rc-qlc 0.3.24__cp311-cp311-macosx_11_0_arm64.whl → 0.3.27__cp311-cp311-macosx_11_0_arm64.whl

qlc/sh/qlc_Z1.sh

@@ -1,4 +1,4 @@
-#!/bin/sh -e
+#!/bin/bash -e
 
 # Source the configuration file to load the settings
 . "$CONFIG_FILE"
@@ -20,7 +20,7 @@ for param in "$@"; do
   log "Subscript $0 received parameter: $param"
 done
 
-log "$0 TEX_DIRECTORY = $TEX_DIRECTORY"
+log "$0 TEX_DIRECTORY = ${TEX_DIRECTORY}"
 pwd -P
 
 # module load for ATOS
@@ -90,10 +90,10 @@ log  "--------------------------------------------------------------------------
 log "Processing ${PLOTTYPE}:"
 
 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"

qlc/sh/qlc_batch.sh

@@ -0,0 +1,61 @@
+#!/bin/bash -e
+SCRIPT="$0"
+# user specific configuration file
+QLC_DIR="$HOME/qlc"
+CONFIG_DIR="$QLC_DIR/config"
+CONFIG_FILE="$CONFIG_DIR/qlc.conf"
+
+# Source the configuration file and automatically export all defined variables
+# to make them available to any subscripts that are called.
+set -a
+. "$CONFIG_FILE"
+set +a
+
+# Source the common functions script to make the 'log' function available
+. "$SCRIPTS_PATH/qlc_common_functions.sh"
+
+log  "________________________________________________________________________________________"
+log  "Start ${SCRIPT} at `date`"
+#log "----------------------------------------------------------------------------------------"
+#log "Copyright (c) 2021-2025 ResearchConcepts io GmbH. All Rights Reserved.                  "
+#log "Questions / comments to: Swen M. Metzger <sm@researchconcepts.io>                       "
+log  "----------------------------------------------------------------------------------------"
+if [ "$1" == "" ] ;then
+log "type, e.g.:"
+log "sqlc b2ro b2rn 2018-12-01 2018-12-21 mars"
+log "sqlc b2ro b2rn 2018-12-01 2018-12-21"
+log " "
+log "Use option 'mars' to retrieve files and then submit a a dependency job once all data have been retrieved."
+log "Or, option 'mars' can be skipped, if all data are already present in $MARS_RETRIEVAL_DIRECTORY"
+log  "________________________________________________________________________________________"
+log  "End   ${SCRIPT} at `date`"
+log  "________________________________________________________________________________________"
+exit 0
+fi
+if [ "$5" == "mars" ] ;then
+jobid='${SLURM_JOB_ID}'
+cat > $HOME/qlc/run/qlc_batch.sh$$<<EOF
+#!/bin/ksh -e
+#SBATCH --job-name=$HOME/qlc/run/qlc_batch.sh$$
+#SBATCH --output=log-%J.out
+#SBATCH --error=err-%J.out
+#SBATCH --export=ALL
+qlc $1 $2 $3 $4 $5
+echo "SLURM_JOB_ID = ${jobid}"
+sbatch --dependency=afterok:${jobid} --mail-user=$USER@ecmwf.int qlc $1 $2 $3 $4
+EOF
+else
+cat > $HOME/qlc/run/qlc_batch.sh$$<<EOF
+#!/bin/ksh -e
+#SBATCH --job-name=$HOME/qlc/run/qlc_batch.sh$$
+#SBATCH --output=log-%J.out
+#SBATCH --error=err-%J.out
+qlc $1 $2 $3 $4
+EOF
+fi
+sbatch $HOME/qlc/run/qlc_batch.sh$$
+squeue -u "$USER"
+log  "________________________________________________________________________________________"
+log  "End   ${SCRIPT} at `date`"
+log  "________________________________________________________________________________________"
+exit 0

qlc/sh/qlc_common_functions.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # Source the configuration file to load the settings
 . "$CONFIG_FILE"
@@ -13,27 +13,13 @@ HOST=`hostname -s  | awk '{printf $1}' | cut -c 1`
 
