Black pass

arcann_training/__main__.py

@@ -23,9 +23,19 @@
 parser = argparse.ArgumentParser(description="Deepmd iterative program suite")
 parser.add_argument("step_name", type=str, help="Step name")
 parser.add_argument("phase_name", type=str, help="Phase name")
-parser.add_argument("-v", "--verbose", type=int, default=0, help="verbosity, 0 (default) or 1 (debug)")
-parser.add_argument("-i", "--input", type=str, default="input.json", help="name of the input file (with ext)")
-parser.add_argument("-c", "--cluster", type=str, default=None, help="name of the fake cluster")
+parser.add_argument(
+    "-v", "--verbose", type=int, default=0, help="verbosity, 0 (default) or 1 (debug)"
+)
+parser.add_argument(
+    "-i",
+    "--input",
+    type=str,
+    default="input.json",
+    help="name of the input file (with ext)",
+)
+parser.add_argument(
+    "-c", "--cluster", type=str, default=None, help="name of the fake cluster"
+)
 
 if __name__ == "__main__":
     args = parser.parse_args()
@@ -58,15 +68,21 @@
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"ARCANN TRAINING PROGRAM SUITE")
-    arcann_logger.info(f"Launching: {step_name.capitalize()} - {phase_name.capitalize()}")
+    arcann_logger.info(
+        f"Launching: {step_name.capitalize()} - {phase_name.capitalize()}"
+    )
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"-" * 88)
 
     steps = ["initialization", "training", "exploration", "labeling", "test"]
     valid_phases = {}
     for step in steps:
         step_path = deepmd_iterative_path / step
-        files = [f.stem for f in step_path.iterdir() if f.is_file() and f.suffix == ".py" and f.stem not in ["__init__", "utils"]]
+        files = [
+            f.stem
+            for f in step_path.iterdir()
+            if f.is_file() and f.suffix == ".py" and f.stem not in ["__init__", "utils"]
+        ]
         valid_phases[step] = files
 
     if step_name not in steps:
@@ -76,7 +92,9 @@
         exit(exit_code)
 
     elif phase_name not in valid_phases.get(step_name, []):
-        arcann_logger.error(f"Invalid phase for step {step_name}. Valid phases are: {valid_phases[step_name]}")
+        arcann_logger.error(
+            f"Invalid phase for step {step_name}. Valid phases are: {valid_phases[step_name]}"
+        )
         arcann_logger.error(f"Aborting...")
         exit_code = 1
         exit(exit_code)
@@ -85,7 +103,9 @@
     else:
         try:
             submodule = importlib.import_module(submodule_name)
-            exit_code = submodule.main(step_name, phase_name, deepmd_iterative_path, fake_cluster, input_fn)
+            exit_code = submodule.main(
+                step_name, phase_name, deepmd_iterative_path, fake_cluster, input_fn
+            )
             del submodule, submodule_name
         except Exception as e:
             exit_code = 1
@@ -96,9 +116,13 @@
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"-" * 88)
     if exit_code == 0:
-        arcann_logger.info(f"{step_name.capitalize()} - {phase_name.capitalize()} finished")
+        arcann_logger.info(
+            f"{step_name.capitalize()} - {phase_name.capitalize()} finished"
+        )
     else:
-        arcann_logger.error(f"{step_name.capitalize()} - {phase_name.capitalize()} encountered an error")
+        arcann_logger.error(
+            f"{step_name.capitalize()} - {phase_name.capitalize()} encountered an error"
+        )
     arcann_logger.info(f"-" * 88)
     arcann_logger.info(f"-" * 88)
 

arcann_training/common/check.py

@@ -71,7 +71,9 @@ def check_atomsk(atomsk_path: str = None) -> str:
         if Path(atomsk_path).is_file():
             return str(Path(atomsk_path).resolve())
         else:
-            logger.warning(f"Atomsk path '{atomsk_path}' is invalid. Deleting the atomsk_path variable. Checking environment variable and system path...")
+            logger.warning(
+                f"Atomsk path '{atomsk_path}' is invalid. Deleting the atomsk_path variable. Checking environment variable and system path..."
+            )
             del atomsk_path
 
