Small fixes to sh docs

src/expreccs/core/expreccs.py

@@ -22,24 +22,24 @@
 from expreccs.visualization.plotting import plot_results
 
 
-def main(argv=None) -> None:
+def main(argv: list[str] | None = None) -> None:
     """Main function for the expreccs executable"""
     cwd = os.getcwd()
-    cmdargs = load_parser(argv)
+    cmdargs = parse_args(argv)
     check_cmdargs(cmdargs)
-    file = cmdargs["input"].split(" ")
-    dic = {"fol": os.path.abspath(cmdargs["output"])}
+    file = cmdargs.input.split(" ")
+    dic = {"fol": os.path.abspath(cmdargs.output)}
     dic["pat"] = os.path.dirname(__file__)[:-5]
-    dic["mode"], dic["plot"] = cmdargs["mode"], cmdargs["plot"]
-    dic["rotate"] = float(cmdargs["transform"])
-    dic["explicit"] = int(cmdargs["explicit"]) == 1
-    dic["zones"] = int(cmdargs["zones"]) == 1
-    dic["freq"] = cmdargs["frequency"].split(",")
-    dic["subfolders"] = int(cmdargs["subfolders"]) == 1
-    dic["nonregular"] = int(cmdargs["nonregular"]) == 1
-    dic["acoeff"] = cmdargs["acoeff"].split(",")
-    dic["boundaries"] = [int(val) for val in cmdargs["boundaries"][1:-1].split(",")]
-    dic["compare"] = cmdargs["compare"]
+    dic["mode"], dic["plot"] = cmdargs.mode, cmdargs.plot
+    dic["rotate"] = float(cmdargs.transform)
+    dic["explicit"] = int(cmdargs.explicit) == 1
+    dic["zones"] = int(cmdargs.zones) == 1
+    dic["freq"] = cmdargs.frequency.split(",")
+    dic["subfolders"] = int(cmdargs.subfolders) == 1
+    dic["nonregular"] = int(cmdargs.nonregular) == 1
+    dic["acoeff"] = cmdargs.acoeff.split(",")
+    dic["boundaries"] = [int(val) for val in cmdargs.boundaries[1:-1].split(",")]
+    dic["compare"] = cmdargs.compare
 
     if dic["compare"]:
         print("\nExecuting the compare functionality in expreccs, please wait.")
@@ -131,7 +131,7 @@ def main(argv=None) -> None:
     os.chdir(cwd)
 
 
-def load_parser(argv):
+def parse_args(argv: list[str] | None = None) -> argparse.Namespace:
     """Argument options"""
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -254,10 +254,10 @@ def load_parser(argv):
         help="Set to '1' for a site with irregular contour, i.e., not defined in a "
         "rectangle",
     )
-    return vars(parser.parse_args(argv))
+    return parser.parse_args(argv)
 
 
-def check_cmdargs(cmdargs: dict[str, str]) -> None:
+def check_cmdargs(cmdargs: argparse.Namespace) -> None:
     """Validate command-line arguments and incompatible operations.
 