 # Function to log messages to a file
 log() {
-  local timestamp
-  timestamp1=$(date +"%Y-%m-%d %H:%M:%S")
-  timestamp2=$(date +"%Y%m%d%H%M")
-# timestamp2=$(date +"%Y%m%d%H")
-  local log_message="[$timestamp1] $1"
-
-  # Create log directory if not existent
-  if  [ ! -d "$WORKING_DIRECTORY/log" ]; then
-	mkdir -p  $WORKING_DIRECTORY/log
-  fi
-  
-  # Specify the log file path
-# local log_file="$WORKING_DIRECTORY/log/qlc_${timestamp2}_$$.log"
-  local log_file="$WORKING_DIRECTORY/log/qlc_${timestamp2}.log"
-  
-  # Append the log message to the log file
-  echo "$log_message"       >> "$log_file"
-# echo "$log_message" | tee -a "$log_file"
- 
-  # Also print the log message to the standard output (console)
-  echo "$log_message"
+  # Create a log message and write to stdout and log file
+  # We use a subshell to ensure all output is captured and redirected atomically
+  (
+      local log_message
+      log_message=$(printf "[%s] %s" "$(date +"%Y-%m-%d %H:%M:%S")" "$*")
+      echo "$log_message"
+  )
 }
 
 # Define the sorting function
@@ -53,15 +39,15 @@ sort_files() {
     # Initialize arrays
     fnam=()
     
-    # workaround for system dependency
+    # workaround for system dependency (obsolete)
 	if [ "${myOS}" == "Darwin" ]; then
-#		var_element=8
-		var_element=9
-		exp_element=10
+#		var_element=9
+#		exp_element=10
+		var_element=7
+		exp_element=8
 	else
-#		var_element=7
-		var_element=8
-		exp_element=9
+		var_element=7
+		exp_element=8
 	fi
 
     # Read the list of files from the file list
@@ -72,6 +58,8 @@ sort_files() {
         var="${parts[$var_element]}"
         fvar+=("$var")
         vars+=" $var"  # Create a space-separated list of variable names
+#       echo "file $file"
+#       echo "var  $var"
     done < "$files_list"
 
     # Get unique variable list

qlc/sh/qlc_main.sh

@@ -1,6 +1,23 @@
-#!/bin/sh -e
+#!/bin/bash -e
 umask 0022
 
+# --- Start: Environment Setup ---
+# Find the Python executable that runs this tool.
+# This ensures that any executables installed in the same environment (like pyferret) are found.
+# Fallback to 'python3' if 'qlc' is not in the path (e.g., during development).
+PYTHON_CMD=$(which python3)
+if command -v qlc >/dev/null 2>&1; then
+    QLC_PATH=$(which qlc)
+    PYTHON_CMD=$(head -n 1 "$QLC_PATH" | sed 's/^#!//')
+fi
+
+# Get the directory of the Python executable.
+PYTHON_BIN_DIR=$(dirname "$PYTHON_CMD")
+
+# Prepend this directory to the PATH for this script and all subscripts.
+export PATH="$PYTHON_BIN_DIR:$PATH"
+# --- End: Environment Setup ---
+
 ARCH="`uname -m`"
 myOS="`uname -s`"
 HOST="`hostname -s`"
@@ -9,14 +26,15 @@ CUSR="`echo $USER`"
 QLC_DIR="$HOME/qlc"
 CONFIG_DIR="$QLC_DIR/config"
 CONFIG_FILE="$CONFIG_DIR/qlc.conf"
-CONFIG_TEX="$CONFIG_DIR/qlc_tex.conf"
 
-# Source the configuration file to load the settings
+# Source the configuration file and automatically export all defined variables
+# to make them available to any subscripts that are called.
+set -a
 . "$CONFIG_FILE"
+set +a
+
 export CONFIG_DIR
 export CONFIG_FILE
-. "$CONFIG_TEX"
-export CONFIG_TEX
 
 # Include common functions
 FUNCTIONS="$SCRIPTS_PATH/qlc_common_functions.sh"
@@ -29,7 +47,7 @@ log  "Start ${SCRIPT} at `date`"
 log  "----------------------------------------------------------------------------------------"
 log  "Purpose of QLC = Quick Look CAMS/IFS results -- ${HOST} on ${myOS} / ${ARCH} - ${CUSR}  "
 log  "           QLC uses subscripts defined in $CONFIG_FILE                                  "
-log  "           see $QLC_DIR/doc/README.md for details                                        "
+log  "           see $QLC_DIR/doc/README.md for details                                       "
 log  "Don^t expect too much, as we follow the KISS principle >Keep it simple, stupid!< ;-) ..."
 log  "________________________________________________________________________________________"
 log  "Copyright (c) 2021-2025 ResearchConcepts io GmbH. All Rights Reserved.                  "
@@ -38,10 +56,14 @@ log  "--------------------------------------------------------------------------
 