     # Check if ATOMSK_PATH is defined and is valid
@@ -127,7 +129,9 @@ def check_vmd(vmd_path: str = None) -> str:
     if vmd_path is not None and vmd_path != "" and Path(vmd_path).is_file():
         return str(Path(vmd_path).resolve())
     else:
-        logger.warning(f"VMD path '{vmd_path}' is invalid. Deleting the vmd_path variable. Checking environment variable and system path...")
+        logger.warning(
+            f"VMD path '{vmd_path}' is invalid. Deleting the vmd_path variable. Checking environment variable and system path..."
+        )
         del vmd_path
 
     # Check if VMD_PATH is defined and is valid
@@ -201,7 +205,12 @@ def check_dcd_is_valid(dcd_path: Path, vmd_bin: Path) -> bool:
     quit
     """
     # Run VMD script from command line
-    result = subprocess.run([vmd_bin, "-dispdev", "text", "-e", "/dev/stdin"], input=vmd_script, text=True, capture_output=True)
+    result = subprocess.run(
+        [vmd_bin, "-dispdev", "text", "-e", "/dev/stdin"],
+        input=vmd_script,
+        text=True,
+        capture_output=True,
+    )
 
     # Check if the output contains "Unable to load file "
     if "Unable to load file " in result.stdout:
@@ -239,7 +248,12 @@ def check_nc_is_valid(nc_path: Path, vmd_bin: Path) -> bool:
     quit
     """
     # Run VMD script from command line
-    result = subprocess.run([vmd_bin, "-dispdev", "text", "-e", "/dev/stdin"], input=vmd_script, text=True, capture_output=True)
+    result = subprocess.run(
+        [vmd_bin, "-dispdev", "text", "-e", "/dev/stdin"],
+        input=vmd_script,
+        text=True,
+        capture_output=True,
+    )
 
     # Check if the output contains "Unable to load file "
     if "Unable to load file " in result.stdout:

arcann_training/common/filesystem.py

@@ -83,7 +83,9 @@ def change_directory(directory_path: Path) -> None:
 
 # Unittested
 @catch_errors_decorator
-def check_directory(directory_path: Path, abort_on_error: bool = True, error_msg: str = "default") -> None:
+def check_directory(
+    directory_path: Path, abort_on_error: bool = True, error_msg: str = "default"
+) -> None:
     """
     Check if the given directory exists and logs a warning or raises an error if it does not.
 
@@ -161,7 +163,9 @@ def check_file_existence(
         if expected_existence:
             message = f"File not found: `{file_path.name}` not in `{file_path.parent}`"
             if abort_on_error:
-                raise FileNotFoundError(message if error_msg == "default" else error_msg)
+                raise FileNotFoundError(
+                    message if error_msg == "default" else error_msg
+                )
             else:
                 logger.warning(message if error_msg == "default" else error_msg)
         else:

arcann_training/common/json.py

@@ -96,7 +96,9 @@ def add_key_value_to_dict(dictionary: Dict, key: str, value: Any) -> None:
 
 # Unittested
 @catch_errors_decorator
-def get_key_in_dict(key: str, input_json: Dict, previous_json: Dict, default_json: Dict) -> Any:
+def get_key_in_dict(
+    key: str, input_json: Dict, previous_json: Dict, default_json: Dict
+) -> Any:
     """
     Get the value of the key from input JSON, previous JSON or default JSON, and validate its type.
 