     The checks cover configuration and model-folder inputs, output names,
@@ -275,41 +275,48 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
     SystemExit
         If an argument is invalid or an incompatible combination is requested.
     """
-    input_value = cmdargs["input"]
+    input_value = cmdargs.input
     if not input_value:
         print("\nInvalid value for '-i', the input cannot be empty.\n")
         raise SystemExit(1)
-    if not cmdargs["output"]:
+
+    if not cmdargs.output:
         print("\nInvalid value for '-o', the output folder cannot be empty.\n")
         raise SystemExit(1)
+
     input_paths = input_value.split()
     if len(input_paths) not in [1, 2]:
         print(
             f"\nInvalid value '-i {input_value}', expected one configuration "
             "file or two model-folder paths separated by a space.\n"
         )
         raise SystemExit(1)
+
     configuration_input = len(input_paths) == 1
     folder_input = len(input_paths) == 2
+
     if configuration_input and not input_paths[0].lower().endswith(".toml"):
         print(
             f"\nInvalid extension for '-i {input_value}', the valid extension "
             "is .toml, or provide paths to the regional and site model "
             "folders.\n"
         )
         raise SystemExit(1)
-    transform = cmdargs["transform"]
+
+    transform = cmdargs.transform
     try:
         transform_value = float(transform)
     except ValueError:
         transform_value = float("nan")
+
     if not math.isfinite(transform_value):
         print(
             f"\nInvalid value '-t {transform}', expected a finite number of "
             "degrees.\n"
         )
         raise SystemExit(1)
-    boundaries = cmdargs["boundaries"]
+
+    boundaries = cmdargs.boundaries
     boundary_pattern = re.fullmatch(
         r"\[\s*-?\d+\s*,\s*-?\d+\s*,\s*-?\d+\s*,\s*-?\d+\s*\]",
         boundaries,
@@ -320,26 +327,34 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
             "brackets, e.g., '-b [0,2,0,0]'.\n"
         )
         raise SystemExit(1)
+
     boundary_values = [int(value.strip()) for value in boundaries[1:-1].split(",")]
     if any(value < -1 for value in boundary_values):
         print(
             f"\nInvalid value '-b {boundaries}', boundary entries must be -1 "
             "or non-negative integers.\n"
         )
         raise SystemExit(1)
-    frequency = cmdargs["frequency"]
-    if not re.fullmatch(r"[1-9]\d*(?:\s*,\s*[1-9]\d*)*", frequency):
+
+    frequency = cmdargs.frequency
+    if not re.fullmatch(
+        r"[1-9]\d*(?:\s*,\s*[1-9]\d*)*",
+        frequency,
+    ):
         print(
             f"\nInvalid value '-f {frequency}', expected positive integers "
             "separated by commas.\n"
         )
         raise SystemExit(1)
+
     frequency_values = [int(value.strip()) for value in frequency.split(",")]
-    acoeff = cmdargs["acoeff"]
+
+    acoeff = cmdargs.acoeff
     try:
         acoeff_values = [float(value.strip()) for value in acoeff.split(",")]
     except ValueError:
         acoeff_values = []
+
     if not acoeff_values or any(
         value < 0 or not math.isfinite(value) for value in acoeff_values
     ):
@@ -348,13 +363,15 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
             "numbers separated by commas.\n"
         )
         raise SystemExit(1)
+
     if len(acoeff_values) not in [1, len(frequency_values)]:
         print(
             f"\nInvalid value '-a {acoeff}', expected one coefficient or one "
             "coefficient for each value provided with '-f'.\n"
         )
         raise SystemExit(1)
-    compare = cmdargs["compare"]
+
+    compare = cmdargs.compare
     if compare:
         compare_options = {
             "-i": ("input", "input.toml"),
@@ -371,7 +388,7 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
         invalid_options = [
             option
             for option, (name, default) in compare_options.items()
-            if cmdargs[name] != default
+            if getattr(cmdargs, name) != default
         ]
         if invalid_options:
             print(
@@ -380,13 +397,16 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
                 f"{', '.join(invalid_options)}.\n"
             )
             raise SystemExit(1)
-        if cmdargs["subfolders"] != "1":
+
+        if cmdargs.subfolders != "1":
             print(
                 "\nInvalid combination, '-c compare' requires the subfolder "
                 "structure and cannot be used with '-s 0'.\n"
             )
             raise SystemExit(1)
+
         return
+
     if folder_input:
         configuration_options = {
             "-m": ("mode", "all"),
@@ -397,7 +417,7 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
         invalid_options = [
             option
             for option, (name, default) in configuration_options.items()
-            if cmdargs[name] != default
+            if getattr(cmdargs, name) != default
         ]
         if invalid_options:
             print(
@@ -406,6 +426,7 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
                 f"{', '.join(invalid_options)}.\n"
             )
             raise SystemExit(1)
+
     if configuration_input:
         folder_options = {
             "-b": ("boundaries", "[0,0,0,0]"),
@@ -418,7 +439,7 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
         invalid_options = [
             option
             for option, (name, default) in folder_options.items()
-            if cmdargs[name] != default
+            if getattr(cmdargs, name) != default
         ]
         if invalid_options:
             print(
@@ -427,7 +448,8 @@ def check_cmdargs(cmdargs: dict[str, str]) -> None:
                 "regional and site model folders.\n"
             )
             raise SystemExit(1)
-    if cmdargs["plot"] != "no" and cmdargs["subfolders"] != "1":
+
+    if cmdargs.plot != "no" and cmdargs.subfolders != "1":
         print(
             "\nInvalid combination, plot generation requires the subfolder "
             "structure and cannot be used with '-s 0'.\n"