 # Check if the required parameters are provided
 if [ $# -eq 0 ]; then
-  log  "Error: No parameters provided. Please provide your parameters in the following syntax:"
-  log  "$0 exp1 exp2  startDate   endDate, e.g.:"
-  log  "$0 b2ro iqi9 2018-12-15 2018-12-31 mars"
-  log  "$0 b2ro iqi9 2019-01-01 2019-01-31"
+  log  "No parameters provided. Please provide your parameters in the following syntax:"
+  log  "qlc exp1 exp2  startDate   endDate [mars]"
+  log  "type, e.g.:"
+  log  "qlc b2ro b2rn 2018-12-01 2018-12-21"
+  log  "qlc b2ro b2rn 2018-12-01 2018-12-21 mars"
+  log  " "
+  log  "Use option 'mars' to retrieve files and then submit a dependency job once all data have been retrieved."
+  log  "Or, option 'mars' can be skipped, if all data are already present in $MARS_RETRIEVAL_DIRECTORY"
   log  "________________________________________________________________________________________"
   log  "End   ${SCRIPT} at `date`"
   log  "________________________________________________________________________________________"
@@ -56,22 +78,20 @@ done
 # Check if the configuration file exists
 if [ -f "$CONFIG_FILE" ]; then
 	# Read and export the variables from the configuration file
-	while IFS= read -r line; do
-		var_name=$(echo "$line" | cut -d= -f1)
-		var_value=$(echo "$line" | cut -d= -f2-)
-
-		# Check if the variable is an array
-		if [[ "$var_value" =~ "^[[:space:]]*\(.*\)[[:space:]]*$" ]]; then
-			eval "array=($var_value)"
-			for element in "${array[@]}"; do
-				log "Configuration file: $var_name=$element"
-#			    export "$var_name"
-			done
-		else
-			log "Configuration file: $var_name=$var_value"
-#		    export "$var_name"
-		fi
-	done < "$CONFIG_FILE"
+	# ----------------------------------------------------------------------------------------
+	# Log the active configuration settings, excluding comments and empty lines
+	log "Active configuration settings from: ${CONFIG_FILE}"
+	grep -v '^\s*#\|^\s*$' "$CONFIG_FILE" | while IFS= read -r line; do
+		log "  ${line}"
+	done
+	log "----------------------------------------------------------------------------------------"
+
+	# Source the configuration file and automatically export all defined variables
+	# to make them available to any subscripts that are called.
+	set -a
+	. "$CONFIG_FILE"
+	set +a
+
 else
   log  "Error: Config file '$CONFIG_FILE' not found."
   exit 1
@@ -110,6 +130,9 @@ for name in "${SUBSCRIPT_NAMES[@]}"; do
 
     if [ "$5" == "mars" ]; then
        log "Only calling the mars retrieval script, the other processes can be called in the second qlc submission step (without option: mars)"
+       log  "----------------------------------------------------------------------------------------"
+       log  "End ${SCRIPT} at `date`"
+       log  "________________________________________________________________________________________"
        exit 1
     fi
           

qlc/sh/tex_template/beamercolorthemeCAMS2_35.sty

@@ -0,0 +1,51 @@
+% Copyright 2007 by Till Tantau
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+% See the file doc/licenses/LICENSE for more details.
+
+\mode<presentation>
+
+
+\setbeamercolor*{palette primary}{use=structure,fg=white,bg=structure.fg!80!green}
+\setbeamercolor*{palette secondary}{use=structure,fg=white,bg=structure.fg!75!green}
+\setbeamercolor*{palette tertiary}{use=structure,fg=white,bg=structure.fg!85!green}
+\setbeamercolor*{palette tertiary}{use=structure,fg=white,bg=structure.fg!80!green}
+%\setbeamercolor*{palette quaternary}{fg=white,bg=green}
+\setbeamercolor*{palette quaternary}{use=structure,fg=white,bg=structure.fg!85!green}
+
+\setbeamercolor*{sidebar}{use=structure,bg=structure.fg}
+\setbeamercolor*{sidebar}{use=structure,fg=blue,fg=structure.fg!80!green}
+  
+\setbeamercolor*{palette}{use=structure,fg=blue,fg=structure.fg!80!green}
+\setbeamercolor*{palette sidebar primary}{use=structure,fg=structure.fg!10}
+\setbeamercolor*{palette sidebar secondary}{fg=white}
+\setbeamercolor*{palette sidebar tertiary}{use=structure,fg=structure.fg!50}
+\setbeamercolor*{palette sidebar quaternary}{fg=white}
+
+\setbeamercolor*{titlelike}{use=structure,fg=structure.fg}
+\setbeamercolor*{titlelike}{use=structure,fg=blue,fg=structure.fg!80!green}
+
+\setbeamercolor*{separation line}{}
+\setbeamercolor*{fine separation line}{}
+
+\setbeamercolor*{block title}{use=structure,fg=white,bg=structure.fg!80!green}
+\setbeamercolor{block title alerted}{use=alerted text,fg=alerted text.fg,bg=alerted text.fg!20!bg}
+\setbeamercolor{block title example}{use=example text,fg=example text.fg,bg=example text.fg!20!bg}
+
+%\setbeamercolor{block body}{use=structure,fg=blue,fg=structure.fg!80!green}
+%\setbeamercolor{block body}{parent=normal text,use=block title,bg=block title.bg!10!bg}
+%\setbeamercolor{block body alerted}{parent=normal text,use=block title alerted,bg=block title alerted.bg!10!bg}
+%\setbeamercolor{block body example}{parent=normal text,use=block title example,bg=block title example.bg!90!bg}
+
+\setbeamercolor{block body}{parent=normal text,use=block title,bg=block title.bg!10!bg}
+\setbeamercolor{section in toc}{use=structure,fg=blue,fg=structure.fg!80!green}
+%\setbeamercolor{subsection in toc}{use=structure,fg=blue,fg=structure.fg!80!green}
+%\setbeamercolor{toc}{use=structure,fg=blue,fg=structure.fg!80!green}
+
+
+\mode
+<all>