@@ -119,7 +121,9 @@ def get_key_in_dict(key: str, input_json: Dict, previous_json: Dict, default_jso
 
     # Check if the key is present in any of the JSON, and set the value accordingly.
     if key in input_json:
-        if ( input_json[key] == "default" or input_json[key] == None ) and key in default_json:
+        if (
+            input_json[key] == "default" or input_json[key] == None
+        ) and key in default_json:
             value = default_json[key]
         else:
             value = input_json[key]
@@ -143,7 +147,12 @@ def get_key_in_dict(key: str, input_json: Dict, previous_json: Dict, default_jso
 
 # Unittested
 @catch_errors_decorator
-def backup_and_overwrite_json_file(json_dict: Dict, file_path: Path, enable_logging: bool = True, read_only: bool = False) -> None:
+def backup_and_overwrite_json_file(
+    json_dict: Dict,
+    file_path: Path,
+    enable_logging: bool = True,
+    read_only: bool = False,
+) -> None:
     """
     Write a dictionary to a JSON file after creating a backup of the existing file.
 
@@ -230,14 +239,18 @@ def load_default_json_file(file_path: Path) -> Dict:
             return json.loads(file_content)
     else:
         # If the file cannot be found, return an empty dictionary and log a warning
-        logging.warning(f"Default file '{file_path.name}' not found in '{file_path.parent}'.")
+        logging.warning(
+            f"Default file '{file_path.name}' not found in '{file_path.parent}'."
+        )
         logging.warning(f"Check your installation")
         return {}
 
 
 # Unittested
 @catch_errors_decorator
-def load_json_file(file_path: Path, abort_on_error: bool = True, enable_logging: bool = True) -> Dict:
+def load_json_file(
+    file_path: Path, abort_on_error: bool = True, enable_logging: bool = True
+) -> Dict:
     """
     Load a JSON file from the given file path and return its contents as a dictionary.
 
@@ -287,13 +300,20 @@ def load_json_file(file_path: Path, abort_on_error: bool = True, enable_logging:
         else:
             # If logging is enabled, log information about the creation of the empty dictionary
             if enable_logging:
-                logging.info(f"Creating an empty dictionary: '{file_path.name}' in '{file_path.parent}'.")
+                logging.info(
+                    f"Creating an empty dictionary: '{file_path.name}' in '{file_path.parent}'."
+                )
             return {}
 
 
 # Unittested
 @catch_errors_decorator
-def write_json_file(json_dict: Dict, file_path: Path, enable_logging: bool = True, read_only: bool = False) -> None:
+def write_json_file(
+    json_dict: Dict,
+    file_path: Path,
+    enable_logging: bool = True,
+    read_only: bool = False,
+) -> None:
     """
     Writes a dictionary to a JSON file, optionally logging the action and setting the file to read-only.
 
@@ -341,7 +361,11 @@ def write_json_file(json_dict: Dict, file_path: Path, enable_logging: bool = Tru
 
             # Collapse arrays/lists in the JSON to a single line
             pattern = r"(\[)(\s*([^\]]*)\s*)(\])"
-            replacement = lambda m: m.group(1) + re.sub(r"\s+", " ", m.group(3)).rstrip() + m.group(4)
+            replacement = (
+                lambda m: m.group(1)
+                + re.sub(r"\s+", " ", m.group(3)).rstrip()
+                + m.group(4)
+            )
             json_str = re.sub(pattern, replacement, json_str)
             json_str = re.sub(r"\],\s+\[", "], [", json_str)
             json_str = re.sub(r"\]\s+\]", "]]", json_str)
@@ -396,14 +420,21 @@ def convert_control_to_input(control_json: Dict, main_json: Dict) -> Dict:
         # Iterate over keys in main_json["systems_auto"]
         for system_auto in main_json.get("systems_auto", {}):
             if system_auto in control_json.get("systems_auto", {}):
-                input_json[key].append(control_json["systems_auto"][system_auto].get(key, None))
+                input_json[key].append(
+                    control_json["systems_auto"][system_auto].get(key, None)
+                )
 
     return input_json
 
 
 # TODO: Add tests for this function
 @catch_errors_decorator
-def replace_values_by_key_name(d: Union[Dict[str, Any], List[Any]], key_name: str, new_value: Any, parent_key: str = "") -> None:
+def replace_values_by_key_name(
+    d: Union[Dict[str, Any], List[Any]],
+    key_name: str,
+    new_value: Any,
+    parent_key: str = "",
+) -> None:
     """
     Recursively finds and replaces the values of all keys (and subkeys) with the specified name within a dictionary or list of dictionaries.
 