tests/scripts/docs_check_outputs.sh

@@ -1,30 +1,32 @@
-files=(
-  "test_outputs/hello_world/hello_world_distance_from_border.png"
-  "test_outputs/hello_world/hello_world_reference_watfluxi+.png"
-  "test_outputs/hello_world/hello_world_regional_watfluxi+.png"
-  "test_outputs/hello_world/hello_world_sensor_pressure_over_time.png"
-  "test_outputs/hello_world/hello_world_site_flux_watfluxi+.png"
-  "test_outputs/hello_world/hello_world_summary_BHP_site_reference.png"
-  "test_outputs/non-regular_boundaries/expreccs_opernum_i,j,1_t0.png"
-  "test_outputs/regular_boundaries/reference_sgas_i,j,1_t90.png"
-  "test_outputs/regular_boundaries/regional_rpr-3.png"
-)
+files="
+test_outputs/hello_world/hello_world_distance_from_border.png
+test_outputs/hello_world/hello_world_reference_watfluxi+.png
+test_outputs/hello_world/hello_world_regional_watfluxi+.png
+test_outputs/hello_world/hello_world_sensor_pressure_over_time.png
+test_outputs/hello_world/hello_world_site_flux_watfluxi+.png
+test_outputs/hello_world/hello_world_summary_BHP_site_reference.png
+test_outputs/non-regular_boundaries/expreccs_opernum_i,j,1_t0.png
+test_outputs/regular_boundaries/reference_sgas_i,j,1_t90.png
+test_outputs/regular_boundaries/regional_rpr-3.png
+"
 
 missing_file="test_outputs/missing_docs_files.txt"
 missing=0
 
 rm -f "$missing_file"
 
-for f in "${files[@]}"; do
-    if [[ ! -f "$f" ]]; then
+printf '%s\n' "$files" | while IFS= read -r f; do
+    [ -z "$f" ] && continue
+    if [ ! -f "$f" ]; then
         echo "$f" >> "$missing_file"
-        ((missing++))
     fi
 done
 
-if (( missing == 0 )); then
+if [ "$missing" -eq 0 ]; then
     echo "All figures and files exist."
+    return 0
 else
     echo "$missing figure(s) or file(s) missing."
     echo "See $missing_file"
+    return 1
 fi

tests/scripts/paper_2025.sh

@@ -7,46 +7,48 @@ python3 $OUT/Case3/run_case3.py &
 python3 $OUT/Case4/run_case4.py &
 wait
 
