rc-qlc 0.3.24__cp310-cp310-win_amd64.whl

qlc/install.py

@@ -0,0 +1,285 @@
+import os
+import sys
+import shutil
+import argparse
+import json
+from pathlib import Path
+try:
+    import tomllib  # Python 3.11+
+except ModuleNotFoundError:
+    import tomli as tomllib  # Python < 3.11
+
+def get_version_from_pyproject(pyproject_path: Path) -> str:
+    with pyproject_path.open("rb") as f:
+        config = tomllib.load(f)
+    return config["project"]["version"]
+
+def read_version_json(version_json_path: Path) -> dict:
+    if not version_json_path.exists():
+        raise FileNotFoundError(f"[ERROR] VERSION.json not found: {version_json_path}")
+    with version_json_path.open("r", encoding="utf-8") as f:
+        return json.load(f)
+
+def get_bin_path():
+    return Path(sys.executable).resolve().parent
+
+def copy_or_link(src, dst, symlink=False):
+    dst.parent.mkdir(parents=True, exist_ok=True)
+    if dst.exists() or dst.is_symlink():
+        dst.unlink()
+    if symlink:
+        dst.symlink_to(src.resolve())
+    else:
+        shutil.copy(src, dst)
+
+def copytree_with_symlinks(src: Path, dst: Path):
+    if dst.exists():
+        shutil.rmtree(dst)
+    dst.mkdir(parents=True)
+
+    for item in src.iterdir():
+        s = src / item.name
+        d = dst / item.name
+        if s.is_symlink():
+            target = os.readlink(s)
+            print(f"[LINK] Preserving symlink {d} → {target}")
+            d.symlink_to(target)
+        elif s.is_dir():
+            copytree_with_symlinks(s, d)
+        else:
+            shutil.copy2(s, d)
+
+def safe_move_and_link(source: Path, target: Path):
+    """
+    Ensures `target` is a symlink to `source`. 
+    If `target` exists but points elsewhere (or is a dir), it gets backed up first.
+    """
+    if target.is_symlink():
+        current = target.resolve()
+        if current == source.resolve():
+            print(f"[SKIP] {target} already links to {source}")
+            return
+        else:
+            print(f"[BACKUP] {target} symlink points to {current}, backing up")
+    elif target.exists():
+        if target.is_dir():
+            # Only backup if it's not the install root (we don't want to mv source itself)
+            if target.resolve() != source.resolve():
+                backup = target.with_name(f"{target.name}_backup")
+                count = 1
+                while backup.exists():
+                    backup = target.with_name(f"{target.name}_backup{count}")
+                    count += 1
+                print(f"[BACKUP] Moving existing directory {target} → {backup}")
+                shutil.move(str(target), str(backup))
+        else:
+            # File or other type — always back up
+            backup = target.with_name(f"{target.name}_backup")
+            count = 1
+            while backup.exists():
+                backup = target.with_name(f"{target.name}_backup{count}")
+                count += 1
+            print(f"[BACKUP] Moving existing file {target} → {backup}")
+            shutil.move(str(target), str(backup))
+
+    print(f"[LINK] {target} → {source}")
+    target.symlink_to(source, target_is_directory=True)
+
+def update_qlc_version(config_path: Path, version: str):
+    if not config_path.exists():
+        raise FileNotFoundError(f"[ERROR] Config file not found: {config_path}")
+
+    lines = config_path.read_text(encoding="utf-8").splitlines()
+    new_lines = []
+    updated = False
+
+    for line in lines:
+        if line.strip().startswith("QLC_VERSION="):
+            new_lines.append(f'QLC_VERSION="{version}"')
+            updated = True
+        else:
+            new_lines.append(line)
+
+    if not updated:
+        print(f"[WARN] QLC_VERSION=... not found in {config_path}")
+    else:
+        config_path.write_text("\n".join(new_lines) + "\n", encoding="utf-8")
+        print(f"[UPDATED] QLC_VERSION set to {version} in {config_path}")
+
+def setup(mode, config_file=None, version="latest"):
+
+    # Define source root
+    qlc_root = Path(__file__).resolve().parent.parent
+    config_src = qlc_root / "qlc" / "config"
+    example_src = qlc_root / "qlc" / "examples"
+    sh_src = qlc_root / "qlc" / "sh"
+    doc_src = qlc_root / "qlc" / "doc"
+
+    from qlc.py.version import QLC_VERSION as version
+
+    # Select appropriate configuration file
+    if mode == "cams":
+        perm_path = Path(os.environ.get("PERM", "/perm")) / os.environ.get("USER", "user")
+        user_home = perm_path