qlc/sh/tex_template/beamerfontthemeCAMS2_35.sty

@@ -0,0 +1,166 @@
+% Copyright 2007 by Till Tantau
+% Copyright 2012,2015 by Vedran Mileti\'c, Joseph Wright
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+% See the file doc/licenses/LICENSE for more details.
+
+\mode<presentation>
+
+
+\setbeamerfont{normal text}{} % ignored currently
+\setbeamerfont{alerted text}{}
+\setbeamerfont{example text}{}
+
+\setbeamerfont{structure}{}
+\setbeamerfont{tiny structure}{size=\tiny}
+
+\setbeamerfont{title}{size=\Large,parent=structure}
+\setbeamerfont{title in head/foot}{}
+\setbeamerfont{title in sidebar}{size=\tiny}
+
+\setbeamerfont{subtitle}{size=\normalsize,parent=title}
+
+\setbeamerfont{author}{}
+\setbeamerfont{author in head/foot}{}
+\setbeamerfont{author in sidebar}{size=\tiny}
+
+\setbeamerfont{institute}{size=\scriptsize}
+\setbeamerfont{institute in head/foot}{}
+\setbeamerfont{institute in sidebar}{}
+
+\setbeamerfont{date}{}
+\setbeamerfont{date in head/foot}{}
+\setbeamerfont{date in sidebar}{}
+
+\setbeamerfont{part name}{size=\LARGE}
+\setbeamerfont{part title}{size=\LARGE,parent=title}
+
+\setbeamerfont{section name}{size=\Large}
+\setbeamerfont{section title}{size=\Large,parent=title}
+
+\setbeamerfont{section in toc}{parent=structure}
+\setbeamerfont{section in toc shaded}{parent=section in toc}
+\setbeamerfont{section in head/foot}{}
+\setbeamerfont{section in sidebar}{size=\tiny}
+\setbeamerfont{section number projected}{size=\small,parent={section in toc,projected text}}
+
+\setbeamerfont{subsection name}{size=\large}
+\setbeamerfont{subsection title}{size=\large,parent=title}
+
+\setbeamerfont{subsection in toc}{}
+\setbeamerfont{subsection in toc shaded}{parent=subsection in toc}
+\setbeamerfont{subsection in head/foot}{}
+\setbeamerfont{subsection in sidebar}{}
+
+\setbeamerfont{subsubsection in toc}{size=\footnotesize}
+\setbeamerfont{subsubsection in toc shaded}{parent=subsubsection in toc}
+\setbeamerfont{subsubsection in head/foot}{}
+\setbeamerfont{subsubsection in sidebar}{}
+
+\setbeamerfont{headline}{parent={tiny structure}}
+\setbeamerfont{footline}{parent={tiny structure}}
+
+\setbeamerfont{sidebar}{size=\Tiny,parent={tiny structure}}
+\setbeamerfont{sidebar left}{parent=sidebar}
+\setbeamerfont{sidebar right}{parent=sidebar}
+
+%\setbeamerfont{frametitle}{parent=structure,size=\footnotesize}
+%\setbeamerfont{frametitle}{parent=structure,size=\Large}
+ \setbeamerfont{frametitle}{parent=structure,size=\normalsize}
+ \setbeamerfont{framesubtitle}{parent=frametitle,size=\footnotesize}
+
+\setbeamerfont{caption}{size=\small}
+\setbeamerfont{caption name}{parent={structure,caption}}
+
+\setbeamerfont{button}{size=\tiny}
+
+\setbeamerfont{block body}{}
+\setbeamerfont{block body alerted}{}
+\setbeamerfont{block body example}{}
+%\setbeamerfont{block title}{size=\large,parent={structure,block body}}
+%\setbeamerfont{block title}{size=\normalsize,parent={structure,block body}}
+%\setbeamerfont{block title}{size=\small,parent={structure,block body}}