-files=(
-    "$OUT/Case4/Case_4_site_pres_pressure.png"
-    "$OUT/Case4/Case_4_reference_saturation.png"
-    "$OUT/Case4/Case_4_difference_site_pres_pressure.png"
-    "$OUT/Case4/Case_4_reference_pressure.png"
-    "$OUT/Case4/Case_4_difference_site_pres_saturation.png"
-    "$OUT/Case4/Case_4_regional_pressure.png"
-    "$OUT/Case4/Case_4_site_pres_saturation.png"
-    "$OUT/Case4/Case_4_regional_saturation.png"
-    "$OUT/Case2/comparegrid_0_40m_sensor_pressure_over_time.png"
-    "$OUT/Case2/comparegrid_0_40m_sensor_gasfluxi+_over_time.png"
-    "$OUT/Case3/compareeveryday_sensor_pressure_over_time.png"
-    "$OUT/Case1/Case_1_maximum_pressure_difference_over_time.png"
-    "$OUT/Case1/Case_1_difference_site_flux_pressure.png"
-    "$OUT/Case1/Case_1_difference_site_flux_gasfluxi+.png"
-    "$OUT/Case1/Case_1_maximum_gasfluxi+_difference_over_time.png"
-    "$OUT/Case1/Case_1_reference_saturation.png"
-    "$OUT/Case1/Case_1_reference_pressure.png"
-    "$OUT/Case1/Case_1_reference_watfluxi+.png"
-    "$OUT/Case1/Case_1_distance_from_border.png"
-    "$OUT/Case1/Case_1_difference_site_flux_saturation.png"
-    "$OUT/Case1/Case_1_difference_site_pres_saturation.png"
-    "$OUT/Case1/Case_1_summary_PR_site_reference.png"
-    "$OUT/Case1/Case_1_difference_site_pres_gasfluxi+.png"
-    "$OUT/Case1/Case_1_difference_site_pres_pressure.png"
-)
+files="
+$OUT/Case4/Case_4_site_pres_pressure.png
+$OUT/Case4/Case_4_reference_saturation.png
+$OUT/Case4/Case_4_difference_site_pres_pressure.png
+$OUT/Case4/Case_4_reference_pressure.png
+$OUT/Case4/Case_4_difference_site_pres_saturation.png
+$OUT/Case4/Case_4_regional_pressure.png
+$OUT/Case4/Case_4_site_pres_saturation.png
+$OUT/Case4/Case_4_regional_saturation.png
+$OUT/Case2/comparegrid_0_40m_sensor_pressure_over_time.png
+$OUT/Case2/comparegrid_0_40m_sensor_gasfluxi+_over_time.png
+$OUT/Case3/compareeveryday_sensor_pressure_over_time.png
+$OUT/Case1/Case_1_maximum_pressure_difference_over_time.png
+$OUT/Case1/Case_1_difference_site_flux_pressure.png
+$OUT/Case1/Case_1_difference_site_flux_gasfluxi+.png
+$OUT/Case1/Case_1_maximum_gasfluxi+_difference_over_time.png
+$OUT/Case1/Case_1_reference_saturation.png
+$OUT/Case1/Case_1_reference_pressure.png
+$OUT/Case1/Case_1_reference_watfluxi+.png
+$OUT/Case1/Case_1_distance_from_border.png
+$OUT/Case1/Case_1_difference_site_flux_saturation.png
+$OUT/Case1/Case_1_difference_site_pres_saturation.png
+$OUT/Case1/Case_1_summary_PR_site_reference.png
+$OUT/Case1/Case_1_difference_site_pres_gasfluxi+.png
+$OUT/Case1/Case_1_difference_site_pres_pressure.png
+"
 
 missing_file="test_outputs/missing_publication_files.txt"
 missing=0
 
-for f in "${files[@]}"; do
-    if [[ ! -f "$f" ]]; then
+printf '%s\n' "$files" | while IFS= read -r f; do
+    [ -z "$f" ] && continue
+    if [ ! -f "$f" ]; then
         echo "$f" >> "$missing_file"
-        ((missing++))
     fi
 done
 
-if (( missing == 0 )); then
+if [ "$missing" -eq 0 ]; then
     echo "All figures and files exist."
+    return 0
 else
     echo "$missing figure(s) or file(s) missing."
     echo "See $missing_file"
+    return 1
 fi