+        selected_conf = config_src / "qlc_cams.conf"
+    elif mode == "test":
+        user_home = Path.home()
+        selected_conf = config_src / "qlc_test.conf"
+    elif mode == "interactive":
+        if not config_file:
+            raise ValueError("You must provide a config file via --interactive=<path>")
+        selected_conf = Path(config_file)
+    else:
+        raise ValueError(f"Unsupported mode: {mode}")
+
+    source = user_home / f"qlc_v{version}"
+
+    if source.exists() and not source.is_symlink():
+        backup = source.with_name(f"{source.name}_backup")
+        count = 1
+        while backup.exists():
+            backup = source.with_name(f"{source.name}_backup{count}")
+            count += 1
+        print(f"[BACKUP] Moving existing install root {source} → {backup}")
+        shutil.move(str(source), str(backup))
+
+    root = source / mode
+#   safe_move_and_link(source, Path.home() / f"qlc_v{version}")
+
+    print(f"[SETUP] Mode: {mode}, Version: {version}")
+    print(f"[PATHS] QLC Root: {root}")
+
+    # Prepare paths
+    config_dst = root / "config"
+    example_dst = root / "examples"
+    bin_dst = root / "bin"
+    log_dst = root / "log"
+    mod_dst = root / "mod"
+    obs_dst = root / "obs"
+    doc_dst = root / "doc"
+    run_dst = root / "run"
+    out_dst = root / "output"
+    plug_dst = root / "plugin"
+
+    # Create distribution directories
+    for path in [bin_dst, log_dst, mod_dst, obs_dst, doc_dst, run_dst, out_dst, plug_dst, example_dst, config_dst]:
+        path.mkdir(parents=True, exist_ok=True)
+
+    # Copy config files
+    if config_dst.exists():
+        copytree_with_symlinks(config_src, config_dst)
+
+    # Copy example files
+    if example_src.exists():
+#       shutil.copytree(example_src, example_dst, dirs_exist_ok=True, symlinks=True)
+        copytree_with_symlinks(example_src, example_dst)
+
+    # Link all documentation files
+#   shutil.copytree(doc_src, doc_dst, dirs_exist_ok=True)
+    for doc_file in doc_src.glob("*"):
+        dst = doc_dst / doc_file.name
+        copy_or_link(doc_file, dst, symlink=True)
+
+    # Link all *.sh files to bin_dst (helpers included)
+    for sh_file in sh_src.glob("*.sh"):
+        dst = bin_dst / sh_file.name
+        copy_or_link(sh_file, dst, symlink=True)
+
+    # Create shell tool links (now handled by entry_points in setup.py)
+    pass
+
+    # In test mode: link obs and mod to examples
+    if mode == "test":
+        # Link sample observation data as requested
+        # 1. $HOME/qlc/obs/data/ver0d/ebas_daily/v_20240216 -> $HOME/qlc/examples/cams_case_1/obs/ebas_daily/v_20240216
+        # 2. $HOME/qlc/obs/data/ver0d/ebas_daily/latest -> v_20240216 (relative)
+        
+        obs_data_source = root / "examples/cams_case_1/obs/ebas_daily/v_20240216"
+        obs_data_dest_dir = root / "obs/data/ver0d/ebas_daily"
+        obs_data_dest_dir.mkdir(parents=True, exist_ok=True)
+        
+        # Create the v_20240216 symlink
+        link1_target = obs_data_dest_dir / "v_20240216"
+        if link1_target.exists() or link1_target.is_symlink():
+            link1_target.unlink()
+        link1_target.symlink_to(obs_data_source.resolve(), target_is_directory=True)
+        print(f"[LINK] {link1_target} -> {obs_data_source}")
+
+        # Create the latest symlink, relative to its location
+        link2_target = obs_data_dest_dir / "latest"
+        if link2_target.exists() or link2_target.is_symlink():
+            link2_target.unlink()
+        link2_target.symlink_to("v_20240216", target_is_directory=True)
+        print(f"[LINK] {link2_target} -> v_20240216")
+
+        # Copy the station file for the test case
+        station_file_source = root / "examples/cams_case_1/obs/ebas_station-locations.csv"
+        station_file_dest = root / "obs/data/ebas_station-locations.csv"
+        if station_file_source.exists():
+            copy_or_link(station_file_source, station_file_dest, symlink=False)
+            print(f"[COPY] {station_file_dest}")
+
+
+        # Link sample model data (unchanged)
+        mod_data_src_root = root / "examples" / "cams_case_1" / "mod"
+        mod_data_dst_root = root / "mod"
+        if mod_data_src_root.is_dir():
+            for model_dir in mod_data_src_root.iterdir():
+                if model_dir.is_dir():
+                    mod_data_dst = mod_data_dst_root / model_dir.name
+                    if mod_data_dst.exists() or mod_data_dst.is_symlink():