+\setbeamerfont{block title}{size=\scriptsize,parent={structure,block body}}
+\setbeamerfont{block title alerted}{parent={block title,alerted text}}
+\setbeamerfont{block title example}{parent={block title,example text}}
+
+\setbeamerfont{item}{parent=structure}
+\setbeamerfont{subitem}{parent=item}
+\setbeamerfont{subsubitem}{parent=subitem}
+
+\setbeamerfont{item projected}{size=\tiny,parent={item,projected text}}
+\setbeamerfont{subitem projected}{parent=item projected}
+\setbeamerfont{subsubitem projected}{parent=subitem projected}
+
+\setbeamerfont{itemize item}{parent=item}
+\setbeamerfont{itemize subitem}{parent=subitem}
+\setbeamerfont{itemize subsubitem}{parent=subsubitem}
+
+\setbeamerfont{enumerate item}{parent=item}
+\setbeamerfont{enumerate subitem}{parent=subitem}
+\setbeamerfont{enumerate subsubitem}{parent=subsubitem}
+
+\setbeamerfont{itemize/enumerate body}{}
+\setbeamerfont{itemize/enumerate subbody}{size=\small}
+\setbeamerfont{itemize/enumerate subsubbody}{size=\footnotesize}
+
+
+\setbeamerfont{description item}{parent=item}
+
+\setbeamerfont{projected text}{parent={tiny structure}}
+
+\setbeamerfont{abstract}{size=\small}
+\setbeamerfont{abstract title}{parent={abstract,structure},size=\normalsize}
+
+\setbeamerfont{verse}{family=\rmfamily,shape=\itshape}
+
+\setbeamerfont{quotation}{shape=\itshape}
+\setbeamerfont{quote}{parent=quotation}
+
+\setbeamerfont{note page}{size=\small}
+\setbeamerfont{note title}{parent=note page}
+\setbeamerfont{note date}{size=\footnotesize}
+
+\def\beamer@tsfont{\sffamily}
+\def\beamer@sfont{\sffamily}
+\def\familydefault{\sfdefault}
+\def\mathfamilydefault{\sfdefault}
+\beamer@sansmathfalse
+
+\ProcessOptionsBeamer
+
+\setbeamerfont{tiny structure}{family=\beamer@tsfont}
+\setbeamerfont{structure}{family=\beamer@sfont}
+
+\def\beamer@ftb@str{
+  \setbeamerfont{structure}{shape=\scshape,family=\rmfamily}
+  \setbeamerfont{section in toc}{size=\large}
+}
+\def\beamer@ftb@tstr{\setbeamerfont{tiny structure}{shape=\scshape,family=\rmfamily}}
+
+\DeclareOptionBeamer{onlysmall}{\let\beamer@ftb@str=\relax}
+\DeclareOptionBeamer{onlylarge}{\let\beamer@ftb@tstr=\relax}
+
+\setbeamerfont{author}{size=\scriptsize}
+\setbeamerfont{author in head/foot}{}
+\setbeamerfont{author in sidebar}{size=\tiny}
+
+\setbeamerfont{date}{size=\scriptsize}
+\setbeamerfont{date in head/foot}{size=\tiny}
+\setbeamerfont{date in sidebar}{}
+
+\ProcessOptionsBeamer
+
+\mode<presentation>
+
+\beamer@ftb@str
+\beamer@ftb@tstr
+
+
+\mode
+<all>
+

qlc/sh/tex_template/beamerthemeCAMS2_35.sty

@@ -0,0 +1,25 @@
+% Copyright 2007 by Till Tantau
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+% See the file doc/licenses/LICENSE for more details.
+
+\mode<presentation>
+
+\newif\ifbeamer@secheader
+\beamer@secheaderfalse
+
+\DeclareOptionBeamer{secheader}{\beamer@secheadertrue}
+\ProcessOptionsBeamer
+
+%\useoutertheme{infolines}
+ \useoutertheme[subsection=false]{smoothbars}
+ \useinnertheme[shadow=false]{rounded}
+ \usecolortheme{CAMS2_35}
+ \usefonttheme{CAMS2_35}
+
+\mode
+<all>