Checking illegal CLI combinations and bash docs scripts

src/pyopmnearwell/core/pyopmnearwell.py

@@ -14,8 +14,40 @@
 from pyopmnearwell.utils.writefile import reservoir_files
 
 
-def main(argv=None) -> None:
+def main(argv: list[str] | None = None) -> None:
     """Main function for the pyopmnearwell executable"""
+    cmdargs = load_parser(argv)
+    check_cmdargs(cmdargs)
+    if int(cmdargs.warnings) == 0:
+        warnings.filterwarnings("ignore")
+    file = cmdargs.input
+    fol = os.path.abspath(cmdargs.output)
+    mode = cmdargs.mode
+    dic: dict[str, Any] = {
+        "pat": os.path.split(os.path.dirname(__file__))[0],
+        "fol": fol,
+        "mode": mode,
+        "write": int(cmdargs.vectors),
+        "runname": pathlib.Path(file).stem,
+    }
+    dic = process_input(dic, file)
+    os.makedirs(fol, exist_ok=True)
+    if mode == "single":
+        dic["fprep"] = fol
+        dic["foutp"] = fol
+    else:
+        dic["fprep"] = f"{fol}/preprocessing"
+        dic["foutp"] = f"{fol}/output"
+    if mode in ["all", "deck", "single"]:
+        os.makedirs(dic["fprep"], exist_ok=True)
+        reservoir_files(dic)
+    if mode in ["all", "flow", "single"]:
+        os.makedirs(dic["foutp"], exist_ok=True)
+        simulations(dic)
+
+
+def load_parser(argv: list[str] | None) -> argparse.Namespace:
+    """CLI arguments"""
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description="Main script to run a near-well system with OPM Flow.",
@@ -60,30 +92,34 @@ def main(argv=None) -> None:
         default="0",
         help="Print Python warnings",
     )
-    cmdargs = vars(parser.parse_known_args(argv)[0])
-    if int(cmdargs["warnings"]) == 0:
-        warnings.filterwarnings("ignore")
-    file = cmdargs["input"]
-    fol = os.path.abspath(cmdargs["output"])
-    mode = cmdargs["mode"]
-    dic: dict[str, Any] = {
-        "pat": os.path.split(os.path.dirname(__file__))[0],
-        "fol": fol,
-        "mode": mode,
-        "write": int(cmdargs["vectors"]),
-        "runname": pathlib.Path(file).stem,
-    }
-    dic = process_input(dic, file)
-    os.makedirs(fol, exist_ok=True)
-    if mode == "single":
-        dic["fprep"] = fol
-        dic["foutp"] = fol
-    else:
-        dic["fprep"] = f"{fol}/preprocessing"
-        dic["foutp"] = f"{fol}/output"
-    if mode in ["all", "deck", "single"]:
-        os.makedirs(dic["fprep"], exist_ok=True)
-        reservoir_files(dic)
-    if mode in ["all", "flow", "single"]:
-        os.makedirs(dic["foutp"], exist_ok=True)
-        simulations(dic)
+    return parser.parse_args(argv)
+
+
+def check_cmdargs(cmdargs: argparse.Namespace) -> None:
+    """Validate command-line arguments.
+
+    The checks cover the input configuration file and output folder.
+
+    Parameters
+    ----------
+    cmdargs
+        Parsed arguments returned by :mod:`argparse`.
+
+    Raises
+    ------
+    SystemExit
+        If an argument is invalid.
+    """
+    input_file = cmdargs.input
+    if not input_file:
+        print("\nInvalid value for '-i', the input file cannot be empty.\n")
+        raise SystemExit(1)
+    if not input_file.lower().endswith(".toml"):
+        print(
+            f"\nInvalid extension for input file '-i {input_file}', "
+            "the valid extension is .toml.\n"
+        )
+        raise SystemExit(1)
+    if not cmdargs.output:
+        print("\nInvalid value for '-o', the output folder cannot be empty.\n")
+        raise SystemExit(1)

tests/conftest.py

@@ -75,7 +75,7 @@ def fixture_run_main(tmp_path_factory) -> pathlib.Path:
     shared_dir: pathlib.Path = tmp_path_factory.mktemp("shared")
     shutil.copy((dirname / "models" / "input").with_suffix(".toml"), shared_dir)
     os.chdir(shared_dir)
-    main()
+    main([])
     return shared_dir
 
 

tests/scripts/docs_all.sh

@@ -1 +1,5 @@
-. tests/scripts/docs_hello_world.sh & . tests/scripts/docs_co2_cyclic_injection.sh
+. tests/scripts/docs_hello_world.sh &
+. tests/scripts/docs_co2_cyclic_injection.sh &
+wait
+
+. tests/scripts/docs_check_outputs.sh

tests/scripts/docs_check_outputs.sh

@@ -0,0 +1,25 @@
+files="
+test_outputs/docs_hello_world/hello_world.png
+test_outputs/docs_co2_cyclic_injection/co2_gas.gif
+"
+
+missing_file="test_outputs/missing_docs_files.txt"
+missing=0
+
+rm -f "$missing_file"
+
+for f in $files; do
+    if [ ! -f "$f" ]; then
+        echo "$f" >> "$missing_file"
+        missing=$((missing + 1))
+    fi
+done
+
+if [ "$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/docs_co2_cyclic_injection.sh

@@ -1,9 +1,5 @@
-WHR="test_outputs/co2_cyclic_injection"
-if [ ! -d "test_outputs" ]; then
-    mkdir "test_outputs"
-fi
-if [ -d $WHR ]; then
-    rm -rf $WHR
-fi
-pyopmnearwell -i examples/co2.toml -o $WHR -m single
-plopm -i $WHR/CO2 -v sgas -m gif -dpi 1000 -interval 50 -loop 1 -d 10,5 -yformat .0f -f 20 -cnum 6 -t "Cyclic injection" -save $WHR/co2_gas
+OUT="test_outputs/docs_co2_cyclic_injection"
+. tests/scripts/initialize_output_folders.sh $OUT
+. tests/scripts/get_plopm.sh
+pyopmnearwell -i examples/co2.toml -o $OUT -m single
+plopm -i $OUT/CO2 -v sgas -m gif -dpi 1000 -interval 50 -loop 1 -d 10,5 -yformat .0f -f 20 -cnum 6 -t "Cyclic injection" -save $OUT/co2_gas

tests/scripts/docs_hello_world.sh

@@ -1,9 +1,5 @@
-WHR="test_outputs/hello_world"
-if [ ! -d "test_outputs" ]; then
-    mkdir "test_outputs"
-fi
-if [ -d $WHR ]; then
-    rm -rf $WHR
-fi
-pyopmnearwell -i examples/h2o.toml -o $WHR -m single
-plopm -i $WHR/H2O -v pressure -s ,,1 -t 'Top view at the end of the simulation' -c bwr -xformat .0f -cformat .0f -save $WHR/hello_world
+OUT="test_outputs/docs_hello_world"
+. tests/scripts/initialize_output_folders.sh $OUT
+. tests/scripts/get_plopm.sh
+pyopmnearwell -i examples/h2o.toml -o $OUT -m single
+plopm -i $OUT/H2O -v pressure -s ,,1 -t 'Top view at the end of the simulation' -c bwr -xformat .0f -cformat .0f -save $OUT/hello_world

tests/scripts/get_plopm.sh

@@ -0,0 +1,3 @@
+if ! command -v plopm &> /dev/null; then
+    pip install git+https://github.com/cssr-tools/plopm.git
+fi

tests/scripts/initialize_output_folders.sh

@@ -0,0 +1,7 @@
+OUTT="$1"
+if [ ! -d "test_outputs" ]; then
+  mkdir "test_outputs"
+fi
+if [ -n "$OUTT" ] && [ -d "$OUTT" ]; then
+  rm -rf "$OUTT"
+fi

tests/scripts/paper_salt-precipitation_all.sh

@@ -1,10 +1,37 @@
-WHR="test_outputs/paper_salt_precipitation"
-if [ ! -d "test_outputs" ]; then
-    mkdir "test_outputs"
-fi
-if [ -d $WHR ]; then
-    rm -rf $WHR
-fi
+NCPUS=${1:-16}
+OUT="test_outputs/paper_salt_precipitation"
+. tests/scripts/initialize_output_folders.sh $OUT
+. tests/scripts/get_plopm.sh
 mkdir "test_outputs/paper_salt_precipitation"
-cp -r publications/Impact_of_Intermittency_on_Salt_Precipitation_During_CO2_Injection_2024_SPE/. $WHR
-python3 $WHR/case1/run_simulations.py & python3 $WHR/case2/run_simulations.py & python3 $WHR/case3/run_simulations.py & python3 $WHR/case4/run_all.py & wait
+cp -r publications/Impact_of_Intermittency_on_Salt_Precipitation_During_CO2_Injection_2024_SPE/. $OUT
+sed -i.bak "s/NPRUNS = 16/NPRUNS = $NCPUS/g" $OUT/case4/including_salt_precipitation/run_simulations.py && rm -f $OUT/case4/including_salt_precipitation/run_simulations.py.bak
+sed -i.bak "s/NPRUNS = 16/NPRUNS = $NCPUS/g" $OUT/case4/neglecting_salt_precipitation/run_simulations.py && rm -f $OUT/case4/neglecting_salt_precipitation/run_simulations.py.bak
+python3 $OUT/case1/run_simulations.py &
+python3 $OUT/case2/run_simulations.py &
+python3 $OUT/case3/run_simulations.py &
+wait
+python3 $OUT/case4/run_all.py &
+wait
+
+files="
+$OUT/case1/nca.png
+"
+
+missing_file="test_outputs/missing_publication_files.txt"
+missing=0
+
+for f in $files; do
+    if [ ! -f "$f" ]; then
+        echo "$f" >> "$missing_file"
+        missing=$((missing + 1))
+    fi
+done
+
+if [ "$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