+                        mod_data_dst.unlink()
+                    mod_data_dst.symlink_to(model_dir.resolve(), target_is_directory=True)
+                    print(f"[LINK] {mod_data_dst} -> {model_dir}")
+
+    # Create a generic qlc.conf symlink
+    config_dir = root / "config"
+    generic_config_path = config_dir / "qlc.conf"
+    if generic_config_path.exists() or generic_config_path.is_symlink():
+        generic_config_path.unlink()
+    
+    if selected_conf.exists():
+        generic_config_path.symlink_to(selected_conf.name)
+        print(f"[LINK] {generic_config_path} -> {selected_conf.name}")
+
+    # Write install info
+    info = {
+        "version": version,
+        "mode": mode,
+        "config": selected_conf.name
+    }
+
+    # Preemptively remove 'qlc_latest' symlink to ensure clean update, mimicking `ln -sf`.
+    qlc_latest_link = Path.home() / "qlc_latest"
+    if qlc_latest_link.is_symlink():
+        qlc_latest_link.unlink()
+
+    safe_move_and_link(root, qlc_latest_link)
+    safe_move_and_link(qlc_latest_link, Path.home() / "qlc")
+
+    (root / "VERSION.json").write_text(json.dumps(info, indent=2))
+    print(f"[WRITE] VERSION.json at {root}")
+
+    version_info = read_version_json(Path.home() / "qlc" / "VERSION.json")
+    update_qlc_version(generic_config_path, version_info["version"])
+
+    print("\n[INFO] QLC installation complete.")
+    print("[INFO] To get started, you may need to open a new terminal or run 'rehash'.")
+    print("[INFO] The following commands are now available: qlc, qlc-py, sqlc, qlc-install")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Install QLC runtime structure")
+    parser.add_argument("--cams", action="store_true", help="Install in CAMS mode")
+    parser.add_argument("--test", action="store_true", help="Install in TEST mode")
+    parser.add_argument("--interactive", type=str, help="Install using custom config path")
+    parser.add_argument("--version", type=str, help="Override QLC version")
+
+    args = parser.parse_args()
+    if args.cams:
+        setup("cams", version=args.version)
+    elif args.test:
+        setup("test", version=args.version)
+    elif args.interactive:
+        setup("interactive", config_file=args.interactive, version=args.version)
+    else:
+        parser.print_help()

qlc/sh/qlc_A1.sh

@@ -0,0 +1,127 @@
+#!/bin/sh -e
+
+# Source the configuration file to load the settings
+. "$CONFIG_FILE"
+# Include common functions
+source $FUNCTIONS
+
+SCRIPT="$0"
+ log  "________________________________________________________________________________________"
+ log  "Start ${SCRIPT} at `date`"
+ log  "Retrieve grib data from MARS archive considering selected nml files (see $CONFIG_FILE)  "
+#log  "----------------------------------------------------------------------------------------"
+#log  "Copyright (c) 2021-2025 ResearchConcepts io GmbH. All Rights Reserved.                  "
+#log  "Questions / comments to: Swen M. Metzger <sm@researchconcepts.io>                       "
+ log  "----------------------------------------------------------------------------------------"
+
+log "$0 MARS_RETRIEVALS = $CONFIG_DIR nml files: ${MARS_RETRIEVALS[*]}"
+pwd -P
+
+# Assign the command line input parameters to variables
+exp1="$1"
+exp2="$2"
+sDat="$3"
+eDat="$4"
+
+myOS="`uname -s`"
+
+exps="$exp1 $exp2"
+for exp in $exps ; do
+  log "Processing experiment: $exp"
+
+  # Create experiment directory if not existent
+  if [ ! -d "$MARS_RETRIEVAL_DIRECTORY/$exp" ]; then
+    mkdir -p $MARS_RETRIEVAL_DIRECTORY/$exp
+  fi
+
+  EXPCLASS=`echo ${exp} | cut -c 1`
+  if [  "${EXPCLASS}" == "b" ]; then
+    XCLASS="nl"
+  elif [  "${EXPCLASS}" == "a" ]; then
+    XCLASS="be"
+  else
+    XCLASS="rd"
+  fi
+  log   ${exp} ${XCLASS}
+
+  for name in "${MARS_RETRIEVALS[@]}"; do
+    nml_name="mars_${name}.nml"
+    log "Processing subscript: $nml_name"
+
+    if [ -f "$CONFIG_DIR/nml/$nml_name" ]; then
+      nml_template="$CONFIG_DIR/nml/$nml_name"
+      nml_file="$MARS_RETRIEVAL_DIRECTORY/$exp/$nml_name"
+
+      # Create a unique flag for this experiment and time period
+      data_retrieved_flag="$MARS_RETRIEVAL_DIRECTORY/$exp/data_retrieved_$sDat-$eDat.flag_${name}"
+
+      # Check for the control file in the mars retrieval directory
+      if [ -f  "$data_retrieved_flag" ]; then
+        ls -lh "$data_retrieved_flag"
+        log "Data retrieval in progress or completed for experiment $exp and namelist case $name."