arcann_training/common/lammps.py

@@ -125,7 +125,14 @@ def read_lammps_data(
     if num_atom_types == None:
         error_msg = "The number of atom types was not found."
         raise ValueError(error_msg)
-    if xlo == None or xhi == None or ylo == None or yhi == None or zlo == None or zhi == None:
+    if (
+        xlo == None
+        or xhi == None
+        or ylo == None
+        or yhi == None
+        or zlo == None
+        or zhi == None
+    ):
         error_msg = f"Invalid box coordinates."
         raise ValueError(error_msg)
     if len(masses) == 0:

arcann_training/common/list.py

@@ -37,7 +37,9 @@
 
 # Unittested
 @catch_errors_decorator
-def exclude_substring_from_string_list(input_list: List[str], substring: str) -> List[str]:
+def exclude_substring_from_string_list(
+    input_list: List[str], substring: str
+) -> List[str]:
     """
     Remove all strings containing a given substring from a list of strings.
 
@@ -74,7 +76,9 @@ def exclude_substring_from_string_list(input_list: List[str], substring: str) ->
 
 # Unittested
 @catch_errors_decorator
-def replace_substring_in_string_list(input_list: List[str], substring_in: str, substring_out: str) -> List[str]:
+def replace_substring_in_string_list(
+    input_list: List[str], substring_in: str, substring_out: str
+) -> List[str]:
     """
     Replace a specified substring with a new substring in each string of a list.
 
@@ -110,13 +114,17 @@ def replace_substring_in_string_list(input_list: List[str], substring_in: str, s
     # if not substring_out:
     #    raise ValueError("Invalid input. substring_out must be a non-empty string.")
 
-    output_list = [string.replace(substring_in, substring_out).strip() for string in input_list]
+    output_list = [
+        string.replace(substring_in, substring_out).strip() for string in input_list
+    ]
     return output_list
 
 
 # Unittested
 @catch_errors_decorator
-def string_list_to_textfile(file_path: Path, string_list: List[str], read_only: bool = False) -> None:
+def string_list_to_textfile(
+    file_path: Path, string_list: List[str], read_only: bool = False
+) -> None:
     """
     Write a list of strings to a text file.
 
@@ -155,7 +163,9 @@ def string_list_to_textfile(file_path: Path, string_list: List[str], read_only:
         error_msg = f"'{file_path}' must be a '{type(Path(''))}'."
         raise TypeError(error_msg)
 
-    if not isinstance(string_list, list) or not all(isinstance(s, str) for s in string_list):
+    if not isinstance(string_list, list) or not all(
+        isinstance(s, str) for s in string_list
+    ):
         error_msg = f"'{string_list}' must be a '{type([])}' of '{type('')}.'"
         raise TypeError(error_msg)
 

arcann_training/common/logging.py

@@ -41,7 +41,12 @@ def setup_logging(verbose: int = 0) -> Dict:
             },
         },
         "handlers": {
-            "console": {"class": "logging.StreamHandler", "level": "INFO", "formatter": "simple", "stream": "ext://sys.stdout"},  # Use standard output (or sys.stderr)
+            "console": {
+                "class": "logging.StreamHandler",
+                "level": "INFO",
+                "formatter": "simple",
+                "stream": "ext://sys.stdout",
+            },  # Use standard output (or sys.stderr)
             "file": {
                 "class": "logging.FileHandler",
                 "level": "INFO",
@@ -50,7 +55,9 @@ def setup_logging(verbose: int = 0) -> Dict:
                 "mode": "a",  # Append mode
             },
         },
-        "loggers": {"": {"handlers": ["console", "file"], "level": "INFO", "propagate": True}},
+        "loggers": {
+            "": {"handlers": ["console", "file"], "level": "INFO", "propagate": True}
+        },
     }
 
     if verbose >= 1: