_date": "${eDat}",
+    "variable": "${myvar_list_string}",
+    "plot_region": "${REGION:-""}",
+    "station_radius_deg": ${STATION_RADIUS_DEG:-0.5},
+    "model_level": ${MODEL_LEVEL:-null},
+    "plot_type": "${PLOT_TYPE:-""}",
+    "time_average": "${TIME_AVERAGE:-""}",
+    "station_plot_group_size": ${STATION_PLOT_GROUP_SIZE:-5},
+    "show_stations": false,
+    "show_min_max": true,
+    "log_y_axis": false,
+    "fix_y_axis": true,
+    "show_station_map": true,
+    "show_station_timeseries_obs": false,
+    "show_station_timeseries_mod": true,
+    "show_station_timeseries_com": false,
+    "save_plot_format": "${PLOTEXTENSION}",
+    "save_data_format": "nc",
+    "multiprocessing": ${MULTIPROCESSING:-false},
+    "n_threads": ${N_THREADS:-4},
+    "debug": ${DEBUG:-false},
+    "global_attributes": {
+      "title": "Air pollutants over ${REGION:-""}, ${myvar_list_string}",
+      "summary": "netCDF output: Model data for ${exp1},${exp2} for selected stations.",
+      "author": "$(echo $USER)",
+      "history": "Processed for CAMS2_35bis (qlc_v${QLC_VERSION})",
+      "Conventions": "CF-1.8"
+    }
+  },
+  {
+    "name": "${TEAM_PREFIX}",
+    "logdir": "${QLC_HOME}/log",
+    "workdir": "${QLC_HOME}/run",
+    "output_base_name": "${hpath}/${QLTYPE}",
+    "station_file": "${STATION_FILE:-""}",
+    "obs_path": "${OBS_DATA_PATH:-""}",
+    "obs_dataset_type": "${OBS_DATASET_TYPE:-""}",
+    "obs_dataset_version": "${OBS_DATASET_VERSION:-""}",
+    "mod_path": "${ANALYSIS_DIRECTORY:-""}",
+    "model": "${MODEL:-""}",
+    "experiments": "${exp1},${exp2}",
+    "exp_labels": "${EXP_LABELS:-""}",
+    "start_date": "${sDat}",
+    "end_date": "${eDat}",
+    "variable": "${myvar_list_string}",
+    "plot_region": "${REGION:-""}",
+    "station_radius_deg": ${STATION_RADIUS_DEG:-0.5},
+    "model_level": ${MODEL_LEVEL:-null},
+    "plot_type": "${PLOT_TYPE:-""}",
+    "time_average": "${TIME_AVERAGE:-""}",
+    "station_plot_group_size": ${STATION_PLOT_GROUP_SIZE:-5},
+    "show_stations": false,
+    "show_min_max": true,
+    "log_y_axis": false,
+    "fix_y_axis": true,
+    "show_station_map": true,
+    "load_station_timeseries_obs": false,
+    "show_station_timeseries_obs": false,
+    "show_station_timeseries_mod": false,
+    "show_station_timeseries_com": true,
+    "save_plot_format": "${PLOTEXTENSION}",
+    "save_data_format": "nc",
+    "multiprocessing": ${MULTIPROCESSING:-false},
+    "n_threads": ${N_THREADS:-4},
+    "debug": ${DEBUG:-false},
+    "global_attributes": {
+      "title": "Air pollutants over ${REGION:-""}, ${myvar_list_string}",
+      "summary": "netCDF output: Collocated model and observation data for selected stations.",
+      "author": "$(echo $USER)",
+      "history": "Processed for CAMS2_35bis (qlc_v${QLC_VERSION})",
+      "Conventions": "CF-1.8"
+    }
+  }
+]
+EOM
 
-	  log "name             : $name"
+log "Generated temporary config file for qlc-py: ${temp_config_file}"
 
-	  # Define the corresponding arrays based on the name
-	  param_var="param_${name}[@]"
-	  ncvar_var="ncvar_${name}[@]"
-	  myvar_var="myvar_${name}[@]"
+# Execute qlc-py with the temporary config file.
+# Note: qlc-py expects the config via stdin when using '--config -'
+log "Executing qlc-py with the multi-entry config file..."
+qlc-py --config "${temp_config_file}"
 
-	  # Use variable indirection to access the arrays
-	  param=("${!param_var}")
-	  ncvar=("${!ncvar_var}")
-	  myvar=("${!myvar_var}")
+# After the run, find the specific final collocation plot(s) and add them to the TeX list.
+log "Searching for final collocation plots in ${hpath}..."
+rm -f "$texPlotsfile" # Start with an empty list
+touch "$texPlotsfile" # Ensure the file exists before grep is called
 
-	  cd $ipath
+# Loop through each variable to control the order of plots in the TeX file
+for var in "${myvar_list_array[@]}"; do
+    log "Ordering plots for variable: $var"
 