+        log "Proceeding without retrieval script qlc_${name}.sh for case $name"
+      else
+        log "Data has not been retrieved. Calling script:"
+        log "$0 for data retrieval for experiment $exp and namelist case $name"
+		  # Replace placeholders in the namelist file
+		  # EXP, SDATE, EDATE, MYPATH, MYFILE
+		  sed -e "s/= EXP,/= $exp,/g" \
+			  -e "s/= XCLASS/= $XCLASS/g" \
+			  -e "s/= SDATE/= $sDat/g" \
+			  -e "s|o/EDATE|o/$eDat|g" \
+			  -e "s/MYFILE_/$exp\_${sDat//[-:]/}-${eDat//[-:]/}_/g" \
+			  -e "s|MYPATH/|${MARS_RETRIEVAL_DIRECTORY}/$exp/|g" \
+			   "$nml_template" > "$nml_file"
+		  log "$nml_file" 
+		  cat "$nml_file"  # Print the modified namelist
+		  log MARS_RETRIEVAL_DIRECTORY $MARS_RETRIEVAL_DIRECTORY
+
+		  # Extract the 'target' value and assign it to a variable
+		  target=$(awk -F'=' '/target/ {gsub("\"", "", $2); print $2}' "$nml_file")
+		  log "mars target file: $target"
+
+        # Create a batch job script
+        MARS_BATCH_SCRIPT="$MARS_RETRIEVAL_DIRECTORY/$exp/mars_$exp_$name.sh"
+        cat > "$MARS_BATCH_SCRIPT" <<EOF
+#!/bin/ksh -e
+#SBATCH --job-name=mars_$exp_$name.sh
+#SBATCH --output=log-%J.out
+#SBATCH --error=err-%J.out
+mars < "$nml_file"
+EOF
+
+        log "----------------------------------------------------------------------------------------"
+        cat  "$MARS_BATCH_SCRIPT"
+        log "----------------------------------------------------------------------------------------"
+        log " $MARS_BATCH_SCRIPT"
+        
+        # Check if pdflatex exists
+        if ! command_exists sbatch; then
+          log "Caution: sbatch command not found" >&2
+          log "Not submitting MARS request on $myOS ..."