-	  # Loop through the variables for this $name
-	  for ((i = 0; i < ${#ncvar[@]}; i++)); do
+    # Helper function to find a plot and add it to the list if it exists and is not already there
+    add_plot_if_found() {
+        local plot_pattern=$1
+        # Use find and sort to ensure a consistent order if multiple files match
+        find "${hpath}" -maxdepth 1 -type f -name "${plot_pattern}" 2>/dev/null | sort | while IFS= read -r plot_file; do
+            if [ -n "$plot_file" ] && ! grep -qF "$plot_file" "$texPlotsfile"; then
+                echo "$plot_file" >> "$texPlotsfile"
+                log "Added plot to TeX list: $plot_file"
+            fi
+        done
+    }
 
-		myvar_name="${myvar[i]}"
-		log "myvar_name       : $myvar_name"
+    # Find plots in the specified order using more precise patterns
+    # 1. Time series plots (individual experiments first, then collocated)
+    add_plot_if_found "*${var}*collocated*regional_mean*.${PLOTEXTENSION}"
+    
+    # 2. Bias plot
+    add_plot_if_found "*${var}*collocated*regional_bias*.${PLOTEXTENSION}"
+    
+    # 3. All statistics plots
+    add_plot_if_found "*${var}*collocated*stats_plot_Error_Metrics*.${PLOTEXTENSION}"
+    add_plot_if_found "*${var}*collocated*stats_plot_Correlation_Metrics*.${PLOTEXTENSION}"
+    add_plot_if_found "*${var}*collocated*stats_plot_Descriptive_Statistics*.${PLOTEXTENSION}"
 
-		tfile="${EVALUATION_PREFIX}_${exp1}-${exp2}_${myvar_name}_${mDate}_${name}_$ext"
-		log "${PLOTTYPE} plot for: $myvar_name - $tpath/$tfile"
-		log "work in progress, plot scripts to be implemented ..."
+    # 4. Value map plots (individual experiments)
+    add_plot_if_found "*${var}*val.${PLOTEXTENSION}"
+    
+done
+
+# ----------------------------------------------------------------------------------------
+# Generate a .tex file with frames for each plot found, for inclusion in the final presentation.
+# ----------------------------------------------------------------------------------------
+log "Generating TeX file for plots: ${texFile}"
+
+# Create the main .tex file for this section with a subsection header
+tQLTYPE=$(echo "$QLTYPE" | sed 's/_/\\_/g')
+cat > "$texFile" <<EOF
+%===============================================================================
+\subsection{${tQLTYPE} -- ${mDate} (${TIME_AVERAGE})}
+EOF
+
+# Loop through the found plot files and generate a TeX frame for each
+if [ -s "$texPlotsfile" ]; then
+  # Read from the ordered file list
+  while IFS= read -r plot_path; do
+    plot_filename=$(basename -- "$plot_path")
+    var_name_tex=""
+    title_prefix=""
 
- 		touch  $tpath/$tfile
- 		ls -lh $tpath/$tfile
+    # Extract the variable name for the title
+    for var in "${myvar_list_array[@]}"; do
+        if [[ "$plot_filename" == *"${var}"* ]]; then
+            var_name_tex=$(echo "$var" | sed 's/_/\\_/g')
+            break
+        fi
+    done
+
+    # Use a case statement for robust title generation
+    case "$plot_filename" in
+        *regional_bias*)
+            title_prefix="Collocation time series bias" ;;
+        *stats_plot_Error_Metrics*)
+            title_prefix="Collocation error stats" ;;
+        *stats_plot_Correlation_Metrics*)
+            title_prefix="Collocation correlation stats" ;;
+        *stats_plot_Descriptive_Statistics*)
+            title_prefix="Collocation descriptive stats" ;;
+        *val.*)
+            title_prefix="Collocation map value plot" ;;
+        *regional_mean*)
+            title_prefix="Collocation time series" ;;
+        *)
+            title_prefix="Collocation station plot" ;;
+    esac
+    
+    title_final="${title_prefix} for ${var_name_tex} of ${exp1} vs ${exp2}"
+
+    # Append the frame to the main .tex file
+    cat >> "$texFile" <<EOF
+%===============================================================================
+\frame{
+\frametitle{${title_final}}
+\vspace{0mm}
+\centering
+\includegraphics[width=0.9\textwidth]{${plot_path}}
+}
+EOF
+    log "Generated TeX frame for $plot_filename"
+  done < "$texPlotsfile"
+  log "Finished generating TeX file."
+  log "${texFile}"
+  cat  "${texFile}"
+else
+  log "No plots found to generate TeX file."
+fi
 
- 	  done # ncvar
-    done # name
-done # exps
+# ----------------------------------------------------------------------------------------
+# End of TeX file generation
+# ----------------------------------------------------------------------------------------
 
-log "$ipath"
-log "$tpath"
+log "$ANALYSIS_DIRECTORY"
+log "$PLOTS_DIRECTORY"
 
 log  "----------------------------------------------------------------------------------------"
 log  "End ${SCRIPT} at `date`"