+#         exit 1
+        else
+          log  "Success: sbatch command found"
+          log  "Submitting MARS request on $myOS:"
+          which sbatch mars squeue scancel
+          sbatch "$MARS_BATCH_SCRIPT"
+          squeue -u "$USER"
+        fi
+
+        # Create the control file in the retrieval directory
+        touch $data_retrieved_flag
+        log "----------------------------------------------------------------------------------------"
+      fi
+    else
+      log "Error: $nml_name not found in $CONFIG_DIR"
+    fi
+  done # name
+  log "$MARS_RETRIEVAL_DIRECTORY/$exp"
+done # exps
+
+log  "----------------------------------------------------------------------------------------"
+log  "End ${SCRIPT} at `date`"
+log  "________________________________________________________________________________________"
+
+exit 0
+

qlc/sh/qlc_B1a.sh

@@ -0,0 +1,123 @@
+#!/bin/sh -e
+
+# Source the configuration file to load the settings
+. "$CONFIG_FILE"
+# Include common functions
+source $FUNCTIONS
+
+SCRIPT="$0"
+ log  "________________________________________________________________________________________"
+ log  "Start ${SCRIPT} at `date`"
+ log  "Process and convert retrieved grib data (MARS_RETRIEVALS as specified in $CONFIG_FILE)  "
+#log  "----------------------------------------------------------------------------------------"
+#log  "Copyright (c) 2021-2025 ResearchConcepts io GmbH. All Rights Reserved.                  "
+#log  "Questions / comments to: Swen M. Metzger <sm@researchconcepts.io>                       "
+ log  "----------------------------------------------------------------------------------------"
+
+log "$0 MARS_RETRIEVAL_DIRECTORY = $MARS_RETRIEVAL_DIRECTORY"
+pwd -P
+
+# module load for ATOS
+myOS="`uname -s`"
+HOST=`hostname -s  | awk '{printf $1}' | cut -c 1`
+#log   ${HOST} ${ARCH}
+if [  "${HOST}" == "a" ] && [ "${myOS}" != "Darwin" ]; then
+module load cdo
+fi
+
+# Check if cdo exists
+if ! command_exists cdo; then
+  log  "Error: cdo command not found" >&2
+  exit 1
+else
+  log  "Success: cdo command found"
+  which cdo
+fi
+
+# Check if ncdump exists
+if ! command_exists ncdump; then
+  log  "Error: ncdump command not found" >&2
+  exit 1
+else
+  log  "Success: ncdump command found"
+  which ncdump
+fi
+
+# Assign the command line input parameters to variables
+exp1="$1"
+exp2="$2"
+sDat="$3"
+eDat="$4"
+sDate="${sDat//[-:]/}"
+eDate="${eDat//[-:]/}"
+mDate="$sDate-$eDate"
+
+exps="$exp1 $exp2"
+for exp in $exps ; do
+  log "Processing experiment: $exp"
+
+  # Create output directory if not existent
+  if [  ! -d "$ANALYSIS_DIRECTORY/$exp" ]; then
+    mkdir -p "$ANALYSIS_DIRECTORY/$exp"
+  fi
+
+  cd "$MARS_RETRIEVAL_DIRECTORY/$exp"
+
+  for name in "${MARS_RETRIEVALS[@]}"; do
+
+	  set +e
+	  # List available GRIB files for selected exp and time period
+#	  grbfiles=($(ls *${mDate}*_${name}_*.grb))
+	  grbfiles=($(ls *${mDate}*_${name}*.grb))
+	  set -e
+
+      log "Processing grbfiles: $grbfiles"
+
+	  if [ ${#grbfiles[@]} -eq 0 ]; then
+		log "No GRIB files found in $MARS_RETRIEVAL_DIRECTORY/$exp"
+	  else
+		log "Files to convert: ${grbfiles[@]}"
+		log  "----------------------------------------------------------------------------------------"
+		for file in "${grbfiles[@]}"; do
+		  # convert grib files to netcdf
+		  log      "$file"
+		  gribfile="$file"
+		  ncfile="${gribfile%.grb}.nc"
+		  if [ ! -f "$ncfile" ]; then
+			log  "Converting $gribfile to $ncfile"
+			cdo -f nc copy  "$gribfile"  "$ncfile"
+			ls -lh          "$ncfile"
+			ncdump -h       "$ncfile"
+		  else
+			log "Nothing to do! NC-file already exists: $ncfile"
+			ls -lh           $ncfile
+	#       ncdump -h        $ncfile
+		  fi
+		  # conversion of tine averaged grib files to netcdf (seasmean)
+		  ncfil2="${gribfile%.grb}_tavg.nc"
+		  if [ ! -f "$ncfil2" ]; then
+			log  "cdo timavg      ${gribfile} ${gribfile%.grb}.grbtavg"
+				  cdo timavg      ${gribfile} ${gribfile%.grb}.grbtavg
+			log  "cdo -f nc copy  ${gribfile%.grb}.grbtavg $ncfil2"
+			  	  cdo -f nc copy  ${gribfile%.grb}.grbtavg $ncfil2
+	#       rm -f           "$gribfile" # Clean up GRIB file
+			ls -lh           $ncfil2
+			ncdump -h        $ncfil2
+		  else
+			log "Nothing to do! NC-file already exists: $ncfil2"
+			ls -lh           $ncfil2
+	#       ncdump -h        $ncfil2
+		  fi
+		done # file
+		log  "----------------------------------------------------------------------------------------"
+	  fi
+
+  done # name
+done # exps
+
+log  "----------------------------------------------------------------------------------------"
+log  "End ${SCRIPT} at `date`"
+log  "________________________________________________________________________________________"
+
+exit 0
+